Inframolecular Protonation Process of Norbadione A: Influence of the Ionic Environment and Stereochemical Consequences

Protoisomerization of indigo di- and monoimines

Indigo di- and monoimines can be protonated to form stable salts in which the central C=C bond has isomerized from a trans to cis configuration. Deprotonation of these salts regenerates the neutral trans species. The protonation chemistry of indigo is also explored.

13C longitudinal relaxation time measurements and DFT-GIAO NMR computations for two ammonium ions of a tetraazamacrocyclic scorpiand system

Abstract

Spin–lattice relaxation times, T₁s, for ¹³C nuclei in two cations H_n1ⁿ⁺ (n = 1, 5) of N-(2-aminoethyl)-cyclam (1, scorpiand) were determined by means of ¹³C{¹H} NMR experiments in aqueous solution at pH 11.5 and 0.2. The theoretical study [modeling with OPLS-AA, B3LYP/6-31G(d) geometry optimizations, dispersion-corrected energies (DFT-D3), and DFT-GIAO predictions of the NMR chemical shifts (including an IEF-PCM simulation of hydration)] was also done for several conformers of the tautomer iso-H₄1⁴⁺ not investigated before. The binding directions in protonated polyamino receptors necessary for efficient complexation of the nitrate anion(s) were briefly outlined, as well. All these results were discussed in terms of ‘abnormal’ ¹³C chemical shift changes found previously for the side-chain carbons of amine 1 in strongly acidic solution (HNO₃). In conclusion, an earlier proposal of its association with NO₃⁻ at pH <1 was rejected. Instead, the participation of small amounts of a micro-species iso-H₄1⁴⁺D_hydr under such conditions can be proposed.

Graphical Abstract

A small contribution of iso-H₄1⁴⁺D_hydr (see figure) to an ionic mixture of pentamine 1 was proposed to explain the ‘abnormal’ ¹³C NMR shifts observed for atoms C11 and C12 in its side-chain arm, at pH <1.

Electronic supplementary material

The online version of this article (doi:10.1007/s10847-013-0298-x) contains supplementary material, which is available to authorized users.

Resolution of microscopic protonation enthalpies of polyprotic molecules by means of cluster expansions

Cluster expansion techniques are used to obtain microconstants and microenthalpies of protonation reactions. The approach relies on the analysis of macroscopic protonation constants and protonation enthalpies within a homologous series. Various linear aliphatic polyamines are considered, including 3,4-tri (spermidine), 3,4,3-tet (spermine), and 2,2,2,2-pent. Besides the full resolution of the microscopic protonation equilibria, one obtains information on the temperature dependence of the microstate probabilities. We find that the concentrations of the dominant microspecies increase with increasing temperature. Due to the large negative protonation enthalpies that are typical for amines, higher temperatures generally favor the less protonated species.

Stereochemical study of iminodihydrofurans based on experimental measurements and SOPPA calculations of (13)C-(13)C spin-spin coupling constants

Configurational assignment and conformational analysis of a series of iminodihydrofurans obtained from cyanoacetylenic alcohols were performed on the basis of experimental measurements and high-level ab initio calculations of their (13)C-(13)C spin-spin coupling constants. The title compounds were shown to form and exist in solution as the individual Z isomers, adopting the orthogonal orientation of the amino, alkylamino and dialkylamino groups and the s-trans orientation of the CONH(2) group at the C(4) position of the 2,5-dihydro-2-iminofuran moiety.

scyllo-inositol pentakisphosphate as an analogue of myo-inositol 1,3,4,5,6-pentakisphosphate: chemical synthesis, physicochemistry and biological applications

myo-Inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P(5)), an inositol polyphosphate of emerging significance in cellular signalling, and its C-2 epimer scyllo-inositol pentakisphosphate (scyllo-InsP(5)) were synthesised from the same myo-inositol-based precursor. Potentiometric and NMR titrations show that both pentakisphosphates undergo a conformational ring-flip at higher pH, beginning at pH 8 for scyllo-InsP(5) and pH 9 for Ins(1,3,4,5,6)P(5). Over the physiological pH range, however, the conformation of the inositol rings and the microprotonation patterns of the phosphate groups in Ins(1,3,4,5,6)P(5) and scyllo-InsP(5) are similar. Thus, scyllo-InsP(5) should be a useful tool for identifying biologically relevant actions of Ins(1,3,4,5,6)P(5), mediated by specific binding sites, and distinguishing them from nonspecific electrostatic effects. We also demonstrate that, although scyllo-InsP(5) and Ins(1,3,4,5,6)P(5) are both hydrolysed by multiple inositol polyphosphate phosphatase (MINPP), scyllo-InsP(5) is not dephosphorylated by PTEN or phosphorylated by Ins(1,3,4,5,6)P(5) 2-kinases. This finding both reinforces the value of scyllo-InsP(5) as a biological control and shows that the axial 2-OH group of Ins(1,3,4,5,6)P(5) plays a part in substrate recognition by PTEN and the Ins(1,3,4,5,6)P(5) 2-kinases.

Synergy of Intramolecular Hydrogen-Bonding Network in myo-Inositol 2-Monophosphate: Theoretical Investigations into the Electronic Structure, Proton Transfer, and pKa

This work demonstrates the pivotal role that an intramolecular hydrogen-bonding network (intra-HBN) plays in the determination of the conformation of myo-inositol 2-monophosphate (Ins(2)P1), a member of the inositol phosphate family of compounds, which are important participants in the role that phosphates play in biological and environmental chemistry. For biologically significant compounds that contain phosphate and hydroxyl groups, Ins(2)P1 is a model system for studying both the primary forces that determine their conformations and their chemical properties from the effect of phosphate group addition. We performed ab initio calculations to determine the intra-HBN within important thermally accessible conformations for neutral Ins(2)P1 and its anions, Ins(2)P1(1-) and Ins(2)P1(2-). The results show that the global minima prefer 1a/5e structures where the phosphate group is in the axial position with all -OH groups in the equatorial positions. The calculations of transition state structures for ring inversion at each ionization state predict an activation energy of 18.16 kcal/mol for the neutral species in water, while the activation energy is lower for the charged compounds, 15.62 kcal/mol for Ins(2)P1(1-) and 12.48 kcal/mol for Ins(2)P1(2-). The pK(a) values of Ins(2)P1 were calculated by modeling the solvent as a polarizable continuum medium (PCM) and as explicit solvent molecules. These values are in good agreement with experimental data. A novel four-center pattern of hydrogen bonding was found to stabilize the system. The intramolecular proton transfer across a low barrier hydrogen bond between the charged phosphate and hydroxyl groups was found to occur under standard conditions with an activation energy that is less than 0.5 kcal/mol.