NMR spectra of salicylohydroxamic acid in DMSO-d6 solution: a DFT study

The ¹H, ¹³C and ¹H, ¹³C COSY NMR spectra of salicylohydroxamic acid (sha) were measured in DMSO-d₆ solution. The B3LYP GIAO method with the 6-311++G(d,p) basis set was chosen to reproduce the experimental spectra. All possible zusammen and entgegen conformers of monomeric sha were computed. After geometry optimisation (B3LYP/6-311++G(d,p)) only nine independent models of the molecule were shown to be stable. Additionally, the NMR chemical shifts of the Onsager model of the most stable monomer were calculated. The computed chemical shifts for the labile protons for all aforementioned geometries meaningfully underestimated experimental results suggesting the existence of the H-bonded structure of sha in DMSO solution. The most probable two dimeric structures along with two solvent-bounded aggregates were subsequently calculated at the same level of theory. The best agreement was obtained for sha H-bonded with two DMSO molecules (confirmed by the absence of concentration effect). The relative error not exceeding 10 and 4% for chemical shifts in ¹H and ¹³C NMR spectra of sha–(DMSO)₂, respectively, showed that the applied method with the B3LYP/6-311++G(d,p) basis set was efficient to predict the NMR shifts of a compound with strong H-bonds. Thus, this allows to assign properly NMR resonances to specific structure formed in DMSO solution.     

Cover Feature: How Many O-Donor Groups in Enterobactin Does It Take to Bind a Metal Cation? (Chem. Eur. J. 28/2019)

The E. coli siderophore enterobactin, the strongest Fe^III chelator known to date, forms hexacoordinate complexes with Si^IV, Ge^IV, and Ti^IV. Synthetic protocols have been developed to prepare non-symmetric enterobactin analogues with varying denticities. Various benzoic acid residues were coupled to the macrocyclic lactone to afford a diverse library of ligands. These enterobactin analogues were bound to Si^IV, Ge^IV, and Ti^IV, and the complexes were investigated through experimental and computational techniques. The binding behavior of the synthesized chelators enabled assessment of the contribution of each of the phenolic hydroxy groups in enterobactin to metal-ion complexation. It was found that at least four O-donors are needed for enterobactin derivatives to act as metal binders. Density functional theory calculations indicate that the strong binding behavior of enterobactin can be ascribed to a diminished translational entropy penalty, a common feature of the chelate effect, coupled with the structural arrangement of the three catechol moieties, which allows the triseryl base to be installed without distorting the preferred local metal-binding geometry of the catecholate ligands.     

Synthesis of 4-phenyl-2h-benzopyrans

Sesamol and other phenols react with equimolar quantities of cinnamaldehyde and morpholine in methanol to yield epimeric 2-morpholinyl-4-phenylbenzopyran derivatives, which are useful intermediates for the synthesis of alcoholic neoflavanoid (4-phenylbenzopyran) compounds.     

Synthesis of 9‐Halogenated 9‐Deazaguanine N7‐(2′‐Deoxyribonucleosides)

The syntheses of N⁷‐glycosylated 9‐deazaguanine 1a as well as of its 9‐bromo and 9‐iodo derivatives 1b , c are described. The regioselective 9‐halogenation with N‐bromosuccinimide (NBS) and N‐iodosuccinimide (NIS) was accomplished at the protected nucleobase 4a (2‐{[(dimethylamino)methylidene]amino}‐3,5‐dihydro‐3‐[(pivaloyloxy)methyl]‐4H‐pyrrolo[3,2‐d]pyrimidin‐4‐one). Nucleobase‐anion glycosylation of 4a – c with 2‐deoxy‐3,5‐di‐O‐(p‐toluoyl)‐α‐D ‐erythro‐pentofuranosyl chloride ( 5 ) furnished the fully protected intermediates 6a – c (Scheme 2). They were deprotected with 0.01M NaOMe yielding the sugar‐deprotected derivatives 8a – c (Scheme 3). At higher concentrations (0.1M NaOMe), also the pivaloyloxymethyl group was removed to give 7a – c , while conc. aq. NH₃ solution furnished the nucleosides 1a – c . In D₂O, the sugar conformation was always biased towards S (67–61%).     

N7-DNA: Synthesis and Base Pairing of Oligonucleotides Containing N7-(2-Deoxy-β-D-erythro-pentofuranosyl)guanine (N7Gd)

The synthesis of oligonucleotides containing N⁷-(2-deoxy-β-D -erythro-pentofuranosyl)guanine (N⁷G_d; 1 ) is described. Compound 1 was prepared by nucleobase-anion glycosylation of 2-amino-6-methoxypurine ( 5 ) with 2-deoxy-3,5-di-O-(4-toluoyl)-α-D -erythro-pentofuranosyl chloride ( 6 ) followed by detoluoylation and displacement of the MeO group ( 8→10→1 ). Upon base protection with the (dimethylamino)methylidene residue (→ 11 ) the 4,4-dimethoxytrityl group was introduced at OH? C(5′) (→ 12 ). The phosphonate 3 and the phosphoramidite 4 were prepared and used in solid-phase oligonucleotide synthesis. The self-complementary dodecamer d(N⁷G? C)₆ shows sigmoidal melting. The T_m of the duplex is 40°. This demonstrates that guanine residues linked via N(7) of purine to the phosphodiester backbone are able to undergo base pairing with cytosine.     

Cadmium(II) and mercury(II) complexes of an NO2S2-donor macrocycle and its ditopic xylyl-bridged analogue

The NO2S2-donor macrocycle (L1) was synthesised from the ring closure reaction between Boc-N-protected 2,2'-iminobis(ethanethiol) (3) and 2,2'-(ethylenedioxy)bis(benzyl chloride) (4) followed by deprotection of the Boc-group. alpha,alpha'-Dibromo-p-xylene was employed as a dialkylating agent to bridge two L1 to yield the corresponding N-linked product (L2). The X-ray structure of L2 (as its HBr salt) is described. A range of Cd(II) and Hg(II) complexes of L1 (6-9) and L2 (10-12) were prepared and characterised. Reaction of HgX2 (X = Br or I) with L1 afforded [Hg(L1)Br]2[Hg2Br6].2CH2Cl2 6 and [Hg(L1)I(2)] 7, respectively. For 6, the Hg(II) ion in the complex cation has a distorted tetrahedral coordination environment composed of S2N donor atoms from L1 and a bromo ligand. In 7 the coordination geometry is highly distorted tetrahedral, with the macrocycle coordinating in an exodentate manner via one S and one N atom. The remaining two coordination sites are occupied by iodide ions. [Hg(L1)(ClO4)]ClO4 8 was isolated from the reaction of Hg(ClO4)2 and L1. The X-ray structure reveals that all macrocyclic ring donors bind to the central mercury ion in this case, with the latter exhibiting a highly distorted octahedral coordination geometry. The O2S2-donors from the macrocyclic ring define the equatorial plane while the axial positions are occupied by the ring nitrogen as well as by an oxygen from a monodentate perchlorato ion. Reaction of Cd(NO3)(2).4H2O with L1 afforded [Cd(L1)(NO3)2](.)0.5CH2Cl2 9 in which L1 acts as a tridentate ligand, binding exo-fashion via its S2N donors. The remaining coordination positions are filled by two bidentate nitrate ions such that, overall, the cadmium is seven-coordinate. Reactions of HgX2(X = Br or I) with L2 yielded the isostructural 2 : 1 (metal : ligand) complexes, [Hg2(L2)Br4] 10 and [Hg2(L2)I(4)] 11. Each mercury ion has a distorted tetrahedral environment made up of S and N donors from an exodentate L2 and two coordinated halides. Contrasting with this, the reaction of L2 with Cd(NO3)(2).4H2O yielded a 1-D coordination network, {[Cd2(L2)(NO3)4].2CH2Cl2}n 12 in which each ring of L2 is exo-coordinated via two S atoms and one N atom to a cadmium ion which is also bound to one monodentate and one bidentate nitrate anion. The latter also has one of its oxygen atom attached to a neighboring cadmium via a nitroso (mu2-O) bridge such that the overall coordination geometry about each cadmium is seven-coordinate. The [Cd(L2)0.5(NO3)2] units are linked by an inversion to yield the polymeric arrangement.     

THEORETICAL PREDICTIONS OF STRUCTURES AND VIBRATIONAL INFRARED FREQUENCIES. I. MERCAPTANS AND SULFIDES

Abstract

We report the computed equilibrium geometries and vibrational infrared frequencies of a group of thirteen mercaptans and sulfides. The computations were based on the Gaussian 86 Program Package utilizing 3-21G basis sets. The theoretical bond distances and bond angles are in agreement with the available experimental data. The agreement between computed frequencies and available experimental values seems reasonable. We also used the computations as guidelines for the assignment of available experimental infrared frequencies. We believe that it is possible to make reliable frequency predictions by combining computations with available experimental data for groups of similar molecules. However, it is necessary to introduce different correction factors for different types of vibrational modes if we use 3-21G basis sets.     

Functionalized Silver-Ion-Mediated α-dC/β-dC Hybrid Base Pairs with Exceptional Stability: α-d-5-Iodo-2′-Deoxycytidine and Its Octadiynyl Derivative in Metal DNA

Silver-mediated α-dC–Ag⁺–β-dC hybrid base pairs decorated with 5-iodo- or 5-octadiynyl residues are well accommodated in duplex DNA. A strong T_m increase and favorable thermodynamic data for duplex DNA were observed after addition of silver ions. The phenomenon is particularly obvious when both nucleobases of the base pairs are functionalized. Neither the position of the base pair, nor the type of 5-substituent had a negative influence. On the contrary, functionalization of conventional silver-mediated β-dC–Ag⁺–β-dC homo base pairs showed a negative impact induced by the bulky substituents. To this end, cytosine modified 12-mer oligodeoxynucleotides were prepared by solid-phase synthesis employing new α-anomeric 2′-deoxycytidine phosphoramidites. A multigram scale synthesis was developed for 5-iodo-α-d -2′-deoxycytidine ( 1 ) employing the direct glycosylation of cytosine with Hoffer's α-d -halogenose followed by separation of anomeric DMT nucleosides. Regarding base-pair stability and functionalization silver-mediated α/β-dC hybrid base pairs were found to be superior to β/β-dC homo pairs. According to their extraordinary properties, they might find applications in DNA diagnostics, material science, or nanotechnology.     

Polymerization of α-Methylstyrene in p-Dioxane with Potassium as Initiator. III. Gel-Permeation Chromatographic Analyses of Polymers

Gel-permeation chromatographic studies on poly-α-methyl-styrene initiated with potassium and potassium-naphthalene in p-dioxane as solvent and polymerized at 5, 15, 25, and 40°C, have been carried out. Bimodal and trimodal distributions are observed in these polymers. It has been shown that these multimodal distributions do not arise because of the monofunctional and bifunctional living ends produced by the reaction of solvent dioxane with the living polymer. These, on the other hand, may be related to the presence of different ion-pairs which contribute to the reaction but to different extents. Contrary to the belief that only contact ion-pairs are responsible for propagation in p-dioxane because of its low dielectric constant, the presence of solvent-separated ion-pairs yielding reversible propagation has been speculated. The different components (D + A), B, and C, similar to the ones present in the a-methyl-styrene-potassium tetrahydrofuran system, have been found in the present study also and are attributed to the dead and a dormant polymer, solvent-separated ion-pair polymer, and that due to a contact pair, respectively. The extent of the formation of component (D + A) has been linked directly to the concentration of living ends. In reactions where naphthalene was used along with potassium for initiation purposes, a unique component yielding reversible propagation was observed. This has been attributed to the presence of polymer due to potassium-naphthalene complex which is different in character to a contact ion-pair but may resemble a solvent-separated ion-pair.