Mixture Of Rotamers Research Articles

Pemuchiamides A and B, Proline-Rich Linear Lipopeptides, Isolated from a Marine Hormoscilla sp. Cyanobacterium.

Pemuchiamides A and B (1 and 2) were isolated from a marine Hormoscilla sp. cyanobacterium collected from Pemuchi Beach on Hateruma Island, Japan. Although 1 and 2 existed as a complex mixture of rotamers in chloroform-d, detailed analyses of their 2D NMR and tandem mass spectra revealed their planar structures, respectively. The absolute configurations of 1 and 2 were established via the degradation and derivatization reactions. Pemuchiamide A (1) exhibited potent growth-inhibitory activity against Trypanosoma brucei rhodesiense, the causative organism of African sleeping sickness, while 2 showed 10-fold weaker activity than 1. This result indicates that the presence of a hydroxy group at the C-3 position of the 4-aminobutanoic acid moiety negatively affects antitrypanosomal activity.

RP-HPLC separation of interconvertible rotamers of a 5-tetrahydroisoquinolin-6-yl-pyridin-3-yl acetic acid derivative and confirmation by VT NMR and DFT study

Due to emergence of drug resistance and drug tolerability, there is urgent need for discovery of new chemical entity for the treatment of HIV infection. As a part of in-house small molecule drug discovery program for HIV infection, sodium-2-(tert-butoxy)− 2-(5-(2-(2-chloro-6-methylbenzyl)− 1,2,3,4-tetrahydroisoquinolin-6-yl)− 4-(4,4-dimethylpiperidin-1-yl)− 2,6-dimethylpyridin-3-yl) acetate (SCMTDDA) was prepared as an intermediate for the synthesis of an API, designed as a HIV-1 integrase inhibitor. Initially, the final compound was isolated as a mixture of rotamers. In the current study, we have developed a simple and efficient achiral, reversed phase (RP) HPLC method to separate the interconvertible rotamers of SCMTDDA. The effect of several parameters, including stationary phase, buffer, modifiers and column temperature, were optimized for the chromatographic separation and it was observed that best separation was achieved on a SunFire C18 column using TFA/acetonitrile (ACN) - methanol (MeOH) (1:1 v/v) as the mobile phase at 10 0C. The chromatographic observations were complemented with variable-temperature NMR and energy barrier calculations using density functional theory (DFT).

Synthesis of [1-8-NαC]-zanriorb A1, alanine-containing analogues, and their cytotoxic and anti-inflammatory activity.

The synthesis of the orbitide[1-8-NαC]-zanriorb A1, isolated from the medicinal plant Zanthoxylum riedelianum, was investigated by solution-phase macrocyclization of a linear peptide and on-resin solid-phase macrocyclization with an acylsulfonamide safety-catch linker. The solution-phase route produced a mixture of proline rotamers, and the main component was assigned as the trans, cis rotamer, identical to the natural product. The on-resin cyclization was less successful, producing mainly a linear peptide, and minor cyclic products as rotameric mixtures. Although the natural product was reported to be significantly cytotoxic against Jurkat leukemia T cells, our synthetic peptides were inactive, suggesting the presence of other rotamers or impurities in the naturally isolated material. Additional analogues of zanriorb A1 were synthesized in which proline and glycine residues were replaced with alanine. While these analogues were not cytotoxic, several of them inhibited the production of nitric oxide in lipopolysaccharide (LPS)-stimulated macrophages. The most active compound, cyclic[Ala5,6,8 ]-zanriorb A1 had an IC50 of 22 μM and was more potent compared with the standard NG-monomethyl-l-arginine acetate (L-NMMA) with an IC50 of 98 μM, indicating their strong anti-inflammatory potential.

Isolation and Characterization of Novel Degradation Products of Valsartan by NMR and High Resolution Mass Spectroscopy: Development and Validation of Valsartan by UPLC

Valsartan is used to treat high blood pressure, heart failure and diabetic kidney disease. It was subjected to forced degradation under acidic, basic and peroxide mediated oxidation. The forced degradation was performed according to ICH guidelines Q1A(R2)−Stability Testing of New Drug Substances and Products. The drug was inert under peroxide mediated hydrolysis, two degradants (DP-Val-1, DP-Val-2) were formed in base hydrolysis and one degradant (DP-Val-3) was formed in acid hydrolysis. These degradants were initially identified through LC-MS and isolated by mass mediated purification system. DP-Val-1 and DP-Val-3 are already reported but their structures were not confirmed by 2D NMR studies. DP-Val-2 is novel degradant and its structure has been elucidated by substantial analysis of high resolution mass spectrometry and 1D, 2D NMR spectroscopy. DP-Val-1 consists of a mixture of rotamers and this hypothesis was confirmed by variable temperature NMR (VT-NMR). A stability indicating RP-UPLC method was developed and validated for assay determination valsartan API drug. A valsartan UPLC method was validated on Acquity BEH C-18 2.1 × 100 mm, 1.7 μm column with shorter runtime of 6 min and the method was validated as per regulatory guidelines in terms of specificity, accuracy, linearity, precision, limit of detection and limit of quantitation.

Helvamide, a new inhibitor of sterol O-acyltransferase produced by the fungus Aspergillus nidulans BF-0142.

A new piperazine derivative designated helvamide was isolated as a pair of rotamers (1 and 2) from the culture broth of the fungus Aspergillus nidulans BF-0142 along with a known helvafuranone (3). The structures of 1 and 2 were elucidated based on spectroscopic analyses by the interpretation of one-dimensional and two-dimensional nuclear magnetic resonance data, ROESY (rotational Overhauser effect spectroscopy) correlations, and a chemical method. Helvamide existed as a rotameric mixture (1 and 2) in dimethyl sulfoxide. Helvamide inhibited sterol O-acyltransferases 1 and 2 (SOAT1 and SOAT2) in enzyme-based and cell-based assays using SOAT1-expressing and SOAT2-expressing Chinese hamster ovary (CHO) cells.

Phosphorus-containing isothiocyanate-derived mercapturic acids as a useful alternative for parental isothiocyanates in experimental oncology

A series of phosphonates, phosphinates and phosphine oxides isothiocyanate-derived mercapturic acids were synthesized. A temperature dependence dynamic proton decoupled 31P NMR studies indicated that in most cases the compounds were obtained as a mixture of rotamers. Moreover, biologically relevant reversibility of mercapturic acids synthesis from the parental isothiocyanates was confirmed. All compounds were evaluated ashighly active antiproliferative agents in vitro in human colon cancer cell lines (LoVo and its doxorubicin-resistant subline LoVo/DX). The cell cycle progression and caspase-3 activity analyses revealed compounds moderate activity as apoptosis inducers and their poor influence on cell cycle progression in the LoVo cells. Our results confirm that isothiocyanate-derived mercapturic acids present a reasonable alternative for the parental compounds, and can replace them in the future studies on isothiocyanates potential as anticancer agents.

Sterically Tuned P‐Phosphanylamino Phosphaalkenes (Me3Si)2C=PN(R)PPh2 and (iPrMe2Si)2C=PN(R)PPh2

Deprotonation of the aminophosphanes Ph2PN(H)R 1a–1h [R = tBu (1a), 1‐adamantyl (1b), iPr (1c), CPh3 (1d), Ph (1e), 2,4,6‐Me3C6H2 (Mes) (1f), 2,4,6‐tBu3C6H2 (Mes*) (1g), 2,6‐iPr2C6H3 (DIPP) (1h)], followed by reactions of the phosphanylamide salts Li[Ph2PNR] 2a, 2b, 2g, and 2h with the P‐chlorophosphaalkene (Me3Si)2C=PCl, and of 2a–2g with (iPrMe2Si)2C=PCl, gave the isolable P‐phosphanylamino phosphaalkenes (Me3Si)2C=PN(R)PPh2 3a, 3b, 3g, and (iPrMe2Si)2C=PN(R)PPh2 4a–4g. 31P NMR spectra, supported by X‐ray structure determinations, reveal that in compounds 2a, 2b, 3a, and 3b, with bulky N‐alkyl groups the Si2C=P–N–P skeleton is non‐planar (orthogonal conformation), whereas 3g, 3h, and 4g with bulky N‐aryl groups exhibit planar conformations of the Si2C=P–N–P skeleton. Solid 3g and 4g exhibit cisoid orientation of the planar C=P–N–C units (planar I) but in solid 3h the transoid rotamer is present (planar II). From 3g, 4d, and 4g mixtures of rotamers were detected in solution by pairs of 31P NMR patterns (3h: line broadening).

3+2] Cycloadditions of N-Protected ‘(S)-Diazoproline’ with Selected Acetylenes

Acetylene carboxylates and an acetylene phosphonate reacted with N-protected (S)-2-(diazoacetyl)pyrrolidines ((S)-diazoprolines) to give optically active bis-heterocyclic pyrazole derivatives in a regioselective [3+2] cycloaddition. The reactions occurred at 60 °C in THF solution in the absence of a catalyst. However, diethyl ethynylphosphonate reacted significantly slower than the carboxylates. The obtained products were shown to exist in CDCl3 solution at room temperature as mixtures of rotamers. The reactions of diethyl ethynylphosphonate with a selected cyclic α-oxodiazo compound, i.e. 2-diazoacenaphthen-1-one, yielded a fused tricyclic pyrazole derivative.

Chemical Biology of N5-Substituted Formamidopyrimidine DNA Adducts.

DNA nucleobases are the prime targets for chemical modifications by endogenous and exogenous electrophiles. Alkylation of the N7 position of guanine and adenine in DNA triggers base-catalyzed imidazole ring opening and the formation of N5-substituted formamidopyrimidine (N5-R-FAPy) lesions. Me-FAPy-dG adducts induced by exposure to methylating agents and AFB-FAPy-dG lesions formed by aflatoxin B1 have been shown to persist in cells and to contribute to toxicity and mutagenicity. In contrast, the biological outcomes of other N5-substituted FAPy lesions have not been fully elucidated. To enable their structural and biological evaluation, N5-R-FAPy adducts must be site-specifically incorporated into synthetic DNA strands using phosphoramidite building blocks, which can be complicated by their unusual structural complexity. N5-R-FAPy exist as a mixture of rotamers and can undergo isomerization between α, β anomers and furanose-pyranose forms. In this Perspective, we will discuss the main types of N5-R-FAPy adducts and summarize the strategies for their synthesis and structural elucidation. We will also summarize the chemical biology studies conducted with N5-R-FAPy-containing DNA to elucidate their effects on DNA replication and to identify the mechanisms of N5-R-FAPy repair.

Synthesis of 3‐Substituted 2‐Indol­inones by a Multicomponent Coupling Isocyanide‐Dependent Microwave‐Assisted Intramolecular Transamidation Process

AbstractA small‐molecule library synthesis of 3‐substituted 2‐indolinones using methyl isocyanide and a microwave‐assisted intramolecular transamidation process with 10 % TFA in dichloroethane has been achieved in 3 steps. A modified Fe0 Bechamp‐type reduction of a substituted bifunctional substrate, o‐nitrobenzaldehyde, renders 3‐substituted 2‐indolinones in yields ranging from 76–91 % (21 examples). Furthermore, it has been determined that symmetrical 2o N‐alkyl or aryl substituents, as a component of the amine starting material, suppresses 3‐substituted 2‐indolinone rotameric mixtures and allows for facile compound 1H NMR characterization. In the absence of methyl isocyanide, 3,4‐dihydroquinazolines or transamidation products predominate under both Brønsted or Lewis acid conditions in reasonable yields.

Rotational Isomers, Intramolecular Hydrogen Bond, and IR Spectra of o-Vinylphenol

Absorption bands of OH stretching vibrations in IR spectra of o-vinylphenol (o-VP) in the weakly polar solvents CCl4 and n-hexane were studied. Several rotamers of the free OH group were observed for o-VP in n-hexane. The fraction of o-VP rotamers with an O-H…�a intramolecular hydrogen bond (IHB) was less than 20% according to experimental estimates for CCl4 solutions and calculations in the gas phase and cyclohexane. The theoretical effective enthalpy of the o-VP IHB was estimated for rotamer A (-�˚ H = 0.20 kcal/mol). basicity of the �a -bond and the geometric cono guration of the functional groups involved in forming the H-bond. The in? uence of substituents on the IHB strength between the OH group and the double-bond �a -electrons was studied by IR spectroscopy using nine o-VPs with variously substituted vinyl groups as examples (4). It was found that two bands were observed as a rule in the high-frequency region of IR spectra of the o-VPs. These were �� (OH)f in the range 3609-3612 cm -1 and �� (OH)b at 3524-3557 cm -1 . The quantity �˚�� (OH) varied in the range 55-85 cm -1 . The intensity ratio of these bands depended strongly on the position and number of alkyl groups in the vinyl substituent. The compound o-VP itself was studied experimentally (4, 5). The �� (OH)f band in IR spectra of its CCl4 solutions was observed at 3611 cm -1 ; �� (OH)b, 3557 with �˚�� (OH) = 54 cm -1 . IR spectra of the o-phenols were examined only in the range 3700-3500 cm -1 . Any absorption bands in the range 3500-3200 cm -1 were not reported (3-5). The enthalpy of the IHB in o-VP was not determined previously although an estimate of this parameter for its homolog o-isopropenylphenol was -�˚ H = 0.76 ± 0.11 kcal/mol (6). A conformational analysis of structurally ? uxional o-VP was recently completed (7). An analysis of the surface potential energy (SPE) of o-VP that was constructed using the B3LYP/6-311G(d) method showed that o-VP existed in the gas phase and in CCl4 solution as a mixture of rotamers A, B, C, and D that were produced by internal rotation of the OH and vinyl groups and three optical isomers A1, B1, and C1 of these rotamers:

Unique Structural Properties of 2,4,6-Tri-tert-butylanilide: Isomerization and Switching between Separable Amide Rotamers through the Reaction of Anilide Enolates

Herein, we report a unique structural property of 2,4,6-tri-tert-butylanilide, which can be separated into its amide rotamers at room temperature. Interconversion between the rotamers of anilide enolates occurs readily at room temperature and their reaction with electrophiles gives mixtures of the rotamers in a ratio that depends on the reactivity of the corresponding electrophile. That is, the reaction of the 2,4,6-tri-tert-butylacetanilide enolate with reactive electrophiles, such as allyl bromide or protic acids, gives mixtures of the anilide rotamers in which the E rotamer is the major component, whereas less-reactive electrophiles, such as 1-bromopropane and 2-iodopropane, yield mixtures of the rotamers in which the Z rotamer is the major component. The rotameric ratio of the product is also strongly dependent on the reactivity of the anilide enolate. Switching between the anilide rotamers can be achieved through protonation of a less-reactive enolate by a less-reactive protic acid and thermal isomerization of the anilide.

ChemInform Abstract: Palladium‐Catalyzed Arylation of Methylene‐Bridged Polyarenes: Synthesis and Structures of 9‐Arylfluorene Derivatives.

AbstractThe reaction of fluorene (I) with various aromatic bromides and chlorides affords arylated products, mostly as mixtures of rotamers.

ChemInform Abstract: Three‐Component Reaction of Triphenylphosphine, Dialkyl Acetylenedicarboxylates, and Heterocyclic Rings and the Related Iminophosphoranes.

AbstractThe title reaction including diester (III) or its diethyl analogue affords phosphorus ylides of type (IV) which exist as mixtures of rotamers.

Antiprotozoal and Antimicrobial Compounds from the Plant Pathogen Septoria pistaciarum

Four new 1,4-dihydroxy-5-phenyl-2-pyridinone alkaloids, 17-hydroxy-N-(O-methyl)septoriamycin A (1), 17-acetoxy-N-(O-methyl)septoriamycin A (2), 13-(S)-hydroxy-N-(O-methyl)septoriamycin A (3), and 13-(R)-hydroxy-N-(O-methyl)septoriamycin A (4), together with the known compounds (+)-cercosporin (5), (+)-14-O-acetylcercosporin (6), (+)-di-O-acetylcercosporin (7), lumichrome, and brassicasterol, were isolated from an ethyl acetate extract of a culture medium of Septoria pistaciarum. Methylation of septoriamycin A (8) with diazomethane yielded three di-O-methyl analogues, two of which existed as mixtures of rotamers. We previously reported antimalarial activity of septoriamycin A. This compound also exhibited significant activity against Leishmania donovani promastigotes. Compounds 5-7 showed moderate in vitro activity against L. donovani promastigotes and chloroquine-sensitive (D6) and -resistant (W2) strains of Plasmodium falciparum, whereas compound 5 was fairly active against methicillin-sensitive and methicillin-resistant strains of Staphylococcus aureus. Compounds 5-7 also displayed moderate phytotoxic activity against both a dicot (lettuce, Lactuca sativa) and a monocot (bentgrass, Agrostis stolonifera) and cytotoxicity against a panel of cell lines.

Strain Effects in Electron Spin Resonance Spectroscopy of Quintet 2,6-Bis(4′-nitrenophenyl)-4-phenylpyridine

Photolysis of 2,6-bis(4'-azidophenyl)-4-phenylpyridine in 2-methyltetrahydrofuran (2MTHF) glass at 7 K leads to quintet 2,6-bis(4'-nitrenophenyl)-4-phenylpyridine as a mixture of rotational isomers. The electron spin resonance (ESR) spectrum of this mixture of rotamers shows a considerable broadening of many transitions in the range of 0-5000 G and cannot be reproduced by computer simulations solely based on the tuning of the spin Hamiltonian parameters g, D(Q), and E(Q) alone or on predictions of DFT calculations. The best modeling of the experimental ESR spectrum is obtained only when the large line-broadening parameter of Γ(E(Q)) = 1200 MHz along with the spin Hamiltonian g = 2.003, D(Q) = 0.154 cm(-1), and E(Q) = 0.050 cm(-1) is used in the spectral simulations. The most accurate theoretical estimations of the magnetic parameters of the dinitrene in a 2MTHF glass are obtained from the B3LYP/6-311+G(d,p)+PBE/DZ/COSMO calculations of the spin-spin coupling parameters D(SS) and E(SS). Such calculations overestimate the E(Q) and D(Q) values of the dinitrene just by 1% and 10%, respectively, demonstrating that contributions of the spin-orbit coupling parameters D(SOC) and E(SOC) to the total D(Q) and E(Q) values are negligibly small. The research shows that ESR studies of polynuclear high-spin nitrenes, obtained by photolysis of rotational isomers of the starting azides, can only be successful if large E(Q) strain effects are taken into account in the spectral simulations.

ChemInform Abstract: Rotational Isomerism in 1,2-Diphenyltetrafluoroethane

Abstract IR and Raman spectra of 1,2-diphenyltetrafluoroethane (in the solid and solution states) are reported and assignment of frequencies made. Comparison of the Raman and IR spectra in both the solid and solution states indicates that the compound exists in the non-polar trans conformation in the solid state and as a rotameric mixture of the polar gauche and trans conformers in solution. Analysis of the dipole moment and Kerr effect data shows that in benzene solution at 25°C, the mixture contains approximately 59% trans and 41% of the gauche rotamer. These results are in reasonable agreement with those predicted by an MMP2 calculation (65% rans , 35% gauche).

ChemInform Abstract: Rotational Isomerism and Crystal Structures of 2-Methyl-2,3,3- trinitrobutane and 2-Methyl-2,3,3-trinitropentane.

Dielectric data show that in benzene and carbon tetrachloride at 25 °C, 2-methyl-2,3,3-trinitrobutane and 2-methyl-2,3,3-trinitropentane exist as “trans” : gauche rotameric mixtures in the approximate ratios of 68 : 32 and 57 : 43 respectively. These experimental results are compared with those predicted by AMPAC (AM1) calculations. X-Ray structure investigations show that in both compounds, the nitro group at C2 is “gauche” with respect to the two nitro groups at C3 in the solid state.

ChemInform Abstract: Enolization in Radical Cations of o-Methylacetophenone and Related Species Under Cryogenic Conditions.

Upon radiolytic ionization of o-methylacetophenone in low temperature matrices, the radical cation of the corresponding enol is formed. The kinetics of this process indicate a significant contribution of quantum-mechanical tunnelling in the hydrogen atom transfer. The same species is also formed by ionizing 1-methyl-1,2-dihydrobenzocyclobutenol but the composition of the rotameric mixture of enol radical cations is different in this case. Analogous experiments with 5,8-dimethyl-1-tetralone demonstrate that enol radical cations are stable in their Z-conformation under cryogenic conditions in contrast to the corresponding neutrals.

Pyrrolizine-1,3-dione

Pyrrolizine-1,3-dione 4 was made by oxidation of the alcohol 2 using pyridinium chlorochromate. The dione 4 shows ketone properties (e.g. formation of DNP derivative 11) and, in common with other pyrrolizinones, the lactam unit is readily ring-opened by methanol under basic conditions. The active methylene unit of 4 couples readily with diazonium salts to provide the hydrazone 15 whose structure was confirmed by X-ray crystallography. The 'Meldrumsated' derivative 18 exists exclusively as the tautomer 18F; flash vacuum pyrolysis (FVP) of 18 at 700 degrees C gives the pyronopyrrolizine 20 exclusively. Reaction of 4 with DMF acetal gives the dimethylaminomethylene derivative 22 which exists as a mixture of rotamers at room temperature.