Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose

The techniques of neutron diffraction with isotopic substitution (NDIS) and molecular dynamics (MD) simulations have been used to examine the rotational conformation of the exocyclic hydroxymethyl group of D-glucopyranose. First order H/D NDIS experiments were performed on the H6 position in 3m aqueous glucose solutions where the average coherent scattering length of the exchangeable hydrogen atoms was zero (i.e., all correlations between exchangeable hydrogen atoms and other atoms cancel and thus are not present in the scattering data). This H6 experimental result suggests that no single conformation for the C4-C5-C6-O6 dihedral reproduces the observed scattering data well, but that a mixture of the gg and gt conformations, which has been suggested by NMR experiments, gives a reasonable agreement between the MD and experimental data.     

Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants

Experimental and theoretical methods have been used to correlate (2)J(HH) and (3)J(HH) values within the exocyclic hydroxymethyl groups (CH(2)OH) of saccharides with specific molecular parameters, and new equations are proposed to assist in the structural interpretation of these couplings. (3)J(HH) depends mainly on the C-C torsion angle (omega) as expected, and new Karplus equations derived from J-couplings computed from density functional theory (DFT) in a model aldopyranosyl ring are in excellent agreement with experimental values and with couplings predicted from a previously reported general Karplus equation. These results confirm the reliability of DFT-calculated (1)H-(1)H couplings in saccharides. (2)J(HH) values depend on both the C-C (omega) and C-O (theta) torsions. Knowledge of the former, which may be derived from other parameters (e.g., (3)J(HH)), allows theta to be evaluated indirectly from (2)J(HH). This latter approach complements more direct determinations of theta from (3)J(HCOH) and potentially extends these more conventional analyses to O-substituted systems lacking the hydroxyl proton. (1)J(CH) values within hydroxymethyl fragments were also examined and found to depend on r(CH), which is modulated by specific bond orientation and stereoelectronic factors. These latter factors could be largely, but not completely, accounted for by C-C and C-O torsional variables, leading to only semiquantitative treatments of these couplings (details discussed in the Supporting Information). New equations pertaining to (2)J(HH) and (3)J(HH) have been applied to the analysis of hydroxymethyl group J-couplings in several mono- and oligosaccharides, yielding information on C5-C6 and/or C6-O6 rotamer populations.     

Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran

High level ab initio computations in vacuum and with the IEFPCM implicit solvent model are carried out on 5-(hydroxymethyl)tetrahydropyran to investigate the effects of water on the exocyclic torsional surface. Rotamer populations evaluated from the omega(C-C-C-O), theta(C-C-C-O) solvent surface agree almost quantitatively with experimental values for the closely related methyl 4-deoxy-alpha-D-xylohexopyranoside. Potentials of mean force obtained from the two surfaces show substantial solvent stabilization of the TG (omega = 180 +/- 60 degrees) rotamer and the barriers at omega= 120 and 240 degrees but solvent destabilization at the cis barrier (omega = 0 degrees). Natural bond orbital analyses indicate that energetics of these effects are largely explained by overstabilization of the vacuum GT (omega= 60 +/- 60 degrees) and GG (omega = 300 +/- 60 degrees) rotamers. Solvent stabilization of theta conformations provides entropic stabilization.     

Benzyl group conformation in 4-benzyl-4-hydroxypiperidines

The high-resolution ¹H and ¹³C NMR spectra of eight 4-benzyl-4-hydroxypiperidines 1–8 were recorded in CDCl₃ and analyzed. In 2, the conformation of the equatorial benzyl group at C(4) was established as an equilibrium mixture of A [the phenyl group is gauche with respect to OH and C(5)] and B [the phenyl group is gauche with respect to OH and C(3)], whereas in 3-alkyl-4-benzyl-4-hydroxypiperidines 3–8, the favored conformation of the benzyl group at C(4) is A. In 1, the axial benzyl group at C(4) adopts the gauche conformations A′ [the phenyl group is gauche with respect to OH and C(3)] and B′ [the phenyl group is gauche with respect to OH and C(5)], in which the phenyl ring of the benzyl group is gauche with respect to the OH group. The HF/DFT B3LYP/6-3G* hybrid calculations of model systems 1′–3′ also support these conformations. The ¹³C data reveal that the equatorial methyl group at C(3) exerts a shielding influence on the methyl-bearing carbon and the magnitude of the α effect was found to be approximately ?1.5 ppm. The parameters of the ¹³C substituent in the benzyl group show that the the α effect of the equatorial benzyl group is considerably higher in 3-ethyl tertiary alcohol 7 than in 3-methyl tertiary alcohol 3 and 4-benzyl-t(4)-hydroxypiperidine 2. This may be explained if we take into account the different conformations of the ethyl group in t(4)-hydroxy-3-ethyl-2,6-diphenylpiperidine 12 and 3-ethyl tertiary alcohol 7.     

On the formation of phenyldiacetylene (C6H5CCCCH) and D5-phenyldiacetylene (C6D5CCCCH) studied under single collision conditions

The crossed molecular beam reactions of the phenyl and D5-phenyl radical with diacetylene (C(4)H(2)) was studied under single collision conditions at a collision energy of 46 kJ mol(-1). The chemical dynamics were found to be indirect and initiated by an addition of the phenyl/D5-phenyl radical with its radical center to the C1-carbon atom of the diacetylene reactant. This process involved an entrance barrier of 4 kJ mol(-1) and lead to a long lived, bound doublet radical intermediate. The latter emitted a hydrogen atom directly or after a few isomerization steps via tight exit transition states placed 20-21 kJ mol(-1) above the separated phenyldiacetylene (C(6)H(5)CCCCH) plus atomic hydrogen products. The overall reaction was determined to be exoergic by about 49 ± 26 kJ mol(-1) and 44 ± 10 kJ mol(-1) as determined experimentally and computationally, thus representing a feasible pathway to the formation of the phenyldiacetylene molecule in combustion flames of hydrocarbon fuel.     

Syntheses and rearrangements of tris(hydroxymethyl)phosphine and tetrakis(hydroxymethyl)phosphonium salts

Abstract

Tetrakis(hydroxymethyl)phosphonium (HOCH₂)₄P⁺ salts, particularly the chloride (THPC) and sulfate (THPS), are among the most accessible organophosphorus compounds that can be made quantitatively from PH₃ and formaldehyde in aqueous media under ambient conditions. These phosphonium salts are air-stable, and are widely used as reactants in organic syntheses, as well as in textile or oil industries. Synthesis of tris(hydroxymethyl)phosphine (THP), an active component of the salts, is more complicated because direct synthesis from PH₃ and CH₂O requires either pressure and high temperature, at which THP rearranges into bis(hydroxymethyl)methylphosphine oxide, CH₃P(O)(CH₂OH)₂, or a metal catalyst that is usually difficult or impossible to recover. Syntheses of THP based on neutralization of the salts are more convenient but require pH control and additional steps to separate THP from CH₂O. This review summarizes literature data on syntheses and purification of the salts and THP, and side reactions such as thermal rearrangement and oxidation.     

Protecting group controlled stereoselective alkylation of asymmetrized bis(hydroxymethyl)propanoates (BHYMP*)

The diastereoselective methylation of the enolates derived from some asymmetrized bis(hydroxymethyl)propanoates (BHYMP*) has been studied. Good results were achieved when one of the two hydroxymethyl groups was unprotected. The induction was interpreted on the basis of an acyclic stereocontrol governed by stereoelectronic effects.     

Chemistry of the versatile (hydroxymethyl)phosphinyl P(O)CH2OH functional group

(Hydroxymethyl)phosphorus compounds are well-known and valuable compounds in general; however the use of (hydroxymethyl)phosphinates R(1)P(O)(OR(2))CH(2)OH in particular has been much more limited. The potential of this functionality has not yet been fully realized because the mild unmasking of the hydroxymethyl group was not available. The mild oxidative conversion of R(1)P(O)(OR(2))CH(2)OH into R(1)P(O)(OR(2))H using the Corey-Kim oxidation is described. Other reactions preserving the methylene carbon are also reported.     

Asymmetric synthesis of 3-amino-4-hydroxy-2-(hydroxymethyl)pyrrolidines as potential glycosidase inhibitors

Three diastereoisomers of 3-amino-4-hydroxy-2-(hydroxymethyl)pyrrolidine have been synthesised by a divergent route starting from trans-4-hydroxy-L-proline. Regio- and stereoselective introduction of the 3-amino and 4-hydroxyl functional groups was achieved using either a tethered aminohydroxylation reaction or by employing intra- and intermolecular epoxide-opening strategies. Preliminary biological data indicate that two of these novel amino pyrrolidines are moderate inhibitors of beta-galactosidase.     

An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA

We show for the first time that it is possible to obtain LNA-like (Locked Nucleic Acid 1) binding affinity and biological activity with carbocyclic LNA (cLNA) analogs by replacing the 2'-oxygen atom in LNA with an exocyclic methylene group. Synthesis of the methylene-cLNA nucleoside was accomplished by an intramolecular cyclization reaction between a radical at the 2'-position and a propynyl group at the C-4' position. Only methylene-cLNA modified oligonucleotides showed similar thermal stability and mismatch discrimination properties for complementary nucleic acids as LNA. In contrast, the close structurally related methyl-cLNA analogs showed diminished hybridization properties. Analysis of crystal structures of cLNA modified self-complementary DNA decamer duplexes revealed that the methylene group participates in a tight interaction with a 2'-deoxyribose residue of the 5'-terminal G of a neighboring duplex, resulting in the formation of a CH...O type hydrogen bond. This indicates that the methylene group retains a negative polarization at the edge of the minor groove in the absence of a hydrophilic 2'-substituent and provides a rationale for the superior thermal stability of this modification. In animal experiments, methylene-cLNA antisense oligonucleotides (ASOs) showed similar in vivo activity but reduced toxicity as compared to LNA ASOs. Our work highlights the interchangeable role of oxygen and unsaturated moieties in nucleic acid structure and emphasizes greater use of this bioisostere to improve the properties of nucleic acids for therapeutic and diagnostic applications.     

Electrolytic methoxylation of 3,4-bis(hydroxymethyl) furan and synthesis of 4,5-bis-(hydroxymethyl) pyridazine

3,4-Bis(hydroxymethyl)furan was electrolytically methoxylated during intense cooling. 4,5-Bis(hydroxymethyl)pyridazine was obtained by reaction of the methoxylation product — 2,5-dimethoxy-3,4-bis (hydroxymethyl)-2,5-dihydrofuran — with hydrazine hydrate.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1306–1307, October, 1970.     

Long-range 4J coupling constants and conformation of the four-membered heterocycles

The correlation between the puckering angle of the four-membered cycle and ⁴J has been obtained from analysis of the PMR spectra of some 2-substituted azetidines and oxetanes. The absolute values of ⁴J_cis and ⁴J_trans were found to decrease with decreasing of the puckering angle.     

Cellulose polymorphism study with sum-frequency-generation (SFG) vibration spectroscopy: identification of exocyclic CH2OH conformation and chain orientation

Sum-frequency-generation (SFG) vibration spectroscopy is a technique only sensitive to functional groups arranged without centrosymmetry. For crystalline cellulose, SFG can detect the C6H₂ and intra-chain hydrogen-bonded OH groups in the crystal. The geometries of these groups are sensitive to the hydrogen bonding network that stabilizes each cellulose polymorph. Therefore, SFG can distinguish cellulose polymorphs (I_β, II, III_I and III_II) which have different conformations of the exocyclic hydroxymethylene group or directionalities of glucan chains. The C6H₂ asymmetric stretching peaks at 2,944 cm^?1 for cellulose I_β and 2,960 cm^?1 for cellulose II, III_I and III_II corresponds to the trans-gauche (tg) and gauche-trans (gt) conformation, respectively. The SFG intensity of the stretch peak of intra-chain hydrogen-bonded O–H group implies that the chain arrangement in cellulose crystal is parallel in I_β and III_I, and antiparallel in II and III_II.     

One-pot cyclization of dilithiated nitriles with isothiocyanates and epibromohydrin. Synthesis of 2-cyano-1-(hydroxymethyl)cyclopropanes and 2-cyanomethylidene-4-(hydroxymethyl)thiazolidines

The cyclization of dilithiated nitriles with epibromohydrin afforded 2-cyano-1-(hydroxymethyl)cyclopropanes. 2-Cyanomethylidene-(4-hydroxymethyl)thiazolidines were prepared by one-pot cyclization of dilithiated nitriles with isothiocyanates and epibromohydrin.