Comparison of azacyclic urea A-98881 as HIV-1 protease inhibitor with cage dimeric N-benzyl 4-(4-methoxyphenyl)-1,4- dihydropyridine as representative of a novel class of HIV-1 protease inhibitors: A molecular modeling study

The functional groups of cage dimeric N-alkyl substituted 3,5-bis(hydroxymethyl)-4-(4-methoxyphenyl)-1,4-dihydropyridines are similar to those of cyclic and azacyclic ureas that are potent inhibitors of HIV-1 protease of the dihydroxyethylene- and hydroxyethylene type, respectively. In the following study the conformity of common functional groups is investigated concerning their orientation in space as well as in the enzyme HIV-1 protease. Starting from X-ray crystal data of the centrosymmetric cage dimeric N-benzyl derivative with ester groups, the derivative with hydroxymethylene groups was built and a systematic conformational search was performed for the conformationally important torsion angles considering electrostatic and van der Waals interactions. From the huge number of conformations those comprising centrosymmetrical and C2-symmetrical energy minima were selected and minimized. The three remaining conformers were fitted to the azacyclic urea A-98881 selected from the HIV-1 protease enzyme- inhibitor complex using the centroids of the corresponding aromatic residues and additionally by the field fit option of the Advanced CoMFA module of SYBYL. Interestingly, the energetically most favourable one, which, additionally, possesses C2-symmetry like the active site cavity of HIV-1 protease, showed the best fit. Comparing the electrostatic potential (EP) of the latter with the EP of A-98881 the aromatic residues show excellent accordance. Slight differences in the extent of the EP were found in the areas of the hydroxymethylene groups of the cage dimer and the single hydroxy group as well as the urea carbonyl group of A- 98881, respectively. In order to compare the binding possibilities to the enzyme HIV-1 protease for the cage dimer and A-98881, their interaction fields with certain probes (CH3 for alkyl, NHamide, and carbonyl, O– of COO–), representing the decisive functional groups of the active site, have been calculated using GRID and projected into the enzyme placing the structures according to the position of A-98881 in the enzyme- inhibitor complex. The strongest calculated fields of the O– probe were found near Asp 25 for both structures. Another respective conformity consists in the overlap of the fields for the NHamide probe near Ile 50 and 50 for the investigated cage dimer and A-98881.     

Conformation and hydrogen bonding for the bicyclic compound 3‐thiabicyclo[3.2.0]heptane‐6,7‐dicarboxylic acid 3,3‐dioxide

The initial goal of this work was to verify the geometry of the product of a photochemical reaction, viz. the title compound, C₈H₁₀O₆S, (II). Our crystallographic study firmly establishes the cis–anti–cis nature of the substituents on the cyclobutane ring. The geometry is also designated as exo, where exo signifies that the five‐membered ring is on the opposite side of the central cyclobutane ring from the carboxylic acid substituents. The structure determination reveals two molecules, A and B, in the asymmetric unit that display substantially different conformations of the bicyclic core: the cyclobutane ring puckering angles are 22 and 3°, and the sulfolane ring conformations are twist (S‐exo) and envelope (S‐endo). Intrigued by this variation, we then compared the conformations of other molecules in the Cambridge Structural Database that have sulfolane rings fused to cyclobutane rings. In this class of compound, there are five examples of saturated cyclobutane rings, with ring puckering angles ranging from 3 to 35°. The sulfolane rings were more similar: four of the six molecules exhibit envelope conformations with S‐endo, as in molecule B of (II). Despite the conformational differences, the hydrogen‐bonding scheme for both molecules is similar: carboxyl –OH groups form hydrogen bonds with carboxyl and sulfone O atoms. Alternating A and B molecules joined by hydrogen bonds between sulfone O atoms and carboxyl –OH groups form parallel chains that extend in the ac plane. Other hydrogen bonds between the carboxyl groups link the chains along the b axis.     

Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations

The cyclic urea inhibitors of HIV-1 protease generally have two hydroxyl groups on the seven-membered ring. In this study, free energy perturbation and continuum electrostatic calculations were used to study the contributions of the two hydroxyl groups to the binding affinity and solubility of a cyclic urea inhibitor DMP323. The results indicated that the inhibitor with one hydroxyl group has better binding affinity and solubility than the inhibitor with two hydroxyl groups. Therefore, removal of one hydroxyl group from DMP323 may help to improve the properties of DMP323. This is also likely to be true for other cyclic urea inhibitors. The study also illustrated the difficulty in accurate modeling of the binding affinities of HIV-1 protease inhibitors, which involves many possible protonation states of the two catalytic aspartic acids in the active site of the enzyme.     

Synthesis of C 2 Symmetric Potential Inhibitors of HIV-1 Protease From D-Mannitol

ABSTRACT

D-Mannitol was used as precursor for the synthesis of acyclic C ₂ symmetric potential HIV-1 protease inhibitors. The 1- and 6-hydroxy groups of D-mannitol were substituted by -NHBoc, -NHValZ, -SAr, -SOAr and -SO₂Ar and the 2-and 5-hydroxy groups were benzylated. In some products one of the central hydroxyl groups was either inverted or deoxygenated. Despite a close structural similarity to previously published inhibitors none of the products showed significant inhibitory activity against HIV-1 protease.

     

Fullerene‐Based Macro‐Heterocycle Prepared through Selective Incorporation of Three N and Two O Atoms into C60

A 14‐membered heterocycle is created on the C₆₀ cage skeleton through a multistep procedure. Key steps involve repeated PCl₅‐induced hydroxylamino N?O bond cleavage leading to insertion of nitrogen atoms, and also piperidine‐induced peroxo O?O bond cleavage leading to insertion of oxygen atoms. The hetero atoms form one pyrrole, two pyran, and one diazepine rings in conjunction with the C₆₀ skeleton carbon atoms. The fullerene‐based macrocycle showed unique reactivities towards fluoride ion and copper salts.     

Synthesis and Structure of (CH3Si)6(NH)9: A Si–N Cage Made from Methyltrichlorosilane and Ammonia

No bulky substituents are bonded to the silicon centers of the cagelike title compound 1 , which is readily formed by reaction of methyltrichlorosilane with ammonia and sodium. According to X-ray structure analysis, 1 consists of two Si₃N₃ rings in the chair conformation that are bridged through the silicon centers by NH groups. The result is a cage in which three bars are missing, as can be seen on the right.     

1‐Phenyl‐5‐(piperidino­methyl)‐1H‐tetrazole

In the mol­ecule of the title 1,5‐disubstituted tetrazole, C₁₃H₁₇N₅, the tetrazole and benzene rings are not coplanar, having a dihedral angle of 42.96 (5)° between them. The piperidine fragment adopts a chair conformation, and there is a non‐classical intramolecular contact between the benzene H atom and the piperidine N atom. Intermolecular C—H⋯π interactions involving the piperidine C—H groups and the benzene rings are responsible for the formation of two‐dimensional networks, extending parallel to the ab plane. These networks are linked together into a three‐dimensional polymeric structure viaπ–π stacking interactions between the tetrazole rings of two adjacent mol­ecules.     

Electronic Effects and the Special Features of Solvation of Alkyl and Hydroxyl Substituted Tetraphenylporphins and Their Complexes with Zinc

Solutions of tetraphenylporphins (H₂TPhP) substituted in one and four phenyl residues by alkyl (CH₃- and -C(CH₃)₃) and hydroxyl groups were studied by electronic spectroscopy and solution thermochemistry. Porphyrin ligands and their complexes with zinc were investigated in solutions in electroneutral (benzene and chloroform) and electron donor (N,N-dimethylformamide, pyridine, and piperidine) solvents. The electronic effects of alkyl and HO groups on the electronic absorption spectra and extracoordination of solvent molecules to the central zinc atom were revealed.     

An FTIR Spectroscopic Study on the Effect of Molecular Structural Variations on the CO2 Absorption Characteristics of Heterocyclic Amines

Herein, the reaction between CO₂ and piperidine, as well as commercially available functionalised piperidine derivatives, for example, those with methyl‐, hydroxyl‐ and hydroxyalkyl substituents, has been investigated. The chemical reactions between CO₂ and the functionalised piperidines were followed in situ by using attenuated total reflectance (ATR) FTIR spectroscopy. The effect of structural variations on CO₂ absorption was assessed in relation to the ionic reaction products identifiable by IR spectroscopy, that is, carbamate versus bicarbonate absorbance, CO₂ absorption capacity and the mass‐transfer coefficient at zero loading. On absorption of CO₂, the formation of the carbamate derivatives of the 3‐ and 4‐hydroxyl‐, 3‐ and 4‐hydroxymethyl‐, and 4‐hydroxyethyl‐substituted piperidines were found to be kinetically less favourable than the carbamate derivatives of piperidine and the 3‐ and 4‐methyl‐substituted piperidines. As the CO₂ loading of piperidine and the 3‐ and 4‐methyl‐ and hydroxyalkyl‐substituted piperidines exceeded 0.5 moles of CO₂ per mole of amine, the hydrolysis of the carbamate derivative of these amines was observed in the IR spectra collected. From the subset of amines analysed, the 2‐alkyl‐ and 2‐hydroxyalkyl‐substituted piperidines were found to favour bicarbonate formation in the reaction with CO₂. Based on IR spectral data, the ability of these amines to form the carbamate derivatives was also established. Computational calculations at the B3LYP/6‐31+G** and MP2/6‐31+G** levels of theory were also performed to investigate the electronic/steric effects of the substituents on the reactivity (CO₂ capture performance) of different amines, as well as their carbamate structures. The theoretical results obtained for the 2‐alkyl‐ and 2‐hydroxyalkyl‐substituted piperidines suggest that a combination of both the electronic effect exerted by the substituent and a reduction in the exposed area of the nitrogen atom play a role in destabilising the carbamate derivative and increasing its susceptibility to hydrolysis. A theoretical investigation into the structure of the carbamate derivatives of these amines revealed shorter N? C bond lengths and a less‐delocalised electron distribution in the carboxylate moiety.     

Synthesis,structural, conformational and pharmacological study of new fentanyl derivatives of the camphidine system

A series of N-phenethyl-8-β-amidocamphidines 4a-f (3-phenethyl-8-β-(N-arylamido)-3-azabicyclo-[3.2.1]octane) has been designed, synthesized and stereochemically characterized as semirigid analogous of the 4-anilidopiperidine analgesics in an attempt to study the influence of certain stereochemical factors on analgesia in this class of compounds. In deuteriochloroform and deuteriobenzene solution, compounds 4a-f display the same preferred conformation. The cyclopentane and piperidine rings adopt an envelope and distorted chair conformation respectively flattened at N-3, with the N and C-8 substituents in equatorial and axial positions with respect to the piperidine ring. In vivo pharmacological testing demonstrated that compounds 4a-f were inactive in the analgesic test, with the exception of compound 4f which showed an ED₅₀ of 250 mg/kg p.o.     

Synthesis,structure, and tautomerism of 3a,7-dimethyl-4,6-diphenyl-2-ethynyl-7a-hydroxyperhydropyrrolo[3,2-c]pyridine

Isomeric [with respect to the fusion of the piperidine and pyrrolidine rings, as well as with respect to the mutual orientation of the substituents attached to the C₍₂₎ and C_(3a) carbon atoms] 3a, 7-dimethyl-4,6-diphenyl2-ethynyl-7a-hydroxyperhydropyrrolo[3,2-c]pyridines were isolated for the first time in the reaction of 3,5-dimethyl-2,6-diphenyl-4-piperidinone oxime with acetylene under the conditions of the Trofimov reaction under pressure. It was established that, in solutions, the isomers of this compound with an axial-equatorial fusion of the rings exist in the form of ring—chain tautomers.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 903–914, July, 1992.     

Chlorination of IPR C100 Fullerene Affords Unconventional C96Cl20 with a Nonclassical Cage Containing Three Heptagons

Chlorination of C₁₀₀ fullerene with a mixture of VCl₄ and SbCl₅ afforded C₉₆Cl₂₀ with a strongly unconventional structure. In contrast to the classical fullerenes containing only hexagonal and pentagonal rings, the C₉₆ cage contains three heptagonal rings and, therefore, should be classified as a fullerene with a nonclassical cage (NCC). There are several types of pentagon fusions in the C₉₆ cage including pentagon pairs and pentagon triples. The three‐step pathway from isolated‐pentagon‐rule (IPR) C₁₀₀ to C₉₆(NCC‐3hp) includes two C₂ losses, which create two cage heptagons, and one Stone–Wales rotation under formation of the third heptagon. Structural reconstruction established C₁₀₀ isomer no. 18 from 450 topologically possible IPR isomers as the starting C₁₀₀ fullerene. Until now, no pristine C₁₀₀ isomers have been confirmed based on the experimental results.     

Reversible Single‐Crystal‐to‐Single‐Crystal Photochemical Formation and Thermal Cleavage of a Cyclobutane Ring

A [2+2] cycloaddition reaction has been observed in a number of solids. The cyclobutane ring in a photodimerized material can be cleaved into olefins by UV light and heat. The high thermal stability of the metal–organic salt K₂SDC (H₂SDC=4,4’‐stilbenedicarboxylic acid) has been successfully utilized to investigate the reversible cleavage of a cyclobutane ring. The two polymorphs of K₂SDC undergo reversible cyclobutane formation by UV light and cleavage by heat in cycles. Of these, one polymorph retains its single‐crystal nature during the reversible processes. Polymorphs are known to show different physical properties and chemical reactivities. This work reveals that the retention of single‐crystal nature is strongly associated with the packing of molecules, which is controlled by kinetics and thermodynamics. The photoemissive nature of the products makes this as a promising material for photoswitches and optical data storage devices.     

Density functional theory study of the styrylbenzoquinoline dyad and the related dibenzoquinolylcyclobutane formed in the [2 + 2] photocycloaddition reaction

The structure and electronic properties of the biphotochromic dyad with two styrylbenzo[f]quinoline photochromes, as well as the corresponding cyclobutane with two benzo[f]quinoline (BQ) substituents, are studied by DFT at the M06-2X/6-31G* level, the cyclobutane being a product of the [2 + 2] photocycloaddition (PCA) reaction of the dyad. According to calculations, the dyad forms π-stacked folded conformers, which, when excited, can form excimers that are precursors of cyclobutane. TD DFT calculations and natural transition orbital (NTO) analysis indicated that the lowest singlet excited S₁ state in the dyad is localized on the SBQ photochrome, including the ethylene group that undergoes PCA. Thus, the conditions for concerted electrocyclic reactions are satisfied, and the direct PCA follows the Woodward–Hoffmann rules. In contrast, in cyclobutane, the S₁ state is localized on the BQ substituent rather than on the cyclobutane core. Therefore, the reverse ring-opening (retro-PCA) reaction cannot follow the Woodward-Hoffmann rules and inevitably involves a step of excitation energy transfer from BQ to cyclobutane, which means the predissociation mechanism.     

The Photocyclodimers of 2,3‐Dihydro‐2,2‐dimethyl‐4H‐pyran‐4‐one

On irradiation (350 nm) in benzene solution, dihydropyranone 3 affords predominantly (75%) the cis‐anti‐cis HH‐dimer 4 , but in smaller amounts (12%) also dimer 5 , wherein one of the six‐membered rings is trans‐fused to the (central) cyclobutane ring. The constitution and configuration of 5 was fully elucidated by NMR‐analysis. On contact with SiO₂, 5 isomerizes quantitatively to the cis‐anti‐cis HT‐dimer 7 , the structure of which was established by X‐ray crystal‐structure determination.     

An unusual acid: (±)‐3‐benzoyl‐1,2‐dimethyl‐8a‐phenyl‐2‐benzo­thieno­[2,3‐b]pyrrole‐1,2‐dicarboxylic anhydride

The title compound, C₂₇H₂₁NO₄S, is a 2‐benzothieno[2,3‐b]pyrrole derivative with several substituents, present in the crystal as a racemate. The tetra­cyclic fused‐ring system shows a `U‐shaped' mol­ecular architecture, since the two rings flanking the central pyrrolidine ring both point in the same direction.     

小环化合物中饱和碳质子化学位移的计算

小环化合物由于其张力、构型、构象和各向异性效应等原因,环碳上质子化学位移缺乏规律性,难以预测,对此作者曾提出一种近似算法。本文根据303种小环化合物中饱和碳质子的化学位移实验数据,将适于计算这类质子化学位移的公式表述为:     

Modulating the Binding of Polycyclic Aromatic Hydrocarbons Inside a Hexacationic Cage by Anion–π Interactions

We report the template‐directed synthesis of BlueCage⁶⁺, a macrobicyclic cyclophane composed of six pyridinium rings fused with two central triazines and bridged by three paraxylylene units. These moieties endow the cage with a remarkably electron‐poor cavity, which makes it a powerful receptor for polycyclic aromatic hydrocarbons (PAHs). Upon forming a 1:1 complex with pyrene in acetonitrile, however, BlueCage?6 PF₆ exhibits a lower association constant K_a than its progenitor ExCage?6 PF₆. A close inspection reveals that the six PF₆^? counterions of BlueCage⁶⁺ occupy the cavity in a fleeting manner as a consequence of anion–π interactions and, as a result, compete with the PAH guests. This conclusion is supported by a one order of magnitude increase in the K_a value for pyrene in BlueCage⁶⁺ when the PF₆^? counterions are replaced by much bulkier anions. The presence of anion–π interactions is supported by X‐ray crystallography, and confirms the presence of a PF₆^? counterion inside its cavity.     

(Z)‐5‐[4‐(Dimethylamino)benzylidene]‐2‐(piperidin‐1‐yl)‐1,3‐thiazolidin‐4(5H)‐one

The molecules of the title compound, C₁₇H₂₁N₃OS, are characterized by a wide C—C—C angle at the methine C atom linking the aryl and thiazolidine rings, associated with a short repulsive intramolecular S...H contact between atoms in these two rings. A single piperidine–arene C—H...π hydrogen bond links pairs of molecules into centrosymmetric dimers.