Metal clips induce folding of a short unstructured peptide into an alpha-helix via turn conformations in water. Kinetic versus thermodynamic products

Short peptides corresponding to two to four alpha-helical turns of proteins are not thermodynamically stable helices in water. Unstructured octapeptide Ac-His1-Ala2-Ala3-His4-His5-Glu6-Leu7-His8-NH(2) (1) reacts with two [Pd((15)NH(2)(CH(2))(2)(15)NH(2))(NO(3))(2)] in water to form a kinetically stable intermediate, [[Pden](2)[(1,4)(5,8)-peptide]](2), in which two 19-membered metallocyclic rings stabilize two peptide turns. Slow subsequent folding to a thermodynamically more stable two-turn alpha-helix drives the equilibrium to [[Pden](2)[(1,5)(4,8)-peptide]] (3), featuring two 22-membered rings. This transformation from unstructured peptide via turns to an alpha-helix suggests that metal clips might be useful probes for investigating peptide folding.     

Stabilisation of a nucleic acid three-way junction by an oligonucleotide containing a single 2'-C to 3'-O-phosphate butylene linkage prepared by a tandem RCM-hydrogenation method

A cyclic dinucleotide with a butylene linker between the upper 2'-C position and the 3'-O-phosphate linkage was synthesised from simple nucleoside building blocks via a tandem ring-closing metathesis and hydrogenation procedure. The major of two phosphorus epimers was incorporated into an oligodeoxynucleotide, as well as into an LNA-DNA mixmer oligonucleotide. These were evaluated as parts in three different secondary structures, a duplex, a bulged duplex and a three-way junction, with both DNA and RNA complements. In the DNA:RNA hybrid molecule, the oligodeoxynucleotide containing this single 2'-C to 3'-O-phosphate butylene linkage was found to stabilise a three-way junction.     

Palladium-catalyzed synthesis of arylamines from aryl halides and lithium bis(trimethylsilyl)amide as an ammonia equivalent

[reaction: see text]. A simple, palladium-catalyzed method to convert aryl halides to the parent anilines using lithium bis(trimethylsilyl)amide (LiN(SiMe3)2) is reported. The reaction is catalyzed by Pd(dba)2 and P(t-Bu)3 and can be run with as little as 0.2 mol % of catalyst. The reaction is faster than competing generation of benzyne intermediates and, therefore, provides the aniline products regiospecifically.     

Molecular orbital interpretation of X-ray emission spectra of ClCN and ONCl

Ab initio as well as semi-empirical SCF MO calculations are presented for ClCN and ONCl. The relative intensities for Cl Kβ emission in the two molecules were calculated. The calculated spectra from the ab initio wavefunctions are in excellent agreement with experiments.     

Crystal structure and magnetic structure of TbOOH

The monoclinic modification of terbium oxide hydroxide, TbOOH, was prepared using hydrothermal technique. The crystal structure was investigated by three-dimensional single-crystal X-ray analysis and was refined to a conventional R-value of 8.1%. The space group is $\text{P2}{}_1\text{m}$, No. 11, with a = 6.04 Å, b = 3.69 Å, c = 4.33 Å, and β = 109.0°. The terbium atom is seven coordinated with oxygen atoms, and the structure is not hydrogen bonded.The compound is antiferromagnetic with a Néel temperature of 10°K. Neutron diffraction powder patterns were measured at 300°K and 4.2°K. The magnetic super lattice reflections were indexed on the basis of a monoclinic unit cell with the dimensions a_M = 2a, b_M = b, c_M = c, and β_M = β, where a, b, c, and β are the dimensions of the chemical unit cell. The structure contains two independent magnetic atoms. A nonclinear antiferromagnetic arrangement of the spins describes the magnetic structure. The spin at one atom has an angle of 43° with the ac plane and the projection of the spin on the ac plane has an angle of 59° with the a axis. The spin on the other atom has an angle of ?43° with the ac plane, the projection having the same angle of 59° with the a axis.     

π‐Facial Selectivity in the Formation of Tricarbonylchromium(0) Complexes of Estra‐1, 3, 5(10), 6‐tetraenes

The preparation of two η⁶‐estra‐1, 3, 5(10), 6‐tetraene tricarbonylchromium complexes 4 and 6 are described. In both cases only one stereoisomer can be isolated, in contrast to other estrane‐tricarbonylchromium complexes, where complexations are non‐stereoselective. X‐ray crystal structural analysis of 4 discloses that only the more sterically hindered β‐facial isomer is formed. It is assumed that the 6, 7‐olefinic moiety exerts a directive influence on the complexation.     

Observations on clear solution silicalite-1 growth by nanoslabs

Several research groups have reported the presence of nanometer-sized particles (nanoslabs) in clear solutions, which precipitate the crystalline MFI (ZSM-5) structure. Debate about the growth mechanism for Al-free ZSM-5 (silicalite-1) has revolved around growth by small silicate units (monomers, dimers, etc.) from solution vs growth by nanoslab addition. A model developed for precipitation of uniform sized colloids by addition of sub-colloidal precursor units has been adapted for this zeolite synthesis system. Parameter values were adjusted for the simulation results to match experimental observations from work reported previously, at least to the extent possible. The model involved the simultaneous solution of up to 6000 ordinary differential equations, and required computation times of up to 24 h. The results shed light on the crystal growth mechanism, but pose questions for further investigations of the nucleation mechanism.     

Genotoxic properties of 2-dodecylcyclobutanone, a compound formed on irradiation of food containing fat

When food containing fat is treated by ionizing radiation, a group of 2-alkylcyclobutanones is formed. These components contain the same number of carbon atoms as their precursor fatty acids and the alkyl group is located in ring position 2. Thus, from palmitic acid 2-dodecylcyclobutanone is derived. To date, there is no evidence that the cyclobutanones occur in unirradiated food. Therefore, these components cannot be considered inherent to food, and for questions pertaining to risk assessment of irradiated food it would be advisable to determine the genotoxic and toxic potentials of cyclobutanones. Measurements of DNA damage in cells exposed to 2-dodecylcyclobutanone, employing the single cell microgel electrophoresis technique, have been carried out. In vitro experiments using rat and human colon cells indicate that 2-docylcyclobutanone in the concentration range of about 0.30 – 1.25 mg/ml induces DNA strand breaks in the cells. Simultaneously, a concentration related cytotoxic effect is observed as was determined by trypan blue exclusion. To which extent these in vitro findings are of relevancy for the in vivo human exposure situation needs to be investigated in further studies. In vivo tests in rats are in progress.     

Über die Wahl der Lösungsmittelsysteme bei der papierchromatographischen Trennung organischer Verbindungen

Zusammenfassung An praktischen Beispielen wurde gezeigt, in welcher Weise die Trennung organischer Verbindungen mittels Papierchromatographie erzielt werden kann. Man ist nicht auf einige bewährte Lösungsmittel systeme allein angewiesen, sondern kann von Fall zu Fall systematisch neue und geeignete Systeme benützen. Es hat sich bewährt, sich nach den elementaren Löslichkeitsregeln für organische Stoffe zu richten, unter der Voraussetzung, daß die zu chromatographierende Verbindung in der stationären Phase gut, in der mobilen Phase dagegen weniger löslich ist. Durch Änderung der stationären Phase (Wasser, nicht wäßriges, polares Lösungsmittel, nicht polares Lösungsmittel) oder der Polarität und Zusammensetzung der mobilen Phase kann man das Wandern der Flecke am Chromatogramm beeinflussen, beliebige R_fWerte erhalten und in vielen Fällen auch eine beliebige Reihenfolge der Verbindungen am Chromatogramm erzielen.Da die Löslichkeit organischer Verbindungen von intermolekularen Kräften abhängig ist, erscheint das Problem im Zusammenhang mit strukturellen Einflüssen sehr kompliziert und muß für jeden Fall auf eigene Weise gelöst werden. Die Löslichkeitseigenschaften können weiter durch Benutzung reaktiver Lösungsmittel beeinflußt werden, die z. B. die Verbindungen in wasserlösliche Salze überführen können. Dabei ist an die möglichen Komplikationen, die bei ionisierbaren Verbindungen durch Dissoziation und Hydrolyse entstehen können, zu achten.Von den Hauptfaktoren, die eine Trennung ermöglichen können, seien die folgenden erwähnt: funktionelle Gruppen, ihre Anzahl, Polarität, gegenseitige Stellung, bzw. ihre Basizität oder Azidität, C-Atomanzahl in homologen Verbindungen, inter- und intramolekulare Wasserstoffbindungen, sterische Faktoren u. a. Es ist dann von der Art des gewählten Lösungsmittelsystems abhängig, welche der genannten Faktoren im Vordergrund stehen und welche beseitigt werden.Wenn die Löslichkeitsunterschiede der zu trennenden Stoffe zu gering sind, um gute Trennungen zu ermöglichen, ist es zweckmäßig, die Verbindungen in solche Derivate zu überführen, deren Strukturunterschiede größer sind.

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Summary Practical examples are given to show how organic compounds can be separated by means of paper chromatography. The operator is not limited to tested solvent systems, but can use new suitable systems as the occasion demands. It has been found best to abide by the elementary rules of solubility of organic compounds, provided the compound to be chromatographed is quite soluble in the stationary phase but less soluble in the mobile phase. By altering the stationary phase (water, nonaqueous, polar solvent, non-polar solvent) or the polarity and composition of the mobile phase, the migration of the stains in the chromatogram can be influenced, selectedR _f -values can be obtained, and in many cases it is also possible to secure a desired succession of the compounds on the chromatogram.Since the solubility of organic compounds depends on intermolecular forces, the problem in connection with structural influences appears very complicated and must be solved individually for each case. Moreover, the solubility characteristics can be affected by using reactive solvents; for instance, the compounds can be converted into water soluble salts. Under such circumstances, sight must not be lost of the complications which may arise because of the dissociation and hydrolysis of ionizable compounds. The following are among the chief factors, which may make a separation possible: functional groups, their number, polarity, relative position, their basicity or acidity, C-atom number in homologous compounds, inter- and intramolecular hydrogen bonds, steric factors, etc. It then depends on the type of solvent system selected, which of these factors are predominant and which can be neglected or eliminated.If the solubility differences are too slight to permit good separations, the compounds to be separated should, if possible, be converted into derivatives whose structural differences are more pronounced.

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Résumé Des exemples pratiques montrent comment il est possible d'effectuer la séparation de combinaisons organiques par Chromatographie sur papier. Il n'est pas uniquement fait appel à des systèmes de solvants éprouvés mais, dans certains cas, de nouveaux systèmes appropriés sont systématiquement utilisés.Il s'est avéré satisfaisant de faire appel aux règles élémentaires de solubilité des substances organiques sous réserve que la combinaison à chromatographier soit suffisamment soluble dans la phase stationnaire et moins soluble dans la phase mobile. En faisant varier la phase stationnaire (eau, solvant non aqueux, solvant polaire, solvant non polaire) ou la polarité et la composition de la phase mobile, il est possible d'influencer la migration des taches du chromatogramme, d'obtenir des valeurs deR _f désirées et, dans de nombreux cas, d'obtenir les combinaisons dans un ordre déterminé sur le chromatogramme.La solubilité des combinaisons organiques étant fonction des forces intermoléculaires il en résulte que le problème se complique considérablement dans la mesure où l'on considère les influences structurelles et que chaque cas particulier doit recevoir une solution qui lui est propre. Les propriétés de solubilité peuvent en outre être influencées par l'emploi de solvants réactifs qui peuvent transformer, par exemple les combinaisons en sels solubles dans l'eau. Il faut alors tenir compte des possibilités de complications qui peuvent apparaître par dissociation et hydrolyse des combinaisons ionisables.Parmi les principaux facteurs qui permettent une séparation, il convient de mentionner les suivants: les groupes fonctionnels, leur nombre, leur polarité, leur position relative, ou encore leur acidité ou leur basicité, le nombre d'atomes de carbone de combinaisons homologues, les liaisons hydrogène inter- et intramoléculaires, les facteurs stériques, etc. Suivant la nature du système solvant choisi pourront alors varier les facteurs dont l'effet est prépondérant et ceux dont l'effet est nul. Lorsque les différences de solubilité des substances à séparer sont trop faibles pour permettre des séparations satisfaisantes, il est commode de transformer les combinaisons en dérivés dont les différences de structure soient plus importantes.

     

Biradicals/zwitterions from thermolysis of enyne-isocyanates. Application to the synthesis of 2(1H)-pyridones, benzofuro[3,2-c]pyridin-1(2H)-ones, 2,5-dihydro-1H-pyrido[4,3-b]indol-1-ones, and related compounds

Thermolysis of benzannulated enyne-isocyanates 13 and enyne-isocyanates 36 and 37 promoted the cycloaromatization reactions to generate in situ O,4-didehydro-2-hydroxyquinolines and O,4-didehydro-2-hydroxypyridines, respectively, as reactive intermediates. These cycloaromatized intermediates could be captured either as biradicals and/or as zwitterions depending on the nature of the substituent at the alkynyl terminus. The intermediate derived from cycloaromatization of 13a bearing a phenyl substituent could be regarded as biradical 14, which then abstracts hydrogen atoms from gamma-terpinene leading to 2(1H)-quinolinone 15. Alternatively, the same intermediate could also be regarded as zwitterion 14', which then undergoes an initial hydride abstraction from gamma-terpinene followed by protonation to produce 15. The presence of a 2-phenylethyl substituent in 13b and 37a or a 2-methylphenyl substituent in 37b also allowed the resulting intermediates to be captured intramolecularly either as biradicals or as zwitterions, producing 2(1H)-quinolinone 19, 2(1H)-pyridone 39, and benzopyranopyridine 43, respectively. On the other hand, with a 2-methoxyphenyl, a 2-(dimethylamino)phenyl, or a 3-methoxypropyl substituent, the chemical behavior of the cycloaromatized adduct could be best accounted for in terms of a zwitterionic intermediate leading to benzofuro[3,2-c]quinolin-6(5H)-one (20), 5,11-dihydro-11-methyl-6H-indolo[3,2-c]quinolin-6-one (25), benzofuro[3,2-c]pyridin-1(2H)-one 44, 2,5-dihydro-2,5-dimethyl-1H-pyrido[4,3-b]indol-1-one 46, and related compounds. Interestingly, thermolysis of 37f bearing a 2-(methoxymethyl)phenyl substituent at the alkynyl terminus produced the unexpected benzopyranopyridine 56 as the major product in a process involving the cleavage of the bond between the methoxyl oxygen and the adjacent methylene carbon. The efficiency and selectivity of the cycloaromatization reaction could also be enhanced by the introduction of 1.1 to 10 equiv of dimethylphenylsilyl chloride to the reaction mixture to capture the resulting zwitterion.