Gem-dimethyl Effect Research Articles

Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)

The high morbidity and mortality associated with SARS-CoV-2 infection, the etiological agent of COVID-19, has had a major impact on global public health. Significant progress has been made in the development of an array of vaccines and biologics, however, the emergence of SARS-CoV-2 variants and breakthrough infections are an ongoing major concern. Furthermore, there is an existing paucity of small-molecule host and virus-directed therapeutics and prophylactics that can be used to counter the spread of SARS-CoV-2, and any emerging and re-emerging coronaviruses. We describe herein our efforts to address this urgent need by focusing on the structure-guided design of potent broad-spectrum inhibitors of SARS-CoV-2 3C-like protease (3CLpro or Main protease), an enzyme essential for viral replication. The inhibitors exploit the directional effects associated with the presence of a gem-dimethyl group that allow the inhibitors to optimally interact with the S4 subsite of the enzyme. Several compounds were found to potently inhibit SARS-CoV-2 and MERS-CoV 3CL proteases in biochemical and cell-based assays. Specifically, the EC50 values of aldehyde 1c and its corresponding bisulfite adduct 1d against SARS-CoV-2 were found to be 12 and 10 nM, respectively, and their CC50 values were >50 μM. Furthermore, deuteration of these compounds yielded compounds 2c/2d with EC50 values 11 and 12 nM, respectively. Replacement of the aldehyde warhead with a nitrile (CN) or an α-ketoamide warhead or its corresponding bisulfite adduct yielded compounds 1g, 1eand1f with EC50 values 60, 50 and 70 nM, respectively. High-resolution cocrystal structures have identified the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and, furthermore, have illuminated the mechanism of action of the inhibitors. Overall, the high Safety Index (SI) (SI=CC50/EC50) displayed by these compounds suggests that they are well-suited to conducting further preclinical studies.

Exploring the gem-dimethyl effect in the formation of imine-based macrocycles and cages

A series of imine-based macrocycles and cages has been synthesized using the gem-dimethyl effect as a platform. Following this strategy, imine-based macrocyclization could be performed even at higher concentration.

Synthesis of Bis(oxazoline) Ligands Possessing C-5 gem-Disubstitution and Their Application in Asymmetric Friedel-Crafts Alkylations.

A series of eight novel bis(oxazoline) ligands incorporating gem-disubstitution on one of the oxazoline rings were prepared from (S)-valine. These ligands are designed as a cost-effective alternative to similar ligands possessing an oxazolinyl C(5)-tert-butyl group derived from expensive (S)-tert-leucine. Four of the ligands possess a C(4)-gem-dimethyl group and four a C(4)-gem-diphenyl group adjacent to the C(5)-isopropyl substituent. Zinc complexes of ligands 11a-h, along with non-C(4)-gem-disubstituted analogues 1a-g, were effective in the Friedel-Crafts alkylation of both indole (up to 74% ee) and 2-methoxyfuran (up to 95% ee) with a series of nitroalkenes. Three of the ligands (11a-c), an iron dichloride complex of ligand 11d and two zinc dichloride complexes, were characterized by X-ray crystallography, one with ligand 11d and the second a bis-tert-butyl-substituted N-methylamine ligand. A direct comparison of the latter structures clearly illustrates the gem-dimethyl effect.

The Oxime Portmanteau Motif: Released Heteroradicals Undergo Incisive EPR Interrogation and Deliver Diverse Heterocycles

ConspectusSelective syntheses are now available for compounds of many classes, based on C-centered radicals, exploiting a diverse range of mechanisms. The prospect for chemistry based around N- and O-centered radicals is probably more favorable because of the importance of heterocycles as biologically active materials. Heteroradical chemistry is still comparatively underdeveloped due to the need for safe and easy ways of generating them. Oxime esters appeared promising candidates to meet this need because literature reports and our EPR spectroscopic examinations showed they readily dissociated on photolysis with production of a pair of N- and O-centered radicals. It soon became apparent that a whole suite of benign oxime-containing molecules could be pressed into service. The bimodality of the oxime motif meant that by suitable choice of functionality the reactions could be directed to yield selectively products from either the N-centered radicals or from the O-centered radicals.We found that on one hand photolyses of acetophenone oxime esters of carboxylic acids yielded alicyclics. On the other hand, aromatic and heteroaromatic acyl oximes (as well as dioxime oxalates) afforded good yields of phenanthridines and related heterocycles. Easily prepared oxime oxalate amides released carbamoyl radicals, and pleasingly, β-lactams were thereby obtained. Oxime carbonates and oxime carbamates, available via our novel 1,1'-carbonyldiimidazole (CDI)-based preparations, were accessible alternatives for iminyl radicals and hence for phenanthridine preparations. In their second modes, these compounds proved their value as precursors for exotic alkoxycarbonyloxyl and carbamoyloxyl radicals.Microwave-assistance was shown to be a particularly convenient procedure with O-phenyl oxime ethers. The iminyl radicals generated from such precursors with alkene, alkyne, and aromatic acceptor substituents furnished pyrrole, quinoline, phenanthridine, benzonaphthiridine, indolopyridine, and other systems. Microwave irradiations with 2-(aminoaryl)alkanone O-phenyl oximes enabled either dihydroquinazolines or quinazolines to be obtained in very good yields.The fine quality of the EPR spectra, acquired during photolyses of all the O-carbonyl oxime types, marked this as an important complement to existing ways of obtaining such spectra in solution. Quantifications enabled SARs to be obtained for key reaction types of N- and O-centered radicals, thus putting mechanistic chemistry in this area on a much firmer footing. Surprises included the inverse gem-dimethyl effect in 5-exo-cyclizations of iminyls and the interplay of spiro- with ortho-cyclization onto aromatics. Insights into unusual 4-exo-cyclizations of carbamoyl radicals showed the process to be more viable than pent-4-enyl 4-exo-ring closure. Another surprise was the magnitude of the difference in CO2 loss rate from alkoxycarbonyloxyl radicals as compared with acyloxyl radicals. Their rapid 5-exo-cyclization was charted, as was their preferred spiro-cyclization onto aromatics. The first evidence that N-monosubstituted carbamoyloxyls had finite lifetimes was also forthcoming.It is evident that oxime derivatives have excellent credentials as reagents for radical generation and that there is ample room to extend their applications to additional radical types and for further heterocycle syntheses. There is also clear scope for the development of preparative procedures based around the alkoxyl and aminyl radicals that emerge downstream from oxime carbonate and oxime carbamate dissociations.

Thorpe-Ingold acceleration of oxirane formation is mostly a solvent effect.

The Thorpe-Ingold hypothesis for the gem-dimethyl effect in the cyclization reactions of 2-chloroethoxide derivatives has been investigated computationally in the gas phase and in aqueous solution. Ab initio MP2/6-311+G(d,p) and CBS-Q calculations reveal little intrinsic difference in reactivity with increasing alpha-methylation for the series of reactants 1-3. However, inclusion of continuum hydration or of explicit hydration through mixed quantum and statistical mechanics (MC/FEP) simulations does reproduce the substantial, experimentally observed rate increases with increasing alpha-methylation. Analysis of the MC/FEP results provides clear evidence that the rate increases stem primarily from increased steric hindrance to hydration of the nucleophilic oxygen atom with increasing alpha-methylation. Thus, the gem-dimethyl acceleration of oxirane formation for 1-3 is found to be predominantly a solvent effect.

5-Exo-Cyclizations of Pentenyliminyl Radicals: Inversion of the gem-Dimethyl Effect

This paper describes how the rates of 5-exo-ring closures of unsaturated iminyl radicals to pyrrolomethyl radicals respond to substituents in the pentenyl chain and at the C=N bond. Benzyl- and acyl oxime esters, as well as dioxime oxalates, were identified as suitable iminyl radical sources for electron paramagnetic resonance (EPR) spectroscopy. Pentenyliminyl radicals with aryl substituents at their C=N bonds, and one with an alkyl substituent at its C=N bond, were studied in solution by steady-state continuous wave EPR spectroscopy. All the pentenyliminyls selectively ring closed in the 5-exo-mode rather than the 6-endo-mode. EPR monitoring of the decay of the 2,2-dimethyl-1-phenylpent-4-enyliminyl radical showed that it underwent bimolecular combination at about the diffusion controlled limit (2kt approximately 3 x 10(8) M(-1) s(-1) at 245 K). The rate constant for 5-exo-ring closure of phenylpentenyliminyl (8.8 x 10(3) s(-1) at 300 K) was a factor of 25 smaller than the rate constant for hex-5-enyl radical cyclization. The rate of cyclization was slower for an iminyl having a Me group at the site of 5-exo-cyclization but faster for an iminyl with an Et substituent at the terminus of the C=C double bond. Surprisingly, the 2,2-dimethyl-1-phenylpent-4-enyliminyl radical, with a bismethyl group in its pentenyl chain, ring closed more slowly than the unsubstituted analogue. DFT computations were in accord with this inverse gem-dimethyl effect and suggested it resulted from steric interaction of the Ph and bis-Me groups which forced the aromatic ring out of the plane of the imine moiety. To check on the role of the Ph substituent, pentenyliminyls lacking this group were sought. A pentenyliminyl radical with an alkyl group in place of the Ph group, and a single Me group in its pentenyl chain, was generated by means of an unsymmetrical dioxime oxalate precursor. The k(c) for this species was a factor of 2.5 larger than k(c) for the original pentenyliminyl, suggesting that the normal positive gem-dimethyl effect does operate for pentenyliminyls lacking the aromatic substituent at the C=N bond. DFT computations also successfully reproduced this trend for model iminyls. It appears that for alkenyliminyl radicals positive or negative gem-dimethyl effects on the cyclization can be induced by appropriate choice of the second substituent on the C=N bond.

Gem-Dimethyl 4-Pentenyl Glycosides: Novel Glycosylating Agents and Anomeric Protecting Groups

Two classes of gem-dimethyl 4-n-pentenyl glycosides (i.e., C2-series and C3-series) have been prepared and studied in both the glycosylation and hydrolysis manifolds utilizing NBS as the sole stoichiometric activator. These novel glycosylating agents, which are analogues of Fraser-Reid's 4-n-pentenyl glycosyl donors, show increased reactivity in side-by-side studies by virtue of the gem-dimethyl effect.

The gem-Dimethyl Effect Revisited

Computation of the ring strain energy of 1,1-dimethylcyclobutane with a variety of methods reveals that there is no significant enthalpic component of the gem-dimethyl effect as measured by the ring strain energy.

Intramolecular Hydroaminations of Aminoalkynes Catalyzed by Yttrium Complexes and Aminoallenes Catalyzed by Zirconium Complexes

It was demonstrated that Y[N(TMS)2]3, the neutral yttrium-diamine complex 13 and yttrium-NPS complexes 15 are efficient precatalysts for intramolecular hydroamination of aminoalkynes involving primary amines. Complex 13 and 15 were quantitatively prepared in situ by direct metalation of the ligands 4 and 9 with 1 equiv of Y[N(TMS)2]3 in benzene-d6 at 120 oC for 5 days and 10 days, respectively, via elimination of (TMS)2NH. 5-Exo- and 6-exo-dig intramolecular hydroamination of aminoalkynes using catalyst 12 and 13 proceeded smoothly to give nitrogen-contained cyclic products in good to excellent yields in all cases. In the case of 7- exo-dig intramolecular hydroamination, the desired product was produced in 41% and 48% yields despite the gem-dimethyl effect. However, treatment of catalyst 15 with aminoalkynes (19 and 22) having a methyl substituent at the carbon adjacent to triple bond and 6-exo-dig intramolecular hydroamination of 21 failed to give the desired products. Zirconium-catalyzed intramolecular hydroamination of aminoallenes (25, 27, and 31) with 5 mol% 16 afforded 2-(trans-1-propenyl)pyrrolidine, 2-isopropylenepyrrolidine, and 2-(trans-1- propenyl)piperidine in 96%, 95%, and 93% yield, respectively. However, subjecting 25 to 5 mol% 15 was unsuccessful to produce the desired product.

Conventional Strain Energy in Dimethyl-Substituted Cyclobutane and the gem-Dimethyl Effect

The gem-dimethyl effect is the acceleration of cyclization by substituents in the chain and is often used in organic synthesis as a ring-closing effect. Calculations on cyclobutane, methylcyclobutane, and 1,1-dimethylcyclobutane are performed. 1,1-Dimethylcyclobutane is a four-membered carbon ring with gem-dimethyl substituents. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, density functional theory (DFT), and second-order perturbation theory (MP2) with two triple-zeta quality basis sets, 6-311G(d,p) and 6-311G+(2df,2pd). Additional single-point calculations are performed using the optimized MP2/6-311G+(2df,2pd) geometries and coupled-cluster theory including single and double excitations and noniterative, linear triple excitations (CCSD(T)). Calculations indicate that 1,1-dimethylcyclobutane is more than 8 kcal mol-1 less strained than cyclobutane, that is, there is at least some thermodynamic component to the gem-dimethyl effect.

The gem-dimethyl effect: amphiphilic bilirubins

New bilirubin congeners ( 1a– 1d ) with the central C(10) CH 2 replaced by C(CH 3) 2 were smoothly synthesized by coupling two identical dipyrrinones with 2,2-dimethoxypropane under acid catalysis. The new yellow pigments, with acid chains varying from acetic ( n=1) to propionic ( n=2) to butyric ( n=3) to hexanoic ( n=5), exhibit unusual amphiphilicity relative to the parent mesobilirubins without the gem-dimethyls and have highly favorable solubility in organic solvents ranging from nonpolar (benzene) to polar (CH 3OH). Like the parent rubins, 1a– 1d can easily bend about the middle but unlike the parents they cannot form mesobiliverdin analogs. NMR spectroscopic analysis and molecular dynamics calculations indicate that, like the parents, 1a– 1d adopt ridge-tile shapes that are stabilized by intramolecular hydrogen bonding. Confirmation of the conformation in 1b comes from its X-ray crystallographic structure.

A large gem‐dimethyl effect in the cyclization of ω‐phenylhydantoic acids: computational modeling of the gem‐dimethyl effect on the acid‐ or base‐catalyzed cyclization of hydantoic acids and esters

AbstractThe rates of the cyclization of methyl‐substituted 5‐phenylhydantoic acids were measured in acid solutions. A particularly strong gem‐dimethyl effect (GDME) was observed with the N‐methyl compounds amounting to an acceleration of six powers of ten for the 2,2,3‐trimethyl derivative. The variations in the free energies of activation for the cyclization of hydantoic acids and esters were modeled by the strain energies of the tetrahedral intermediates and of the reactants calculated by the MM3 force field. The neutral tetrahedral intermediate T0 was used for reaction series involving acid catalysis and the negatively charged intermediate T− for base catalysis. Very good agreement with the experimental GDME was obtained for the acid‐catalyzed cyclizations of the complete series of the N‐methyl‐substituted substrates, showing that the accelerations result from a greater strain increase in the reactants. The results with T− are closely parallel, indicating that the loss of GDME observed under base catalysis with 2,2,3‐trimethylhydantoate esters is not due to intramolecular strain in T−. A linear correlation (slope 1.22, r = 0.934) is obtained for a plot of the free energy variations against strain energies for the reaction series of 5‐phenylhydantoic acids when the data for the strongly deviating parent acid is excluded. Excellent LFERs are obtained between the reaction series of esters and acids. The observed large rate enhancements induced by N‐substituents explain the switches to cyclization routes in synthetic reactions. Copyright © 2004 John Wiley & Sons, Ltd.

Thorpe-Ingold effects in cyclizations to five-membered and six-membered rings containing planar segments. The rearrangement of N(1)-alkyl-substituted dihydroorotic acids to hydantoinacetic acids in base.

While the gem-dimethyl effect (GDME) is quantitatively similar for cyclizations to cyclopentane and cyclohexane rings and their homomorphs, in systems containing planar segments the GDME is stronger for the formation of five-membered rings. Planar pentagons have smaller angles than planar hexagons and their formation is helped by the decrease in the potential internal bond angle caused by substituents, as suggested by Thorpe and Ingold for small rings. The phenomenon is illustrated with crystal structure data on five-membered hydantoins and six-membered dihydrouracils containing four-atom planar segments. Such a Thorpe-Ingold effect explains the rearrangement in base of N-alkyl substituted dihydroorotic acids 1 to hydantoinacetic acids 3. The reaction involves initial hydrolysis to N-(N-alkylcarbamoyl)aspartic acids 2 and their subsequent cyclization. The unsubstituted N-carbamoylaspartic acid 2a is stable in 1 M KOH, the N(1)-methyl and ethyl compounds 2b and 2c are in equilibrium with the hydantoinacetic acids 3, while the cyclization of the N(1)-isopropyl and cyclohexyl derivatives 2d and 2e is irreversible. Experimental data on equilibria and pK(a)s for ionization of the carboxy and NH groups allow equilibria and rates involving the N-unsubstituted compounds to be estimated and compared with those for the N-alkyl derivatives. The strongest effect is observed on the equilibrium [3(2-)]/2[(2-)], where substitution of H by methyl increases K 600-fold. In vitro the kinetic regioselectivity for acid catalyzed cyclization of N-carbamoylaspartic to hydantoinacetic acid against dihydroorotic acid is only 10:1. This, together with the weaker acidity of the remote carboxyl group, favours cyclization to dihydroorotic acid under biological conditions.

Hemilabile ligands in organolithium chemistry: substituent effects on lithium ion chelation.

The lithium diisopropylamide-mediated 1,2-elimination of 1-bromocyclooctene to provide cyclooctyne is investigated using approximately 50 potentially hemilabile polyethers and amino ethers. Rate laws for selected ligands reveal chelated monomer-based pathways. The dependence of the rates on ligand structure shows that anticipated rate accelerations based on the gem-dimethyl effect are nonexistent and that substituents generally retard the reaction. With the aid of semiempirical and DFT computational studies, the factors influencing chelation are discussed. It seems that severe buttressing within chelates of the substitutionally rich ligands precludes a net stabilization of the chelates relative to nonchelated (eta(1)-solvated) forms. One ligand-MeOCH(2)CH(2)NMe(2)-appears to promote elimination uniquely by a higher-coordinate monomer-based pathway.

Electrochemically-induced spirolactonization of alpha-(methoxyphenoxy)alkanoic acids into quinone ketals.

Anodic oxidation of two series of alpha-(2)- and alpha-(4-methoxyphenoxy)alkanoic acids were studied both at the analytical and preparative scales in order to delineate mechanistic aspects of electrochemically induced spirolactonization and to develop synthetically useful orthoquinone bis- and monoketals. Although alpha-monomethylated carboxylic acids and acetic acid derivatives do not undergo any spiroannulation, alpha-dimethylated carboxylic acids furnished spirolactones in high yields. A gem-dimethyl effect is invoked to explain these differences in cyclization capacity. Electrooxidation conditions can be selected to furnish either quinone spirolactone bis- or monoketals. Chemoselective monohydrolysis of bisketals can also be accomplished in a stepwise fashion to furnish the corresponding spirolactone monoketals, but the ortho compound unfortunately dimerized in situ via a Diels-Alder process. An ECEC pathway is proposed to rationalize the observed spirolactonizations on the basis of cyclic voltammetry analyses.

The gem-dimethyl effect in reactions through tetrahedral intermediates: cyclizations of some ethyl 2,3-disubstituted-5-(p-nitrophenyl) hydantoates

The gem-dimethyl effect in reactions through tetrahedral intermediates: cyclizations of some ethyl 2,3-disubstituted-5-(p-nitrophenyl) hydantoates

Crystal Structure and Conformation of a Dipyrrylmethane. The gem-Dimethyl Effect

Crystal Structure and Conformation of a Dipyrrylmethane. The gem-Dimethyl Effect

Crystal Structure and Conformation of a Dipyrrylmethane. The gem-Dimethyl Effect

A crystal structure determination of the new dipyrrylmethane diethyl-2,3,5,5,7,8-hexamethyl-5,10-dihydrodipyrrin-1,9-dicarboxylate (1) is only the third reported for a dipyrrylmethane and the first with a gem-dimethyl group at the bridging carbon atom. Conformation determining torsion angles are compared to those from molecular mechanics calculations and to the corresponding data for an analogous dipyrrylmethane (2) with no gem-dimethyl moiety. The crystal structures of 1 and 2 differ significantly: 1 adopts the +ac,+ac or −ac,−ac conformation, whereas 2 exists in the −ac,+sc conformation in an intermolecularly hydrogen bonded dimer. There is no evidence for hydrogen bonding in crystals of 1, and its ac conformation is unlike that found about the central core of bilirubin (sc,sc). Taken collectively, the data indicate that the presence of a sterically demanding and potentially conformation distorting gem-dimethyl group located at the bridging carbon of a dipyrrylmethane (i) stabilizes a conformation that brings the pyrrole NH groups syn to the gem-dimethyls and (ii) would destabilize the ridge-title conformation of 10,10-dimethylbilirubin.

A normal gem-dimethyl effect in the base-catalyzed cyclization of ω-( p-nitrophenyl)hydantoic acids: evidence for hindered proton transfer in the permethylated esters †

The cyclization of hydantoic acids 2-UA and 3-UA – kinetics, solvent kinetic isotope effects (SKIE) and buffer catalysis – were studied in an attempt to explain the disappearance of the gem-dimethyl effect (GDME) in the specific base-catalyzed cyclization of hydantoic esters. pH-Rate profiles for both acids (after correction for ionization and for reversibility at high pH) show two regions of unit slope corresponding to different mechanisms. For 2-UA at high pH and 3-UA at lower pH the mechanism is considered to involve rate-determining attack by the ureido anion on the neutral carboxy group, consistent with the observed inverse SKIE. The normal GDME of 15 provides strong evidence that anomalies observed with the esters do indeed result from steric hindrance to proton transfer. The change to rate determining departure of OH− with 2-UA is caused at low pH by acid catalysis of the reversion of the tetrahedral intermediate (T−) to reactants, while with 3-UA at high pH this takes place through T2−. The GDME favours attack on the carboxylate anion but makes ring opening more difficult, thus decreasing acid inhibition. The observed β = 0.44 for general base catalysis of the cyclization of 2-UA is consistent with concerted deprotonation and attack of the ureido group. With 3-UA two simultaneous general base-catalyzed reactions take place: slow deprotonation of the ureido group (β = 1.0) and attack of the ureide anion on the carboxy anion aided by the buffer conjugate acid. The estimated GDME is 2800 for the equilibrium between acid anion and hydantoin, but only 45 and 15 for catalysis by H3O+ and OH−, respectively: both reactions are presumed to go through early transition states.

Multiple changes in rate-determining step in the acid and base catalyzed cyclizations of ethyl N-(p-nitrophenyl)hydantoates caused by methyl substitution

The slopes of the pH-rate profiles for the cyclization of 2-methyl- and 2,3-dimethyl hydantoates 1-NPU and 2-NPU between pH 1 and 7 change from 1 to 0 and then back to 1. A reaction first order in H+ was observed with the latter compound. The 2,2,3-trimethyl derivative 3-NPU showed only one reaction first order in OH-, but complex acid catalysis is described by slopes 0, -1, 0, and finally -1 again. The cyclizations were general base catalyzed, with Brønsted β values of 0.5-0.6. The OH- catalysis at higher pH for 1-NPU and 2-NPU showed inverse solvent kinetic isotope effects and deviated from the Brønsted relationships, while that for 3-NPU showed a normal effect and complied with the Brønsted relationship. The accelerations due to the gem-dimethyl effect were lost with the OH- and general base-catalyzed reactions of 3-NPU. This behaviour is due to a change from the rate-determining formation of the tetrahedral intermediate with 1-NPU and 2-NPU to the rate-determining breakdown with 3-NPU, due to steric hindrance to protonation of the leaving ethoxy group. The OH- reaction at higher pH involves attack of the ureide anion with 1-NPU and 2- NPU, becoming concerted with deprotonation when catalyzed by general bases and changing to acid inhibition of the anion of the tetrahedral intermediate at low pH. With 3-NPU at higher pH, T- is in equilibrium and the conjugate acids of the general bases accelerate its breakdown by protonating the ethoxy group. Acid catalysis of the cyclization of 3-NPU at higher pH is also protonation of the leaving group from T0 changing to the rate-determining formation of T at lower pH. The latter mechanism is preferred for the cyclization of 2-NPU.Key words: gem-dimethyl effect, mechanism, general base catalysis, proton transfer, steric hindrance.