Scaffold diversity through intramolecular cascade reactions of solid-supported cyclic N-acyliminium intermediates

The solid-phase synthesis of pharmacologically interesting heterocycles is presented. The formation of a series of (5,5)-, (5,6)-, (6,5)-, and (6,6)-fused bicyclic ring systems was systematically studied by implementation of a common strategy involving N-acyliminium intermediates. These are highly reactive and transformed further in intramolecular cascade reactions with strong as well as weak C, N, S, and O-nucleophiles. The methodology was successfully applied to the conversion of peptidomimetics into constrained small molecule core structures, such as the hexahydropyrrolo[2,1- b][1,3]oxazines, generally with full control of diastereoselectivity (>20:1) and in purities above 90%.     

A novel reaction cascade leading to a spontaneous intramolecular dipolar cycloaddition through simultaneous generation of 1,3-dipole and dipolarophile

Ornithine methyl ester reacts with aromatic aldehydes to generate bis-Schiff bases, which depending on the structure of the aromatic aldehyde, further undergo an intramolecular cycloaddition through the transient formation of a reactive 1,3-dipole.     

Self-assembled heterotrimeric collagen triple helices directed through electrostatic interactions

Collagen, a fibrous protein, is an essential structural component of all connective tissues such as cartilage, bones, ligaments, and skin. Type I collagen, the most abundant form, is a heterotrimer assembled from two identical alpha1 chains and one alpha2 chain. However, most synthetic systems have addressed homotrimeric triple helices. In this paper we examine the stability of several heterotrimeric collagen-like triple helices with an emphasis on electrostatic interactions between peptides. We synthesize seven 30 amino acid peptides with net charges ranging from -10 to +10. These peptides were mixed, and their ability to form heterotrimers was assessed. We successfully show the assembly of five different AAB heterotrimers and one ABC heterotrimer. The results from this study indicate that intermolecular electrostatic interactions can be utilized to direct heterotrimer formation. Furthermore, amino acids with poor stability in collagen triple helices can be "rescued" in heterotrimers containing amino acids with known high triple helical stability. This mechanism allows collagen triple helices to have greater chemical diversity than would otherwise be allowed.     

Controlling the DNA binding specificity of bHLH proteins through intramolecular interactions

Reversible control of the conformation of proteins was employed to probe the relationship between flexibility and specificity of the basic helix-loop-helix protein MyoD. A fusion protein (apaMyoD) was designed where the basic DNA binding helix of MyoD was stablized by an amino-terminal extension with a sequence derived from the bee venom peptide apamin. The disulfide-stabilized helix from apamin served as a nucleus for a helix that extended for a further ten residues, thereby holding apaMyoD's DNA recognition helix in a predominantly alpha-helical conformation. The thermal stability of the DNA complexes of apaMyoD was increased by 13 degrees C relative to MyoD-bHLH. Measurements of the fluorescence anisotropy change on DNA binding indicated that apaMyoD bound to E-box-containing DNA sequences with enhanced affinity relative to MyoD-bHLH. Consequently, the DNA binding specificity of apaMyoD was increased 10-fold.     

Molecular layer-by-layer self-assembly of water-soluble perylene diimides through pi-pi and electrostatic interactions

A layer-by-layer deposition process has been carried out for two oppositely charged water-soluble perylene diimide dyes without the use of intervening polyelectrolyte layers. The strong pi-pi interactions between the perylene moieties help stabilize the layers and simultaneously diminish the fluorescence quantum yield of the array without strongly affecting the absorption or fluorescence spectra. There is an alternation of fluorescence intensity according to which perylene species is on the outer layer, which is interpreted as the effect of facile energy transfer between the perylenes.     

Synthesis of 3-substituted isocoumarins via a cascade intramolecular Ullmann-type coupling-rearrangement process

A simple and highly efficient strategy for the synthesis of 3-substituted isocoumarins through a copper(I)-catalyzed reaction of 1-(2-halophenyl)-1,3-diones has been developed. The procedure is based on a cascade copper-catalyzed intramolecular Ullmann-type C-arylation and rearrangement process. This methodology is tolerant of a wide range of substrates and applicable to library synthesis.     

Accurate modeling of the intramolecular electrostatic energy of proteins

The (?, ψ) energy surface of blocked alanine (N-acetyl–N′-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization-induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization-induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.     

On a semiclassical interpretation of inter- and intramolecular interactions

The semiclassical models considered here are composed by charge distributions coming from ab initio quantum-mechanical calculations on actual molecular systems. These charge distributions interact with one another according to the laws of classical electrostatics. This article describes some results of a systematic examination of the performances of this model in a variety of cases, with the aim of putting in evidence the usefulness and the limits of this inherently approximate representation of chemical interactions. Intermolecular interactions are examined first; the test cases are interactions of neutral molecules with H⁺, Li⁺, and C1^?, and the formation of H-bonded complexes. Attention is paid mainly to the energetics of the processes; each interacting molecule is considered as a unique entity and classical molecular reactivity indexes (electrostatic potential V, polarization term P) are introduced to compute the interaction energy, to interpret the details of the interaction process, and then to elaborate on less expensive computational procedures. Intramolecular interactions are considered. Attention is paid to the question of defining chemical groups starting from SCF molecular wavefunctions. The transferability and conservation degree of groups derived from localized orbitals of actual molecules is examined in detail, taking as tests their ability to reproduce charge distribution, one-electron observables, and energy. The effect of classical fields on these groups is then examined, taking into consideration external fields originated either by a point charge or by a solvent, and internal fields deriving from substitution of chemical groups. The intergroup analysis is then extended to the case of bimolecular reaction acts by considering the whole system as a supermolecule. Approximate computational procedures able to reproduce the main features of these interactions are proposed and tested. All through the article the performances of the classical models are compared with ab initio SCF calculations (mainly of low or intermediate quality).     

Selective recognition of tryptophan through inhibition of intramolecular charge-transfer interactions in an aqueous medium

[reaction: see text] A novel donor-acceptor conjugate 1 was synthesized, and its interactions with various amino acids have been investigated as compared to the model system 2. The conjugate 1 unusually forms an intramolecular charge-transfer complex in the aqueous medium and undergoes selective binding interactions with tryptophan. The uniqueness of this system is that it selectively recognizes tryptophan among all other amino acids and involves synergistic effects of pi-stacking, electrostatic, and donor-acceptor interactions.     

Investigation of the influence of intramolecular electrostatic interactions on the conformational equilibrium in pyrimidine nucleosides by the PMR method

The influence of solvents on the PMR spectra of uridine and cytidine has been studied. Because of intramolecular electrostatic interactions (IEIs) between the 2-keto oxygen and the freely rotating 2-hydroxyl, the position of the conformational equilibrium in the pyrimidine nucleosides but not in purine and deoxy nucleosides, depends substantially on the dielectric constant of the solvent and the size of the partial negative charge on the 2-keto oxygen of the base. It has been shown that an increase in the IEI leads to an increase in the 3-endo (N) population of the ribose ring and to an increased influence of the temperature on the state of the conformational equilibrium.All-Union Scientific-Research Institute of Applied Biochemistry, Olaine. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 362–366, May–June, 1981.     

Investigation of the influence of intramolecular electrostatic interactions on the conformational equilibrium in pyrimidine nucleosides by the PMR method

The influence of solvents on the PMR spectra of uridine and cytidine has been studied. Because of intramolecular electrostatic interactions (IEIs) between the 2-keto oxygen and the freely rotating 2-hydroxyl, the position of the conformational equilibrium in the pyrimidine nucleosides but not in purine and deoxy nucleosides, depends substantially on the dielectric constant of the solvent and the size of the partial negative charge on the 2-keto oxygen of the base. It has been shown that an increase in the IEI leads to an increase in the 3′-endo (N) population of the ribose ring and to an increased influence of the temperature on the state of the conformational equilibrium.     

Supramolecular helix of an amphiphilic pyrene derivative induced by chiral tryptophan through electrostatic interactions

An amphiphilic pyrene derivative (PyDNH3) bearing positively charged ammonium cations has been synthesized and characterized. Self-assembly of PyDNH3 in the presence of chiral tryptophan derivatives was investigated in ethanol/water by optical and chiroptical spectra, indicating the formation of helical aggregates. Scanning electron microscope (SEM) images showed the formation of ring-shape structures.     

Study of intramolecular interactions in aspirin

A detailed quantum chemical study of the solvent effects in the intramolecular hydrogen bonding, conformational stability, and reactivity of aspirin has been performed using density functional theory (DFT) at the B3LYP/6‐31G(d) theory level. Seven conformational isomers, three of them presenting intramolecular hydrogen bonds, have been located. Thermochemical functions have been computed, and relative energies and free enthalpies have been determined in gas and aqueous phases. Several molecular properties have been calculated to predict the ability of aspirin to acylate cyclooxygenase (COX) enzymes. A six‐membered‐ring hydrogen‐bonded conformer was found to be the most reactive species. The solvation in aqueous phase increases the reactivity and strengthens intramolecular hydrogen bonding.     

Causation in a cascade: the origins of selectivities in intramolecular nitrone cycloadditions

The factors controlling chemo-, regio-, and stereoselectivity in a cascade of reactions starting from a bis(cyanoalkenyl)oxime and proceeding via nitrone cycloadditions have been unraveled through a series of density functional theory calculations with several different functionals. Both kinetic and thermodynamic control of the reaction cascade are important, depending upon the conditions. Kinetic control was analyzed by the distortion/interaction model and found to be dictated by differences in distortions of the cycloaddends in the transition states. A new mechanism competing with that originally proposed in the application of these reactions to the histrionicotoxin synthesis was discovered in these studies.     

Synthesis of fused piperidinones through a radical-ionic cascade

Azabicyclo[4.3.0]nonanes were assembled, from chiral allylsilanes possessing an oxime moiety, using a stereocontrolled formal [2 + 2 + 2] radical-ionic process. The cascade involves the addition of an alpha-iodoester to the less substituted end of the enoxime which is then followed by a 5-exo-trig cyclization onto the aldoxime function, producing an alkoxyaminyl radical species which finally lactamizes to afford the titled piperidinone. High levels of stereoinduction were observed, demonstrating the ability of a silicon group located at the allylic position to efficiently control the stereochemistry of the two newly created stereogenic centers. When the radical cascade was extended to ketoximes, the resulting sterically hindered alkoxyaminyl radical did not react further with the initiator Et3B to produce the expected nucleophilic amidoborane complex. In sharp contrast, this long-lived radical recombined with the initial alpha-stabilized ester radical to produce a cyclopentane incorporating two ester fragments.     

A new strategy toward indole alkaloids involving an intramolecular cycloaddition/rearrangement cascade

The intramolecular Diels-Alder reaction between an amidofuran moiety tethered onto an indole component was examined as a strategy for the synthesis of Aspidosperma alkaloids. Furanyl carbamate 23 was acylated using the mixed anhydride 26 to provide amidofuran 22 in 68% yield. Further N-acylation of this indole furnished 27 in 88% yield. Cyclization precursors were prepared by removing the carbamate moiety followed by N-alkylation with the appropriate alkyl halides. Large substituent groups on the amido nitrogen atom causes the reactive s-trans conformation of the amidofuran to be more highly populated, thereby facilitating the Diels-Alder cycloaddition. The reaction requires the presence of an electron-withdrawing substituent on the indole nitrogen in order for the cycloaddition to proceed. Treatment of N-allyl-bromoenamide 48 with n-Bu(3)SnH/AIBN preferentially led to the 6-endo trig cyclization product 50, with the best yield (91%) being obtained under high dilution conditions. The initially generated cyclohexenyl radical derived from 48 produces the pentacyclic heterocycle 50 by either a direct 6-endo trig cyclization or, alternatively, by a vinyl radical rearrangement pathway.     

Restoration of protein foam stability through electrostatic propylene glycol alginate-mediated protein–protein interactions

The action of propylene glycol alginate in the enhancement of foam stability of a destabilised Tween 20/bovine serum albumin mixed system was evaluated. A significant increase in the foam stability was observed in the presence of low concentrations of propylene glycol alginate. A pseudo-plateau level of foam stability was obtained in the presence of approximately 0.8 μg/ml propylene glycol alginate in the solution used to form the foam. Foam stability enhancement due to bulk viscosity changes and surface effects were elucidated. The increase in foam stability was investigated by reference to the properties of thin liquid films and the macroscopic interface of test solutions. Propylene glycol alginate was found to slow the rate of thin film drainage, increase the equilibrium thickness of the films, slow the lateral diffusion of a fluorescent probe molecule located in the adsorbed layer and increase the elasticity of the interface. Data are consistent with propylene glycol alginate-induced crosslinking of protein in the adsorbed layer. This polysaccharide presents a means for controlling protein foam stability.