Restricted Conformational Freedom Research Articles

Sterically Congested Phosphite Ligands: Synthesis, crystallographic characterization, and observation of unprecedented eight‐Bond 31P,31P coupling in the 31P‐NMR spectra

AbstractThe synthesis and characterization of 2‐{1‐{3,5‐bis(1,1‐dimethylethyl)‐2‐{[2,4,8,10‐tetrakis(1,1‐dimethylethyl)dibenzo[d,f][1,3,2]dioxaphosphepin‐6‐yl]oxy}phenyl}ethyl}‐4,6‐bis(1,1‐dimethylethyl)phenyl diphenyl phosphite (6) is described. In the 31P‐NMR spectrum (1H‐decoupled) of 6, an unprecedented eight‐bond P,P coupling of J = 72.8 Hz is observed. In the X‐ray crystal structure of 6, an intramolecular P–P distance of 3.67 Å is found, which is within the sum of the van‐der‐Waals radii of the P‐atoms. The observed intramolecular P–P distance suggests that a through‐space coupling mechanism is operative. The solid‐state conformation of 6 is compared to the conformation obtained by semi‐empirical MO geometry optimizations (PM3 method). The calculated geometry suggests that the solid‐state structure is near a true energy minimum, but that crystal‐packing forces decrease the intramolecular P–P distance in the solid state. In the absence of crystal‐packing forces, however, the collisional and vibrational energy available in solution may lead to the population of states with a shortened intramolecular P–P distance in 6. The proximity of the P‐atoms in 6 is due to restricted conformational freedom resulting from steric congestion within the molecule. The free energy of activation (ΔG* = 10.2 and 10.8 kcal/mol for unequal populations of exchanging conformers) for ring inversion of the dibenzo[d,f][1,3,2]dioxaphosphepin ring in 6 is determined by variable‐temperature 31P‐NMR spectroscopy. Semi‐empirical MO calculation on model compounds suggest that the structure of the transition state for ring inversion has the two aryl rings and O‐atoms in a common plane, with the P‐atom lying above this plane.

Conformational properties of semirigid antipsychotic drugs: the pharmacophore for dopamine D2 antagonist activity

Conformational energy calculations using the MM2-87 program have been performed on the tetracyclic spiro amines 1 (A23887) and 2 (A31472) which have previously been shown to have considerable affinity for dopamine D-2 receptors. These compounds are important for defining the pharmacophore for D-2 antagonist activity due to their limited conformational freedom. Possible foldings of the multicyclic structure were energy minimized and the barriers for inversion and for rotation of the ammonium group were computed. The conformational properties of 1 and 2 are consistent with a pharmacophore recently proposed by Liljefors and Bøgesø. The greater affinity of (S)-octoclothepin for D-2 receptors as compared with its enantiomer was attributed to the latter having an incorrect orientation of the ammonium hydrogen despite the correct folding of the tricyclic structure. Other D-2 antagonists with limited conformational freedom such as butaclamol, isobutaclamol, loxapine, clozapine, and resolved cyproheptadine analogues were also found to be consistent with the pharmacophore. In addition, 1, 2, and their enantiomers were tested on radioligand binding assays for dopamine D-1, dopamine D-2, noradrenergic alpha-1, serotonergic 5-HT2, muscarinic, and sigma receptors. 1 and 2 have greater affinities than their enantiomers in the D-1, D-2, alpha-1, and 5-HT2 assays though there was little difference between 2 and its enantiomer in the latter two assays. In the muscarinic assays, 2 and its enantiomer, which were approximately equipotent, had greater affinity than 1 and its enantiomer. None of the compounds had substantial affinity for sigma receptors. Since the same enantiomers of 1, 2, butaclamol, and the resolved cyproheptadine analogues also have greater affinities for D-1 receptors, the conformational requirements of D-1 ligands appear to be quite similar to those of D-2 ligands.

Conformational analysis of amine-cured epoxy resins

Analysis using molecular mechanics has been performed on the six-bond aliphatic link segment formed when diglycidyl ether of bisphenol-A (DGEBA) is cured with aromatic amines. It is found to have restricted conformational freedom owing to coulombic repulsion between oxygen and nitrogen atoms. Hence the segment can be approximated by a virtual bond about 9.5 Å long. The study of the local network structure is therefore simplified.

Molecular conformations of dibucaine in solution as determined by NMR lanthanide—induced shifts and conformational energy calculations

AbstractProton lanthanide‐induced shifts (LIS) were measured for Yb(fod)3‐dibucaine complexes in CDCl3 solution. The data were used in conjunction with empirical energy calculations to determine the preferred conformations of dibucaine. The energy calculations and the LIS analysis were in agreement in showing that the plane of the amide group makes an angle of approximately 60° with the plane of the quinoline ring, and also that the two carbon‐carbon bonds between the amide group and the tertiary amine nitrogen are both in gauche configurations. Energy calculations showed that the diethyl tertiary zmine group has very restricted conformational freedom owing to internal steric constraints. The butyl ether group has considerable flexibility but is forced out of the plane of the quinoline ring by steric effects.

Mean geometry of the thiopeptide unit and conformational features of dithiopeptides and polythiopeptides

The mean geometry of the thiopeptide [C aNC(S)C a] unit has been derived from an analysis of X-ray crystal structure data, as well as MM2 and Gaussian 80 82 calculations. The conformational flexibilities of dithiopeptides with glycyl- and alanyl-side chains have been investigated by molecular mechanics. Minimum energy conformations were examined using interactive computer graphics molecular modeling techniques. Alanyl-dithiopeptide substitution within an oligopeptide results in considerable restriction of conformational freedom whereas the effect is minimal for glycyl-dithiopeptide substitution. Polyglycyl-thiopeptide adopts a left-handed three or fourfold or right-handed threefold helical structure with favorable interchain CS…HN hydrogen bond interactions. A poly-L-alanyl-thiopeptide prefers a left-handed threefold poly-L-proline-like helical structure.

Conformational analysis of the octamer d(G-G-C-C-G-G-C-C) in aqueous solution. A one-dimensional and two-dimensional proton NMR study at 300 MHz and 500 MHz.

Proton NMR studies in H2O and 2H2O were carried out on the self-complementary DNA octamer d(G-G-C-C-G-G-C-C) and compared with similar studies on the dimethylated analogue d(G-G-m5C-m5C-G-G-C-C) [Sanderson, M. R., Mellema, J.-R., van der Marel, G. A., Wille, G., van Boom, J. H. & Altona, C. (1983) Nucleic Acids Res. 11, 3333-3346]. Base, H1', H2' and H2" resonances were assigned by means of two-dimensional nuclear Overhauser spectroscopy (NOESY) and correlated spectroscopy (COSY) experiments. Chemical shift vs temperature profiles were used to analyze the temperature-dependent conformational behaviour and to extract thermodynamic parameters for the duplex-to-coil transition. Analysis of proton-proton couplings were used to discriminate between J1'2' and J1'2" and between the H2' and H2" resonances as well as to obtain conformational parameters of the sugar rings. From the NOESY and COSY experiments, the temperature profiles and the analysis of the coupling data it is concluded that: (a) the compound adopts a B-DNA-type helix in solution; (b) the sugar rings in the intact duplex display limited conformational freedom; (c) methylation of the cytosine bases at the C5 position has no measurable effect on the conformational behaviour of the octamer, nor on the conformation of the sugar rings; however, methylation does increase the stability of the duplex in aqueous solution under conditions of low salt concentration.

Molecular determinants for drug–receptor interactions. Part 7. 500 MHz1H nuclear magnetic resonance spectra of the narcotic agonists morphine and oxymorphone and of the morphine-related antagonist nalorphine by two-dimensional1H–1H chemical shift correlation spectroscopy

The high frequency (500 MHz)1H n.m.r. spectra of the narcotic agonists morphine and oxymorphone and of the mixed agonist–antagonist nalorphine (hydrochloride salts) were run in 2H2O and fully analysed in terms of chemical shifts and coupling constants. Detection of correlated resonances, relative signs of coupling constants and assignments of multiplets were made possible by two-dimensional (2D) homonuclear shift spectroscopy. The coupling constant determined provided evidence that the piperidine ring adopts a slightly distorted-chair conformation in all these compounds. Selective broadening of the signals of the protons in the 10, 15, 16, and 17 positions was observed in the morphine and nalorphine spectra at 296 K. This was consistent with an inversion process occurring between the two configurational isomers with axial and equatorial N-alkyl group. Resolved patterns were attained at 345 and 330 K for morphine and nalorphine, respectively. This demonstrated that the increase of temperature was sufficient to make the inversion process rates fast on the n.m.r. time-scale. All portions of the spectrum of oxymorphone were sharp at 296 K, showing that a single diastereoisomer (equatorial N-alkyl group) is present for this molecule. A possible correlation was proposed between restricted conformational freedom along the chain of the N-alkyl group and the relative narcotic antagonist potency of nalorphine, naloxone, and naltrexone.

Intramolecular electron transfer in donor-acceptor systems. Porphyrins bearing trinitroaryl acceptor group

Porphyrins bearing picryl group in ortho, meta, and para positions of one of the mesoaryl groups of tetraphenylporphyrin (TPP) were synthesized in the free-base form. The metal [Cu(II) and Zn(II)] derivs. of the free-base picrylporphyrins (PPc) were prepd. The broadened Soret absorption, the decreased optical absorbance values of Q bands, and the reduced singlet emission quantum yields of PPc indicate the existence of intramol. interaction. The extent of this interaction is greater than those obsd. for the intermol. systems and varies with the position at which the picryl moiety is attached to the porphyrin as ortho > meta > para. The energies of the redox states, E(CT) of P+Pc-, calcd. from the electrochem. redox potentials depend on the nature of the metal ion as free-base PPc > CuPPc > ZnPPc. The nature of intramol. interaction between the picryl moiety and porphyrin unit is essentially $\pi-\pi$ (CT). Conclusive evidence for light-induced electron transfer in ZnPPc is presented from EPR studies. The decay profiles of the EPR signals vary with the position of the picryl moiety as ortho < para < meta. Computer simulation of structures substantiated by the 1H NMR results point out the restricted conformational freedom of the picryl moiety in ZnPPc. Arguments based on symmetry considerations of HOMO of the excited singlet state PPc and LUMO of picryl group indicate plane-to-plane orientation of the donor and acceptor in the picrylporphyrins.

Synthesis and conformation of sequential basic polypeptides with branched and linear side chains

Polypeptides (Lys-X-Ala)n and (Lys-X-Gly)n in which X represents residues of isoleucine and norleucine, respectively, and polypeptide (Tle-Lys-Ala)n, were synthesized via polymerization of 1-hydroxysuccinimidyl esters of the appropriate tripeptides to complete previously studied series. Circular dichroism (CD) spectra of the respective polymers were measured as a function of pH and salt concentration of the medium. The results were correlated with those obtained previously with the same series containing different amino acid residues at the X-position. The helix forming ability of the polypeptides (Lys-X-Ala)n with linear X side chain was found to be independent of the length. In the series (Lys-X-Gly)n the unordered conformation was the most probable one except (Lys-Ile-Gly)n. This polymer assumed the β conformation even in low salt solution at neutral pH. An agreement with some theoretical work concerned with the restriction of conformational freedom of amino acid residue branching at Cβ atom with our experimental results is evident.

Boundary refinement of the lysozyme antigenic site around the disulphide bond 6-127 (site 1) by 'surface-simulation' synthesis.

1. We have previously shown that an antigenic site (site 1) in native lysozyme resides around the disulphide bond 6-127 and, by classical synthesis of nine disulphide peptides, the antigenic site was accurately narrowed down to the structure Cys((6))-Arg((14))-[Cys((6))-Cys((127))] -Gly((126))-Arg((128)). Only a few residues on this disulphide peptide were proposed to be involved in the reactivity with antibody. However, this lacked direct verification and the role of Arg-128 remained uncertain. 2. In the present work, several peptides were designed and synthesized by the surface-simulation concept devised in our laboratory. These enabled the precise definition of the site as well as the investigation of its conformational and directional requirements. 3. The results showed that the antigenic site (site 1) is made up of the spatially contiguous surface residues: Arg-125, Arg-5, Glu-7, Arg-14, Lys-13. The surface-simulation synthetic peptide Arg-Gly-Gly-Arg-Gly-Glu-Gly-Gly-Arg-Lys (which does not exist in native lysozyme, but copies a surface region of it) accounted entirely for the maximum expected reactivity of the site (i.e. about one-third of the total antigenic reactivity of lysozyme). An immunoadsorbent of the peptide also removed about one-third of the total lysozyme antibodies. 4. The antigenic site exhibited restricted conformational freedom. The achievement of the full reactivity of the site by surface-simulation synthesis requires the appropriate choice of spacer separation between its reactive residues. The surface-simulation synthetic site exhibits the same mono-directional preference (Arg-125 to Lys-13) for the rabbit and goat antisera so far tested. The site describes a line which encircles a part (3.01 nm in C((alpha))-to-C((alpha)) distance from Arg-125 to Lys-13) of the surface of the molecule.

Enzymic and immunochemical properties of lysozyme: XIX. Definition of the direction and conformational restrictions of the antigenic site around the disulfide bonds 64–80 and 76–94 (site 2) by ‘surface-simulation’ synthesis

We have previously shown that an antigenic reactive site is situated in native lysozyme around the disulfide bonds 64–80 and 76–94 and we also established that the site comprised the spatially contiguous surface residues: Trp-62, Lys-97, Lys-96, Asn-93, Thr-89 and Asp-87. The identity of the site was confirmed by the ‘surface-simulation’ synthetic approach that we recently devised in which the aforementioned six residues were linked directly via peptide bonds into a single peptide (Phe-Gly-Lys-Lys-Asn-Thr-Asp) with an intervening spacer where appropriate and substituting tryptophan by phenylalanine. The peptide does not exist in native lysozyme but simulates a surface region of the protein. In the present work, several surface-simulation synthetic peptides were synthesized in order to investigate the conformational restrictions of the site and to determine if the spatially constructed antigenic site has a preferred ‘direction’. The results showed that the above peptide possessed the maximum inhibitory activity towards the lysozyme immune reaction and, remarkably, accounted quantitatively for the maximum expected reactivity of the site (i.e. about a third of the total antigenic reactivity of lysozyme). An immunoadsorbent of the peptide also removed about a third of the total lysozyme antibodies. The antigenic site exhibited restricted conformational freedom. Deletion of the glycine spacer between phenylalanine and lysine had a vastly detrimental effect on the immunochemical reactivity of the peptide. Furthermore, when the above sequence was reversed the immunochemical reactivity of the resultant peptide was drastically decreased with goat antisera but was unchanged with rabbit antisera. The antigenic site therefore exhibits a preferred ‘direction’ towards the goat antisera and none towards the rabbit antisera tested. The site describes a line which encircles part (27.3 Å in extended C a -to-C a distance from Trp-62 to Asp-87) of the surface of the native molecule.

ChemInform Abstract: ANALOGS OF BRADYKININ WITH RESTRICTED CONFORMATIONAL FREEDOM

Three analogs of bradykinin have been synthesized which bear an alpha-methyl group in the place of an alpha proton at position, 4, 5, or 8. Such analogs possess restricted conformational freedom and are of interest for three reasons. (1) They may provide information about the receptor-bound conformation of the peptide. (2) They may provide a route to antagonists of the native peptide. (3) They may be degraded slowly by proteolytic enzymes. None of the analogs described here antagonized the action of bradykinin, but one exhibited tissue specificity and decreased pulmonary inactivation in the rat.

Analogs of bradykinin with restricted conformational freedom.

Three analogs of bradykinin have been synthesized which bear an alpha-methyl group in the place of an alpha proton at position, 4, 5, or 8. Such analogs possess restricted conformational freedom and are of interest for three reasons. (1) They may provide information about the receptor-bound conformation of the peptide. (2) They may provide a route to antagonists of the native peptide. (3) They may be degraded slowly by proteolytic enzymes. None of the analogs described here antagonized the action of bradykinin, but one exhibited tissue specificity and decreased pulmonary inactivation in the rat.

A 13C spin-lattice relaxation study of dipeptides containing glycine and proline: mobility of the cyclic proline side chain.

AbstractMolecular dynamics of the cyclic dipeptides cyclo(Gly‐L‐Pro), cyclo‐(L‐Pro‐L‐Pro), and cyclo(L‐Pro‐D‐Pro) and the linear dipeptides L‐Pro‐Gly and cis and trans Gly‐L‐Pro were studied in neutral aqueous solution by 13C nuclear magnetic resonance. Spinlattice relaxation times (T1) were determined for each individual carbon atom. The correlation times, τ, were derived from a semiquantitative analysis of the T1 data. The correlation times of the proline ring carbons, β, γ, and δ suggest that the cyclic dipeptides have more restriction of conformational freedom in the proline ring than the linear dipeptides. This effect is most pronounced on the γ carbon.

The origin of rotational barriers in amides and esters

We discuss in this article the origin and magnitude of the single bond rotational barrier in amides and esters. The high rotational barrier of amides is biochemically manifested in the limited conformational freedom of proteins, Since there are only two instead of three bonds to rotate about per arnino acid residue. On the basis of thermochemical estimates with model compounds, we find that the resonance energy of esters is somewhat higher than that of amides. However, the experimental rotational barrier for the former is considerably lower than the latter. We suggest esters have lower rotational barriers than the corresponding amides because they retain a large fraction of the resonance energy in the transition state. Justification is offerred using an orbital delocalization argument.

Conformational studies of anthrax polypeptide, subtilis polypeptide, and synthetic poly- -L-glutamic acid.

AbstractPoly‐γ‐L‐glutamic acid has been synthesized by the activated pentachlorophenyl ester polymerization method and the molecule weight of the polymer was found to be 16,000. Comparative conformational studies on the synthetic and on the native polyglutamic acid mbtained from B. anthracis and B. subtilis were carried out using optical rotatory dispersion, circular dichroism, peptide absorption spectrum, and titration data. These results show that poly‐γ‐glutamic acid does not exhibit any conformational order under the conditions of investigation. At low degrees of ionization, restriction of conformational freedom via random “hypercoiling” of the chain appears likely.