Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile

Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH+(H2O) consistent with the formation of a weak carbon-based CHδ+··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH+··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH+(CH3OH) and pyrimidineH+(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared towater. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4 •+ ion by weak CHδ+··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvatedstructures where the water molecules are bonded to each other and the ion is external to thewater cluster. Dissociative proton transfer reactions C4N2H4 •+(H2O)n−1 + H2O → C4N2H3 • + (H2O)nH+ and C4N2H5 +(H2O)n−1 + H2O → C4N2H4 + (H2O)nH+ are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5 +(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks

Proton-bound dimers of nitrogen heterocyclic molecules: Substituent effects on the structures and binding energies of homodimers of diazine, triazine, and fluoropyridine

The bonding energies of proton-bound homodimers BH+B were measured by ion mobilityequilibrium studies and calculated at the DFT B3LYP/6-311++G* * level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°dissoc) of the proton-bound dimers (BH+B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°dissoc for (1,3-diazine)2H+, i.e., (pyrimidine)2H+ and (3-F-pyridine)2H+ are 22.7 and 23.0 kcal/mol, respectively. The measured ΔH°dissoc for the pyrimidine ·+(3-F-pyridine) radical cation dimer (19.2 kcal/mol) is signifcantly lower than that of the proton-bound homodimers of pyrimidine and 3-F-pyridine, reflecting the stronger interaction in the ionic H-bond of the protonated dimers. The calculated binding energies for (1,2-diazine)2H+, (pyridine)2H+, (2-F-pyridine)2H+, (3-F-pyridine)2H+, (2,6-di-F-pyridine)2H+, (4-F-pyridine)2H+, (1,3-diazine)2H+, (1,4-diazine)2H+, (1,3,5-triazine)2H+, and (pentafluoropyridine)2H+ are 29.7, 24.9, 24.8, 23.3, 23.2, 23.0, 22.4, 21.9, 19.3, and 18.1 kcal/mol, respectively. The electron-withdrawing substituents form internal dipoles whose electrostatic interactions contribute to both the decreased proton affinities of (B) and the decreased binding energies of the protonated dimers BH+B. The bonding energies also vary with rotation about the hydrogen bond, and they decrease in rotamers where the internal dipoles of the components are aligned efficiently for inter-ring repulsion. For compounds substituted at the 3 or 4 (meta or para) positions, the lowest energy rotamers are T-shaped with the planes of the two rings rotated by 90° about the hydrogen bond, while the planar rotamers are weakened by repulsion between the ortho hydrogen atoms of the two rings. Conversely, inortho-substituted (1,2-diazine)2H+ and (2-F-pyridine)2H+, attractive interactions between the ortho (C–H) hydrogen atoms of one ring and the electronegative ortho atoms (N or F) of the other ring are stabilizing, and increase the protonated dimer binding energies by up to 4 kcal/mol. In all of the dimers, rotation about the hydrogen bond can involve a 2–4 kcal/mol barrier due to the relative energies of the rotamers

Ultrafast radiationless decay mechanisms through conical intersections in cytosine: Computational insight and topological analysis of the charge density distributions

27-34<span style="font-size:9.0pt;mso-fareast-font-family:Calibri;mso-bidi-font-family: Calibri;mso-ansi-language:EN-US;mso-bidi-language:AR-SA" lang="EN-US">The quantum theory of atoms-in-molecules (QTAIM) in conjunction with the DFT/B3LYP/6-311++G(2d,2p) wave function are used to compute the atomic, bonded and non-bonded interactions, distributions of the charge density, (r)<span style="font-size:9.0pt;mso-fareast-font-family:Calibri;mso-bidi-font-family: Calibri;mso-ansi-language:EN-US;mso-bidi-language:AR-SA;mso-bidi-font-weight: bold" lang="EN-US">, and its Laplacian, 2(r), for the ground equilibrium structure of cytosine. The study has been further extended to include two conical intersection (CI) structures that underlie the radiationless decay of cytosine. Complete Active Space Multi-configuration SCF level of theory with the 6-311++G** basis set are used to identify, characterize and to optimize the geometrical structures of the conical intersections between So and S1. In the case of cytosine, all ring bond critical points show 2(r)<span style="font-size:9.0pt; mso-fareast-font-family:Calibri;mso-bidi-font-family:Calibri;mso-ansi-language: EN-US;mso-bidi-language:AR-SA" lang="EN-US"> <span style="font-size: 9.0pt;font-family:Symbol;mso-ascii-font-family:" times="" new="" roman";mso-fareast-font-family:="" calibri;mso-hansi-font-family:"times="" roman";mso-bidi-font-family:calibri;="" mso-ansi-language:en-us;mso-bidi-language:ar-sa;mso-char-type:symbol;="" mso-symbol-font-family:symbol;mso-bidi-font-weight:bold"="" lang="EN-US"><<span style="font-size:9.0pt;mso-fareast-font-family:Calibri;mso-bidi-font-family: Calibri;mso-ansi-language:EN-US;mso-bidi-language:AR-SA;mso-bidi-font-weight: bold" lang="EN-US"> 0<span style="font-size:9.0pt;mso-fareast-font-family:Calibri;mso-bidi-font-family: Calibri;mso-ansi-language:EN-US;mso-bidi-language:AR-SA" lang="EN-US"> <span style="font-size:9.0pt;mso-fareast-font-family:Calibri;mso-bidi-font-family: Calibri;mso-ansi-language:EN-US;mso-bidi-language:AR-SA" lang="EN-US">indicating covalent binding and accumulation of the electron density in the bonding regions. On the other hand, the C1-O11 bond shows, depletion of charge density, indicating the increased ionic character of this bond. This point might very well underlie the reactivity and the low keto-enol barrier in cytosine. Contour plots and relief maps have been analyzed for regions of valence shell charge concentrations and depletions in the ground state and the three CI structures of cytosine. NBO analysis reveals that the conformational and overall stability of the studied cytosine conformations is facilitated by the competitive conjugative and the lone-pair interactions. In cytosine, there is a delicate balance between these two forces, whereas, in each of the two CI configurations there is one dominant force that underlies the stability of the cytosine structure. The present work indicates that the QTAIM provide not only a graphical presentation of very important critical points on the PES but also unique quantitative descriptors of CI's that characterize it. </span

UV excitations of halons

International audienceIn the present study, we examined the UV excitations of a newly introduced molecular set, Halons-9, composed of nine gaseous halon molecules. The performance of the density functional-based multi-reference configuration interaction method (DFT/MRCI) and time-dependent density functional theory with CAM-B3LYP functional (TD-CAM-B3LYP) in the computation of singlet and triplet excited states of this set was evaluated against coupled-cluster with singles and doubles (CCSD). Excited states up to the corresponding ionization limits, including both localized and delocalized excitations, have been benchmarked. TD-CAM-B3LYP significantly underestimates excitation energies of the higher mixed valence-Rydberg and Rydberg states, with computed mean absolute deviations from the equation of motion (EOM)-CCSD results 1.06 and 0.76 eV, respectively. DFT/MRCI gives a significantly better description of higher excited states, albeit still poor, compared to the TD-CAM-B3LYP. The mean absolute deviations of mixed valence-Rydberg and Rydberg states from the reference EOM-CCSD values are 0.66 and 0.47 eV, respectively. The performance of DFT/MRCI for description of strongly correlated states with valence-Rydberg mixing is still not satisfactory enough. On the other hand, oscillator strengths of most of singlet states obtained with both methods are close to the EOM-CCSD values. The largest deviations, occurring in the case of several high-lying multiconfigurational states, are of an order of magnitude

The Thermodynamic and Kinetic Properties of 2-Hydroxypyridine/2-Pyridone Tautomerization: A Theoretical and Computational Revisit

The gas-phase thermal tautomerization reaction between 2-hydroxypyridine (2-HPY) and 2-pyridone (2-PY) was investigated by applying 6-311++G** and aug-cc-pvdz basis sets incorporated into some density functional theory (DFT) and coupled cluster with singles and doubles (CCSD) methods. The geometrical structures, dipole moments, HOMO-LUMO energy gaps, total hyperpolarizability, kinetics and thermodynamics functions were monitored against the effects of the corrections imposed on these functionals. The small experimental energy difference between the two tautomers of 3.23 kJ/mol; was a real test of the accuracy of the applied levels of theory. M062X and CCSD methods predicted the preference of 2-HPY over 2-PY by 5–9 kJ/mol; while B3LYP functional favoured 2-PY by 1–3 kJ/mol. The CAM-B3LYP and ωB97XD functionals yielded mixed results depending on the basis set used. The source of preference of 2-HPY is the minimal steric hindrance and electrostatic repulsion that subdued the huge hyperconjugation in 2-PY. A 1,3-proton shift intramolecular gas-phase tautomerization yielded a high average activation of 137.152 kJ/mol; while the intermolecular mixed dimer interconversion gave an average barrier height of 30.844 kJ/mol. These findings are boosted by a natural bond orbital (NBO) technique. The low total hyperpolarizabilities of both tautomers mark out their poor nonlinear optical (NLO) behaviour. The enhancement of the total hyperpolarizability of 2-HPY over that of 2-PY is interpreted by the bond length alternation

Towards Understanding the Decomposition/Isomerism Channels of Stratospheric Bromine Species: Ab Initio and Quantum Topology Study

The present study aims at a fundamental understanding of bonding characteristics of the C–Br and O–Br bonds. The target molecular systems are the isomeric CH3OBr/BrCH2OH system and their decomposition products. Calculations of geometries and frequencies at different density functional theory (DFT) and Hartree–Fock/Møller–Plesset (HF/MP2) levels have been performed. Results have been assessed and evaluated against those obtained at the coupled cluster single-double (Triplet) (CCSD(T)) level of theory. The characteristics of the C–Br and O–Br bonds have been identified via analysis of the electrostatic potential, natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM). Analysis of the electrostatic potential (ESP) maps enabled the quantitative characterization of the Br σ-holes. Its magnitude seems very sensitive to the environment and the charge accumulated in the adjacent centers. Some quantum topological parameters, namely Ñ2ρ, ellipticity at bond critical points and the Laplacian bond order, were computed and discussed. The potential energy function for internal rotation has been computed and Fourier transformed to characterize the conformational preferences and origin of the barriers. NBO energetic components for rotation about the C–Br and O–Br bonds as a function of torsion angle have been computed and displayed

Electronic structure and acid–base properties of Kojic acid and its dimers. A DFT and quantum topology study

<p>Kojic acid is a polyfunctional heterocyclic compound, with several important reaction centres; it has a wide range of applications in the cosmetic, medicine, food, agriculture and chemical industries. The present study aims at better insight into its electronic structure and bonding characteristics. Thus, density functional theory at the M06-2x /6-311++G^** level of theory is used to investigate its ground state electronic and acid–base properties. Protonation and deprotonation enthalpies are computed and analysed. The ability of Kojic acid to form both water complexes and dimers is explored. Several different complexes and dimer structures were examined. Natural bond order and quantum topology features of the charge density were analysed. The origin of the stability of the studied complexes and dimer structures can be traced to hydrogen bonding, π-conjugative and non-covalent dispersive interactions.</p

Eclipsed Acetaldehyde as a Precursor for Producing Vinyl Alcohol

Abstract: The MP2 and DFT/B3LYP methods at 6-311++G(d,p) and aug-cc-pdz basis sets have been used to probe the origin of relative stability preference for eclipsed acetaldehyde over its bisected counterpart. A relative energy stability range of 1.02 to 1.20 kcal/mol, in favor of the eclipsed conformer, was found and discussed. An NBO study at these chemistry levels complemented these findings and assigned the eclipsed acetaldehyde preference mainly to the vicinal antiperiplanar hyperconjugative interactions. The tautomeric interconversion between the more stable eclipsed acetaldehyde and vinyl alcohol has been achieved through a four-membered ring transition state (TS). The obtained barrier heights and relative stabilities of eclipsed acetaldehyde and the two conformers of vinyl alchol at these model chemistries have been estimated and discussed

Hybrid Antibody–Aptamer Assay for Detection of Tetrodotoxin in Pufferfish

The marine toxin tetrodotoxin (TTX) poses a great risk to public health safety due to its severe paralytic effects after ingestion. Seafood poisoning caused by the consumption of contaminated marine species like pufferfish due to its expansion to nonendemic areas has increased the need for fast and reliable detection of the toxin to effectively implement prevention strategies. Liquid chromatography-mass spectrometry is considered the most accurate method, although competitive immunoassays have also been reported. In this work, we sought to develop an aptamer-based assay for the rapid, sensitive, and cost-effective detection of TTX in pufferfish. Using capture-SELEX combined with next-generation sequencing, aptamers were identified, and their binding properties were evaluated. Finally, a highly sensitive and user-friendly hybrid antibody–aptamer sandwich assay was developed with superior performance compared to several assays reported in the literature and commercial immunoassay kits. The assay was successfully applied to the quantification of TTX in pufferfish extracts, and the results obtained correlated very well with a competitive magnetic bead-based immunoassay performed in parallel for comparison. This is one of the very few works reported in the literature of such hybrid assays for small-molecule analytes whose compatibility with field samples is also demonstrated.info:eu-repo/semantics/publishedVersio

Evidence for the Formation of Pyrimidine Cations from the Sequential Reactions of Hydrogen Cyanide with the Acetylene Radical Cation

Herein, we report the first direct evidence for the formation of pyrimidine ion isomers by sequential reactions of HCN with the acetylene radical cation in the gas phase at ambient temperature using the mass-selected variable temperature and pressure ion mobility technique. The formation and structures of the pyrimidine ion isomers are theoretically predicted via coupled cluster and density functional theory calculations. This ion–molecule synthesis may indicate that pyrimidine is produced in the gas phase in space environments before being incorporated into condensed-phase ices and transformed into nucleic acid bases such as uracil