Showing papers on "Intramolecular force published in 1968"

Studies of inter- and intramolecular interaction in mononucleotides by proton magnetic resonance.

Abstract: The interaction and conformation of 5’, 3’-, and 2’-nucleoside monophosphates in aqueous solutions have been studied mainly by pmr at varying concentrations and pH. The chemical shifts of the base protons and H-1 ’ protons of the adenine nucleotides were found to shift upfield at increasing concentration in a manner analogous to adenosine. This result indicates that the AMP molecules also associate to form vertical stacks with similar geometry in solution, a conclusion also supported by the vapor pressure osmometry data. The phosphoryl substitution at the 5 ’ or 3‘ position reduces the tendency of association to about 30-40z as compared to the corresponding adenine nucleosides. Substitution of the phosphoryl group at the 2‘ position has a greater influence in reducing the association, especially in the dianionic form. The 5 ‘-phosphoryl group (not the 3‘or 2’-phosphate) was found to have a specific deshielding effect on the H-8 proton (and not H-2) of the 5’-purine nucleotides and on the H-6 proton (and not H-5) of the 5’-pyrimidine nucleotides. This deshielding effect is largest (-0.2 ppm) when the phosphate is in the dianion form (above pD 7.4), less when in the monoanion form (-0.12 ppm, below p D 5.9), and least as the monomethyl ester (-0.07 ppm). These data indicate that the 5’-nucleotides must be in the “anti” conformation. The mechanism of this phosphate deshielding effect is discussed based on the observation that this effect appears to be dependent on the “acidity” of the sensitive protons. Comparison of the pmr data on the ribose and deoxyribose 5’-nucleotides suggests the presence of intramolecular hydrogen bonding between the 2‘-OH group and the N-3 of the purine or the 2-keto of the pyrimidine. or the past few years the properties of various purine F bases a n d purine and pyrimidine nucleosides in aqueous solutions have been studied extensively by vapor pressure osmometry a n d by proton magnetic resonance. *-’ The results conclusively show that these compounds, especially the purines and the purine nucleosides, associate extensively in water primarily by way of vertical stacking of base rings. In the studies of cooperative binding of adenosine to polyuridylic acid,* the stacking energy has been shown to be the major factor contributing to the conformational stability of nucleic acid. In the continuation of our recent research on the purine a n d pyrimidine nucleosides by pmr,607 we report here the investigation on the solution properties of purine and pyrimidine mononucleotides. We have studied the influence of the charged phosphate group upon the stacking interactions of these mononucleotides. I n addition, we have found a specific intramolecular deshielding of the H-6 proton of pyrimidine nucleotides a n d the H-8 proton of purine nucleotides by the 5’-phospha te group. This finding indicates t ha t in aqueous solution the 5 ’-nucleotides are in “anti” conformation. Also, comparison of the da ta on the deoxyribonucleotides a n d the ribonucleotides suggests the possibility of intramolecular hydrogen bonding of the 2’-hydroxyl g roup to the bases in these compounds. (1) (a) Supported in part by a program project grant, National Institutes of Health (GM 10802-04), and by grants from the National Science Foundation (GB-5483 and GB-767). (b) Resented in part at the Ninth Annual Biophysics Meeting, San Francisco, Calif., 1965. (2) P. 0. P. Ts’o, I. S. Melvin, and A. C. Olson, J . Amer. Chem. SOC., 85. 1289 (1 963). (3) P. 0. P. Ts’o and S. I. Chan, ibid., 86, 4176 (1964). (4) S. I. Chan, M. P. Schweizer, P. 0. P. Ts’o, and G. K. Helmkamp, (5) M. P. Schweizer, S. I. Chan, and P. 0. P. Ts’o, ibid., 87, 5241 (6) 0. Jardetzky, Biopolym. Symp., 1, 501 (1964). (7) A. D. Broom, M. P. Schweizer, and P. 0. P. Ts’o, J . Arner. Chem. (8) W. M. Huang and P. 0. P. Ts’o, J . Mol. Biol., 16, 523 (1966). ibid., 86, 4182 (1964).

Some aspects of stereochemistry and hydrogen bonding of carbohydrates related to polysaccharide conformations

Abstract: Some general rules governing hydrogen bonding at the ring oxygens of furanosides, pyranosides, and bridge oxygens of glycosides have been formulated from existing data on crystal structures of carbohydrates. Ring oxygens of the majority of the glycopyranosides in the hemiacetal or acetal form are involved in hydrogen bonding such that the hydrogen bond direction is usually equatorial to the ring plane and not axial. In contrast, there are no known examples of ring oxygens of glycofuranosides and methyl-glycopyranosides displaying hydrogen bonding in the crystal. Also, the bridge oxygens of glycosides are not involved in hydrogen bonding. The observed shortening in the exocyclic and endocyclic anomeric C(1)O bonds and the geminal CO bonds indicate that compounds with two oxygen atoms attached to the same saturated carbon atom may participate in double-bond-no-bond resonance interaction in the same manner as difluoromethane. It is also possible that under these circumstances the carbon atom exhibits greater than tetracovalency. The “anomeric effect” may also be related to (a) the differences in the “double bonding” or bond shortening in the anomeric CO bonds of the anomeric glycopyranosides, (b) the shorter intramolecular O(1)…O(5) non-bonded interaction, and (c) the smaller O(1)C(1)O(5) valence angle in the equatorial anomer compared to the axial anomer. An analysis has been made of the energetically preferred conformations about the glycosyl and glycosidic bonds of 1,4- and 1,3-polysuc-charides. In the 1a, 4e-glycopyranosides the projected angle ϕ1 [O(5)C(1)OR, where R = C or H] is positive, while it is negative in the 1e, 4e-glycopyranosides. Angle ϕ2 [C(1)OC(4′)C(3′)] is positive in both the 1,4-anomeric polyglycosides. 1e, 4e- and 1a, 4e -polysaccharides are stabilized by intramolecular O(5)…HO(3′) and O(2′)…O(3′) hydrogen bonding, respectively, and generate linear and helical (cyclic) structures, respectively. 1e, 3e- and 1a, 3e-polysaccharides may be stablized by one of two possible intramolecular hydrogen-bonding schemes such that the 1a, 3e -polysaccharides generate helical structures while the 1a, 3e-polysaccharides generate nonhelical structures. The conformation about the C(5)C(6) bond in the pyranosides falls into two groups where the angle ϕ00 [O(5)C(5)C(6)O(6)] is either positive, ∼+60 ± 30°, or negative, ∼–60 ± 30°, the former conformation being found more frequently. In the furanosides the latter conformation is preferred.

The crystal structure of α-glycylglycine

Abstract: The cystal structure of the α crystal form of glycylglyeine, -CO 2 CH 2 NHCOCH 2 NH 3 + , has been investigted. The cell dimensions are a = 7·70, b = 9·57, c = 9·48 A β = 124°35'. The space group is P2 1 /a with four molecules per cell. Mo kα rays were used. The trial structure was derived by use of part-cell Patterson methods and modlfied Banerjee equations. Final refinement was by block-diagnol anisotropic least-squares adjustment to an R of 12·3 and yielded standard deviations of about 0·007A in bond lengths.The intramolecular chemical bond lengths and interbond angles agree well with those found for the same molecule in the previously reported β crystal form but the configuration of the molecule is somewhat different. There is an angle of about 22·4° between the plane of the amide group and that of the carboxyl group. In the β crystal these group were coplanar within experimental error. Since the α form is probably the stable form, this distortion presumbly permits better molecular packing with stronger hydrogen bonds and van Waals interactions.

Nonempirical Molecular‐Orbital Calculations for Protonated Formaldehyde, Acetaldehyde, and Formic Acid

Abstract: Nonempirical molecular‐orbital calculations based on the Roothaan scheme are reported for protonated species of formaldehyde, acetaldehyde, and formic acid. In these calculations a small Gaussian basis is used, which is obtained from optimized atomic orbitals. The results are interpreted with the help of a Mulliken‐type population analysis. A number of structural parameters was obtained by minimization of the total energy. Values found for the C–O distances are: 1.23 A in formaldehyde, 1.27 A in protonated formaldehyde, 1.31 A in protonated formic acid. In all protonated molecules the C–O–H angle was close to 120°. For protonated acetaldehyde the stability of the configuration [Complex Equation] was found to be greater than that of [Complex Equation] by 1.4 kcal/mole. For protonated formic acid the stablest system was found to be [Complex Equation] followed by [Complex Equation] which is 1.5 kcal/mole higher in energy. The other possible structure [Complex Equation] was found to be another 6.0 kcal/mole higher in energy. The mechanism of the intramolecular interconversion that transforms one configuration of the protonated system into another depends on the strength of the C– bond. In protonated aldehydes a rotation around the C–O bond is rather difficult and has an energy barrier of 25–30 kcal/mole. A motion in the plane, however, requires only 17–18 kcal/mole, so that it is likely that in aldehyde systems this motion causes the interconversion. In protonated formic acid the C–O bond is not as strong as in aldehydes, and a rotation around the C–O bond requires only 15 kcal/mole, while the motion in the plane still requires 17 kcal/mole.

Nuclear magnetic resonance studies on niobium and tantalum penta-alkoxides

Abstract: Variable-temperature n.m.r. studies have proved the double alkoxide-bridged bi-octahedral (edge-shared) structure of the dimeric penta-alkoxides M2(OR)10, where M = Nb or Ta and R = Me, Et, or Bui. Rapid intramolecular double exchange of alkoxide groups occurs between (i) the two types of terminal group and (ii) the terminal and bridging groups and the activation energies Ett and Etb were evaluated for Ta2(OMe)10. The presence of a monomer–dimer equilibrium was proved for the pentaisopropoxides and from equilibrium constants at various temperatures the enthalpy of dissociation of the dimer was evaluated. The monomeric t-butoxides showed a rapid intramolecular exchange down to –90°. Alcohol interchange with dimeric species was slower than with monomers.

Photochemische Reaktionen: 46. Mitteilung [1]: Zur Photochemie von α,β‐ungesättigten γ‐Aldehydoketonen I. Die UV.‐Bestrahlung von 3,19‐Dioxo‐17β‐acetoxy‐Δ4‐androsten

Abstract: Irradiation of 3,19-dioxo-17β-acetoxy-Δ4-androstene (2) at room temperature in either of its two absorption bands centered at about 245 and 315 nm, respectively, led to products 21, 22, and 23 (Chart 3). Compounds 21 and 22 result from rearrangements involving intramolecular formal 1,2- (21) and 1,3-shifts (22) of the angular formyl group, and the formation of compound 23 proceeds through the elimination of the formyl radical and the incorporation of a hydrogen from the medium. Evidence favors the latter process to be a secondary radical reaction rather than a primary photochemical step.

Die Dienol‐Benzol‐Umlagerung von Allyldienolen: aromatische [1,2]‐, [3,3]‐ und [3,4]‐sigmatropische Umlagerungen

Abstract: The dienol-benzene rearrangement of syn and anti-4-allyl-4-methylcyclohexa-2,5-dien-1-ol (syn and anti 15) occurs by formation of a benzonium ion intermediate in p-toluene-sulphonic acid in ether below 0° and leads to a mixture of 2-, 3- and 4-allyltoluenes in the ratio 54:10:36. By the introduction of 14C-, D- and methyl labelled dienols it is shown that only the allyl group migrates and that this rearrangement is an intramolecular, one-step process. The formation of 2-allyltoluene occurs with retention, whereas the 3- and 4-allyltoluenes are formed by inversion of the carbon skeleton of the migrating allyl group. These rearrangements can be therefore classified as suprafacial, aromatic sigmatropic reactions of the order [1,2], [3,3] and [3,4]. The transition state can be postulated as representing a positively charged complex consisting of interacting allyl and tolyl radicals. The interaction of the two parts is controlled by the symmetry of the highest occupied π-orbitals (ψ3 for toluene and ψ2 for the allyl group) in agreement with the Woodward-Hoffmann rules. The better “distribution” of the charge in the transition state of these reactions in comparison to the ground state is chiefly responsible for the CoPE-like [3,3] sigmatropic reaction occurring at low temperatures. In general, sigmatropic reactions in charged systems are faster. The rearrangement of syn and anti 2-allyl-2-methylcyclohexa-3,5-dien-1-ol (syn and anti 28) gives results similar to those obtained with the para-allyldienols. The thermal rearrangement of 15 and 28 gives 3-allyltoluene by a [3,3] sigmatropic Cope rearrangement followed by elimination of water.

Spectroscopic studies of inorganic fluoro-complexes. Part II. 19F nuclear magnetic resonance studies of tin(IV) fluoro-complexes

Abstract: Approximately 100 anions of the general type SnF6–nXn2– have been characterised in solution by 19F n.m.r. spectroscopy, where X is one of a wide range of unidentate ligands or half a bidentate ligand. Complexes containing two different groups X, and mononegative anions containing a neutral ligand, have also been studied. cis/trans ratios have been obtained for many of the geometrical isomers. 19F chemical shifts and tin–fluorine and fluorine–fluorine coupling constants are reported. The 19F chemical shifts δ(relative to the SnF62– ion) of a fluorine atom in these complexes are given, to a good approximation, by δ=pC+qT, where C and T are constants characteristic of the ligand X, and p and q are the number of substituents cis and trans to the fluorine atom respectively. It is suggested that the effect of ligands in cis-positions is largely due to intramolecular van der Waals interactions. Approximate equilibrium constants have been obtained for the displacement of fluoride ion from SnF62– by chloride, bromide, and hydroxide ions, and by water.

Elektronen‐Donator‐Acceptor‐Komplexe bei Polypeptiden II. Problemstellung und orientierende Versuche mit Acceptoren des neuen Phtalimid‐ Typs

Abstract: Phthalimides, 4-nitrophthalimides, and tetrachlorophthalimides (exemplified by methyl Nα-phthalyl-glycinate, 4-nitrophthalimide, ethyl Nα-(4-nitrophthalyl)-glycinate, and methyl Nα-tetrachlorophthalyl-glycinate) give colored molecular complexes with Nα-benzyloxycarbonyl-ar-pentamethyl-phenylalanine, Nα-acetyl-p-dimethylamino-phenylalanine, and Nα-acetyl-tryptophane, as well as with the simpler compounds hexamethylbenzene, N, N-dimethylaniline, N, N-dimethyl-p-toluidine, and indole, in various organic solvents. The association constants are small, and vary between 0.4 and 1.2 l/mol as measured spectroscopically. Enthalpies of complex formation lie between (−) 0.5 and (−) 2.5 kcal/mole. They are within the range assumed for VANDER WAALS interactions between hydrophobic side-chains of amino-acids. This is essential if one would want to use such complexes as intra- or intermolecular conformational probes in synthetic polypeptides. The broad absorption maxima of the complexes lie between 350 and 490 nm, extinction coefficients are in the range reported for charge transfer complexes, 500 to 2000. Assignment of the long wavelength absorption to a charge transfer transition seems quite justified by the calculated values of energy coefficients (HMO-method) for the new class of phthalimide acceptors and the donors, as well as by the applicability of the BRIEGLEB relationship between h νmax, ionisation energy, electron affinity, and distance between the planes of donor and acceptor in the complex between ethyl Nα-(4-nitrophthalyl)-glycinate and hexamethylbenzene. On the basis of absorption maxima, the relative acceptor strengths are: 4- nitrophthalimide > tetrachlorophthalimide > phthalimide. Phthalyl, nitrophthalyl, and tetrachlorophthalyl derivatives of tryptophane, pentamethylphenylalanine, and p-dimethylamino-phenylalanine are colored compounds and behave like intramolecular charge transfer complexes. The syntheses of all required compounds are described. N-Ethoxycarbonyl derivatives of 4-nitrophthalimide and of tetrachlorophthalimide are used to prepare 4-nitrophthalyl and tetrachlorophthalyl derivatives of amino-acids.

Solvent effects on the conformations of ortho-substituted acetanilides

Abstract: In acetanilides bearing nitro, halogen, alkoxyl, or carboxyl substituents in the ortho position, the intramolecular hydrogen bond is disrupted by polar solvents and the acetamido group adopts a pos...

Electronic structures of the Meisenheimer and Janovsky complexes

Abstract: In order to study the electronic spectra and stabilities of the Meisenheimer and Janovsky complexes, the π-electron structures of the 1,3,5-trinitro-, 1,3-dinitro-, 1,5-dinitro-, 2,4-dinitro-, and 3-nitropentadienyl anions were calculated by the method of composite molecules. The Pariser-ParrPople type SCF-CI calculation was also performed for the 1,3,5-trinitropentadienyl anion. The lower electronic transitions of these ions are assigned as due to charge-transfer from the pentadienyl group to the nitro group. Calculated transition energies and intensities agree well with the observed values so far as comparison can be done. Relative stabilities of these ions can well be predicted in terms of intramolecular charge-transfer in the ground state, the extent of which is mostly determined by the mode of substitution of nitro groups. The calculated bond order can well explain the bond lengths in the pentadienyl part determined by the X-ray crystal analysis technique.

Intramolecular Interaction between Hydroxyl Group and Carbonyl Moiety in Keto-alcohols

Abstract: The O–H stretching absorption (νO–H) spectra of some keto-alcohols have been examined. The νO–H shift to the lower frequency due to the intramolecular O–H··· bonding can roughly be correlated to the geometry of the hydroxyl group relative to the n-electrons on the carbonyl oxygen. When the bonding is forbidden because of the conformational restriction, a weaker interaction between the hydroxyl group and the π-electrons on the carbonyl group is observable as the lower shift of the νO–H by 10–30 cm−1 as far as the conformation is favorable for the interaction.