Lone Pair-lone Pair Repulsion Research Articles

Rapid assessment of conformational preferences in biaryl and aryl carbonyl fragments.

The ability to rapidly assess the preferred conformation of key fragments in a structure “by visual inspection” is a very useful starting point in the process of drug design. With the ability to do so, one could address questions like: “How could we avoid planarity in a molecule?”, “Will a molecule change its conformational preference if we make it more or less basic?” or “How does this electronic repulsion affect the conformational preference in the system?” in timely fashion. In this paper, we describe how the conformational energy profile (CEP, plot of energy as a function of dihedral bond angle) of a fragment can be interpreted through the understanding the interplay between resonance stabilization, steric effects and electrostatic interactions. Fifty-nine biaryl and aryl carbonyl fragments present in oral drugs or which are close derivatives thereof were selected. Calculation of their CEPs using ab initio methodology allowed us to conclude the relative importance of these factors in the conformational preference of these fragments as follows: “steric repulsion > lone pair—lone pair repulsion > lone pair—fluorine repulsion > resonance stabilization” and to formulate “rules of thumb” that the practicing medicinal/organic chemist can apply when analysing molecules that contain these fragments.

Azapeptide Synthesis Methods for Expanding Side-Chain Diversity for Biomedical Applications.

Mimicry of bioactive conformations is critical for peptide-based medicinal chemistry because such peptidomimetics may augment stability, enhance affinity, and increase specificity. Azapeptides are peptidomimetics in which the α-carbon(s) of one or more amino acid residues are substituted by nitrogen. The resulting semicarbazide analogues have been shown to reinforce β-turn conformation through the combination of lone pair-lone pair repulsion of the adjacent hydrazine nitrogen and urea planarity. Substitution of a semicarbazide for an amino amide residue in a peptide may retain biological activity and add benefits such as improved metabolic stability. The applications of azapeptides include receptor ligands, enzyme inhibitors, prodrugs, probes, and imaging agents. Moreover, azapeptides have proven therapeutic utility. For example, the aza-glycinamide analogue of the luteinizing hormone-releasing hormone analogue Zoladex is a potent long-acting agonist currently used in the clinic for the treatment of prostate and breast cancer. However, the use of azapeptides was hampered by tedious solution-phase synthetic routes for selective hydrazine functionalization. A remarkable stride to overcome this bottleneck was made in 2009 through the introduction of the submonomer procedure for azapeptide synthesis, which enabled addition of diverse side chains onto a common semicarbazone intermediate, providing a means to construct azapeptide libraries by solution- and solid-phase chemistry. In brief, aza residues are introduced into the peptide chain using the submonomer strategy by semicarbazone incorporation, deprotonation, N-alkylation, and orthogonal deprotection. Amino acylation of the resulting semicarbazide and elongation gives the desired azapeptide. Since the initial report, a number of chemical transformations have taken advantage of the orthogonal chemistry of semicarbazone residues (e.g., Michael additions and N-arylations). In addition, libraries have been synthesized from libraries by diversification of aza-propargylglycine (e.g., A3 coupling reactions, [1,3]-dipolar cycloadditions, and 5-exo-dig cyclizations) and aza-chloroalkylglycine residues. In addition, oxidation of aza-glycine residues has afforded azopeptides that react in pericyclic reactions (e.g., Diels-Alder and Alder-ene chemistry). The bulk of these transformations of aza-glycine residues have been developed by the Lubell laboratory, which has applied such chemistry in the synthesis of ligands with promising biological activity for treating diseases such as cancer and age-related macular degeneration. Azapeptide analogues of growth hormone-releasing peptide-6 (His-d-Trp-Ala-Trp-d-Phe-Lys-NH2, GHRP-6) have for example been pursued as ligands of the cluster of differentiation 36 receptor (CD36) and show promising activity for the development of treatments for angiogenesis-related diseases, such as age-related macular degeneration, as well as for atherosclerosis. Azapeptides have also been employed to make a series of conformationally constrained second mitochondria-derived activator of caspase (Smac) mimetics that exhibit promising apoptosis-inducing activity in cancer cells. The synthesis of cyclic azapeptide derivatives was used to make an aza scan to study the conformation-activity relationships of the anticancer agent cilengitide, cyclo(RGDf-N(Me)V), and its parent counterpart cyclo(RGDfV), which exhibit potency against human tumor metastasis and tumor-induced angiogenesis. Innovations in the synthesis and application of azapeptides will be presented in this Account, focusing on the creation and use of side-chain diversity in medicinal chemistry.

Adjacent Lone Pair (ALP) Effect: A Computational Approach for Its Origin.

The adjacent lone pair (ALP) effect is an experimental phenomenon in certain nitrogenous heterocyclic systems exhibiting the preference of the products with lone pairs separated over other isomers with lone pairs adjacent. A theoretical elucidation of the ALP effect requires the decomposition of intramolecular energy terms and the isolation of lone pair-lone pair interactions. Here we used the block-localized wavefunction (BLW) method within the ab initio valence bond (VB) theory to derive the strictly localized orbitals which are used to accommodate one-atom centered lone pairs and two-atom centered σ or π bonds. As such, interactions among electron pairs can be directly derived. Two-electron integrals between adjacent lone pairs do not support the view that the lone pair-lone pair repulsion is responsible for the ALP effect. Instead, the disabling of π conjugation greatly diminishes the ALP effect, indicating that the reduction of π conjugation in deprotonated forms with two σ lone pairs adjacent is one of the major causes for the ALP effect. Further electrostatic potential analysis and intramolecular energy decomposition confirm that the other key factor is the favorable electrostatic attraction within the isomers with lone pairs separated.

Synthetic and Structural Studies of 1,8‐Chalcogen Naphthalene Derivatives

Four novel 1,8-disubstituted naphthalene derivatives 4-7 that contain chalcogen atoms occupying the peri positions have been prepared and fully characterised by using X-ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Molecular distortion due to noncovalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X-ray data for 4-7 was compared to the series of known 1,8-bis(phenylchalcogeno)naphthalenes 1-3, which were themselves prepared from novel synthetic routes. A general increase in the E...E' distance was observed for molecules containing bulkier atoms at the peri positions. The decreased S...S distance from phenyl-1 and ethyl-4 analogues is ascribed to a weaker chalcogen lone pair-lone pair repulsion acting in the ethyl analogue due to the presence of two equatorial S(naphthyl) ring conformations. Two novel peri-substituted naphthalene sulfoxides of 1, Nap(O=SPh)(SPh) 8 and Nap(O=SPh)(2) 9, which contain different valence states of sulfur, were prepared and fully characterised by using X-ray crystallography and multinuclear NMR spectroscopy, IR spectroscopy and MS. Molecular structures were analysed by using naphthalene ring torsions, peri-atom displacement, splay angle magnitude, S...S interactions, aromatic ring orientations and quasi-linear O=S...S arrangements. The axial S(naphthyl) rings in 8 and 9 are unfavourable for S...S contacts due to stronger chalcogen lone pair-lone pair repulsion. Although quasi-linear O=S...S alignments suggest attractive interaction is conceivable, analysis of the B3LYP wavefunctions affords no evidence for direct bonding interactions between the S atoms.

Synthetic and Structural Studies of 1-Halo-8-(alkylchalcogeno)naphthalene Derivatives

A series of eight 1-halo-8-(alkylchalcogeno)naphthalene derivatives (1-8; halogen=Br, I; alkylchalcogen=SEt, SPh, SePh, TePh) containing a halogen and a chalcogen atom occupying the peri positions have been prepared and fully characterised by using X-ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Naphthalene distortion due to non-covalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X-ray data for 1, 2, 4 and 5-8 were compared. Molecular structures were analysed in terms of naphthalene ring torsions, peri-atom displacement, splay angle magnitude, X...E interactions, aromatic ring orientations and quasi-linear X...E-C arrangements. A general increase in the X...E distance was observed for molecules that contain bulkier atoms at the peri positions. The I...S distance of 4 is comparable with the I...Te distance of 8, and is ascribed to a stronger lone pair-lone pair repulsion due to the presence of an axial S(naphthyl) ring conformation. Density functional theory (B3LYP) calculations performed on 5-8 revealed Wiberg bond index values of 0.05-0.08, which indicate minor interactions taking place between the non-bonded atoms in these compounds.

Revision of the Dissociation Energies of Mercury Chalcogenides—Unusual Types of Mercury Bonding

Mercury chalcogenides HgE (E=O, S, Se, etc.) are described in the literature to possess rather stable bonds with bond dissociation energies between 53 and 30 kcal mol(-1), which is actually difficult to understand in view of the closed-shell electron configuration of the Hg atom in its ground state (...4f(14)5d(10)6s(2)). Based on relativistically corrected many body perturbation theory and coupled-cluster theory [IORAmm/MP4, Feenberg-scaled IORAmm/MP4, IORAmm/CCSD(T)] in connection with IORAmm/B3LYP theory and a [17s14p9d5f]/aug-cc-pVTZ basis set, it is shown that the covalent HgE bond is rather weak (2-7 kcal mol(-1)), the ground state of HgE is a triplet rather than a singlet state, and that the experimental bond dissociation energies have been obtained for dimers (or mixtures of monomers, dimers, and even trimers) Hg2E2 rather than true monomers. The dimers possess association energies of more than 100 kcal mol(-1) due to electrostatic forces between the monomer units. The covalent bond between Hg and E is in so far peculiar as it requires a charge transfer from Hg to E (depending on the electronegativity of E) for the creation of a single bond, which is supported by electrostatic forces. However, a bonding between Hg and E is reduced by strong lone pair-lone pair repulsion to a couple of kcal mol(-1). Since a triplet configuration possesses somewhat lower destabilizing lone pair energies, the triplet state is more stable. In the dimer, there is a Hg-Hg pi bond of bond order 0.66 without any a support. Weak covalent Hg-O interactions are supported by electrostatic bonding. The results for the mercury chalcogenides suggests that all experimental dissociation energies for group-12 chalcogenides have to be revised because of erroneous measurements.

Measures to evaluate heteroaromaticity and their limitations: Story of skeletally substituted benzenes

Ab initio HF, MP2, CCSD(T) and hybrid density functional B3LYP calculations were performed on a series of skeletally mono- and di-substituted benzenes, (CH)5Z and (CH)4Z2, Z = C-, N, O+, Si-, P, S+, Ge-, As, Se+, BH-, NH+, AlH-, SiH, PH+, GaH-, GeH and AsH+. Various measures of aromaticity such as the bond length equalization, homodesmic equations, singlet-triplet energy difference (AE s-t), chemical hardness (η) and out-of-plane distortive tendency are critically analysed. The relative energy ordering in skeletally disubstituted benzenes displays trends that are inexplicable based on conventional wisdom. In general, the orthoisomer is found to be the least stable when the substituent is from the second row, whereas if the substituent is from the fourth row, the ortho-isomer is the most stable. Various qualitative arguments, including (a) lone pair-lone pair repulsion, (b) the sum of bond strengths in the twin Kekule forms, and (c) the rule of topological charge stabilization (TCS), are used to explain the observed relative energy trends. The rule of TCS in conjunction with the sum of bond strengths is found to predict the relative energy ordering reasonably well. The reactivity of this class of compounds is assessed based on their singlet-triplet energy differences, chemical hardness and the frequencies corresponding to out-of-plane skeletal distortions. These reactivity indices show less kinetic stability for the compounds with substituents from the fourth row and point to the fact that the thermodynamically most stable compounds need not be the least reactive ones. The ‡Es-t values indicate that the π-framework of benzene weakens upon skeletal substitutions.

Nonbonded P···P and P···Se Interactions in Naphthalene 1,8-Positions: Role of Lone-Pair Orbitals

The lone pair-lone pair repulsion plays an important role in the nonbonded P;;;P interaction in naphthalene 1,8-positions. The conformations around P and Se in 8-(PhSe)-1-(Ph 2 P=O)C 10 H 6 are determined by the attractive O;;;Se--C 3c-4e type interaction. The P;;;Se interaction in the 1,8-positions is also discussed.

Bond dissociation energies of H2NX compounds: comparison with CH3X, HOX, and FX compounds

The bond dissociation energies (BDE) of H{sub 2}NNH{sub 2}, HONH{sub 2} and FNH{sub 2} have been calculated using Pople`s G1 procedure, and the known BDE for hydrazine is well reproduced. The BDE`s of MeX, H{sub 2}NX, HOX and FX derivatives where X = Me, H{sub 2}N, HO, and F, are compared, and the differences are related to changes in hybridization, internal Coulombic stabilization and lone pair-lone pair repulsion. 20 refs., 6 figs., 6 tabs.

Kinetic Study on the Alkaline Hydrolysis of S,S-Diaryl-N-halosulfilimines

Abstract Kinetics for the alkaline hydrolysis of S,S-diaryl-N-bromosulfilimines were carried out in aqueous methanol. The observed pseudo-first-order rate constants were found to give a linear correlation with the concentration of sodium hydroxide, k=k1+k2[NaOH]. The first-order rate constants k1 showed a large negative Hammett ρ value (−2.43) for the substituent effect on the phenyl group, nearly zero activation entropy (−0.9±13.1 JK−1mol−1) and a relatively large m value (0.638) against the solvent ionizing power Y value suggesting that the reaction process for k1 close to SNl. The salt effect, the deuterium solvent isotope effect and the steric effect are also in accord with the SNl mechanism. On the other hand, the second-order rate constants k2 revealed a small Hammett ρ value, a negative activation entropy (−44.0±4.0 JK−1mol−1), a small m value (0.153) and a steric deceleration by ortho substituents showing that the reaction for k2 is SN2-like. The salt effect and the solvent isotope effect are also compatible with the SN2-like mechanism. Meanwhile, the k1 for S,S-diphenyl-N-halosulfilimines remarkably increased in the order of N-iodo<N-bromo<N-chloro. This reactivity might be due to the lone pair-lone pair repulsion at the reactant state. From these observations, the alkaline hydrolysis of S,S-diaryl-N-halosulfilimines was confirmed to proceed via concurrent two mechanisms, the SN2′-like mechanism involving nitridosulfonium cation (>+S≡N) as an intermediate and the SN2′-like mechanism with the transition state in which the N-X bond cleavage is more progressed than the S–O bond formation with nucleophiles (−OH, −OMe).