Molecular dynamics of 6‐methyl‐2‐phenyl‐2,3‐dihydro‐4H‐chromen‐4‐one and 6‐methyl‐2‐(4‐nitrophenyl)‐2,3‐dihydro‐4H‐chromen‐4‐one (flavanone) derivatives in a solution studied by NMR spectroscopy

Molecular dynamics of benzoxazepin, oxime, pyrazole, and thiosemicarbazone derivatives of some flavanones have been investigated in a solution using NMR. The results confirm the formation of different O–H···O, O–H···N, N···H–N type intramolecular hydrogen bonds in the pyrazole and oxime molecules. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined. Copyright © 2013 John Wiley & Sons, Ltd.     

Semi‐synthesis and NMR spectral assignments of flavonoid and chalcone derivatives

Previous investigations of the aerial parts of the Australian plant Eremophila microtheca and Syzygium tierneyanum resulted in the isolation of the antimicrobial flavonoid jaceosidin ( 4 ) and 2′,6′‐dihydroxy‐4′‐methoxy‐3′,5′‐dimethyl chalcone ( 7 ), respectively. In this current study, compounds 4 and 7 were derivatized by acetylation, pivaloylation, and methylation reactions. The final products, 5,7,4′‐triacetoxy jaceosidin ( 10 ), 5,7,4′‐tripivaloyloxy jaceosidin ( 11 ), 5,7,4′‐trimethoxy jaceosidin ( 12 ), 2′,6′‐diacetoxy‐4′‐methoxy‐3′,5′‐dimethyl chalcone ( 13 ), 2′‐hydroxy‐4′‐methoxy‐6′‐pivaloyloxy‐3′,5′‐dimethyl chalcone ( 14 ), and 2′‐hydroxy‐4′,6′‐dimethoxy‐3′,5′‐dimethyl chalcone ( 15 ) were all fully characterized by NMR and MS. Derivatives 10 and 13 have been previously reported but were only partially characterized. This is the first reported synthesis of 11 and 14 . The natural products and their derivatives were evaluated for their antibacterial and antifungal properties, and the natural product, jaceosidin ( 4 ) and the acetylated derivative, 5,7,4′‐triacetoxy jaceosidin ( 10 ), showed modest antibacterial activity (32–128 µg/ml) against Staphylococcus aureus strains. Copyright © 2016 John Wiley & Sons, Ltd.     

Molecular dynamics of cis‐1‐(2‐hydroxy‐5‐ methylphenyl)ethanone oxime and N‐(2‐hydroxy‐4‐methylphenyl)acetamide in solution studied by NMR spectroscopy

The formation of hydrogen bonds and molecular dynamics for the molecules cis‐1‐(2‐hydroxy‐5‐methylphenyl)ethanone oxime ( I ) and N‐(2‐hydroxy‐4‐methylphenyl)acetamide ( II ) have been investigated in solution using NMR. The results confirm the formation of O? H···O, O? H···N and O···H? N type inter‐ and intramolecular hydrogen bonds. Spin‐lattice relaxation times (T₁), activation energy of molecular dynamics and energy of intramolecular hydrogen bonds have been determined. Copyright © 2010 John Wiley & Sons, Ltd.     

1H and 13C chemical shifts for acridines: Part XVII. (1,3‐Benzothiazol‐2‐yl)amino‐9(10H)‐acridinone derivatives

The ¹H and ¹³C NMR resonances for 16 acridin‐9(10H)‐ones substituted with amino or (1,3‐benzothiazol‐2‐yl)amino groups were completely and unequivocally assigned by the concerted application of gs‐COSY, gs‐HMQC and gs‐HMBC experiments. Evidence for hydrogen bond and amino–imino tautomerism is presented for 1‐ and 4‐substituted acridin‐9(10H)‐ones. Copyright © 2002 John Wiley & Sons, Ltd.     

Theoretical study on keto–enol tautomerism and isomerization in pyruvic acid

Isomerization and tautomerism of 12 isomers of pyruvic acid including 4 keto and 8 enol forms were studied at the MP2 and B3LYP levels of theory using 6‐311++G(2df,p) basis set, separately. Activation energy (E_a), imaginary frequency (υ), and Gibbs free energy (ΔG^#) of the considered isomerization and tautomerism reactions were calculated. Interconversion of the enol forms proceeds through two paths: (i) proton transfer and (ii) internal rotation. Activation energies for the proton transfer paths were in the range of 125–145 kJ/mol and for the internal rotation paths were in the range of 5–45 kJ/mol. Keto–enol tautomerism of pyruvic acid proceeds only through proton transfer route and their activation energies were in the range of 200–300 kJ/mol. Effect of microhydration on the transition state structures and activation energies was also investigated. It was found that the presence of a water molecule catalyzes the isomerization and tautomerism reactions of pyruvic acid so that the activation energies decrease. © 2013 Wiley Periodicals, Inc.     

Synthesis and properties of polyimides derived from 1,4‐bis(4‐aminophenoxy)‐2‐(6‐oxido‐6H‐dibenz[c,e] [1,2]oxaphosphorin‐6‐yl) phenylene

A new phosphorus‐containing aromatic diamine, 1,4‐bis(4‐aminophenoxy)‐2‐(6‐oxido‐6H‐dibenz[c,e] [1,2]oxaphosphorin‐6‐yl) phenylene ( 3 ) was synthesized by the nucleophilic aromatic substitution of 2‐(6‐oxido‐6H‐dibenz[c,e] [1,2]oxaphosphorin‐6‐yl)‐1,4‐dihydroxy phenylene ( 1 ) with 4‐fluoronitrobenzene, followed by catalytic hydrogenation. Light color, flexible, and creasable polyimides with high molecular weight, high glass transition, high thermal stability, improved organosolubility, and good oxygen plasma resistance were synthesized from the condensation of ( 3 ) with various aromatic dianhydrides in N,N‐dimethylacetamide, followed by thermal imidization. The number‐average molecular weights of polyimides are in the range of 7.0–8.3 × 10⁴ g/mol, and the weight‐average molecular weights are in the range of 12.5–16.5 × 10⁴ g/mol. The T_gs of these polyimides range from 230 to 304 °C by differential scanning calorimetry and from 228 to 305 °C by DMA. These polyimides are tough and flexible, with tensile strength at around 100 MPa. The degradation temperatures (T_d 5%) and char yields at 800 °C in nitrogen range from 544 to 597 °C and 59–65 wt %, respectively. Polyimides 5c and 5e , derived from OPDA and 6FDA, respectively, with the cutoff wavelength of 347 and 342 μm, respectively, show very light color. These polyimides also exhibit good oxygen plasma resistance. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2897–2912, 2007     

NMR Studies of Active‐Site Properties of Human Carbonic Anhydrase II by Using 15N‐Labeled 4‐Methylimidazole as a Local Probe and Histidine Hydrogen‐Bond Correlations

By using a combination of liquid and solid‐state NMR spectroscopy, ¹⁵N‐labeled 4‐methylimidazole (4‐MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF₃/CDF₂Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active‐site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4‐MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen‐bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen‐bond geometries is obtained by establishing a correlation between published ¹H and ¹⁵N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen‐bond geometries of His64 in the active site of HCA II and of 4‐MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.­ 2007 , 282, 9646) can be explained with a wet, polar, nonaqueous active‐site conformation in the inward conformation, similar to the properties of 4‐MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.     

NMR study on 9‐S and 9‐R oxirane derivatives of ascomycin

Structure elucidation of 9‐S and 9‐R oxirane derivatives of ascomycin, a 23‐membered immunomodulating macrolactam, was performed using NMR spectroscopy. The total ¹H and ¹³C signal assignments required the gradient‐selected versions of COSY (gs‐COSY), heteronuclear multiple quantum‐correlation spectroscopy (gs‐HSQC), heteronuclear multiple‐bond correlation spectroscopy (gs‐HMBC), and nuclear Overhauser methods. The data sets then were used to examine the dependence of ketone–hemiketal and cis–trans amide equilibria on the substitution pattern and the absolute configuration of the chiral oxirane. Copyright © 2002 John Wiley & Sons, Ltd.     

Unveiling the “Three‐Finger Pharmacophore” Required for p53–MDM2 Inhibition by Saturation‐Transfer Difference (STD) NMR Initial Growth‐Rates Approach

Inhibitors of the p53‐MDM2 protein–protein interaction are emerging as a new and validated approach to treating cancer. Herein, we describe the synthesis and inhibitory evaluation of a series of isoquinolin‐1‐one analogues, and highlight the utility of an initial growth‐rates saturation‐transfer difference (STD) NMR approach supported by protein–ligand docking to investigate p53‐MDM2 inhibition. The approach is illustrated by the study of compound 1 , providing key insights into the binding mode of this kind of MDM2 ligands and, more importantly, readily unveiling the previously proposed three‐finger pharmacophore requirement for p53‐MDM2 inhibition.     

Tautomerization in 2,7,12,17‐Tetraphenylporphycene and 9‐Amino‐2,7,12,17‐tetraphenylporphycene: Influence of Asymmetry on the Direction of the Transition Moment

Femtosecond transient absorption anisotropy studies have been performed for two porphycenes of different symmetry. In 2,7,12,17‐tetraphenylporphycene, the chemical identity of two trans forms implies a change in the S₀–S₁ transition‐moment direction upon tautomerization. Exploiting this phenomenon, the rates of double hydrogen transfer in both the S₀ and S₁ states (1.4×10¹² s^?1 and 2.7×10¹¹ s^?1, respectively) have been determined by performing time‐resolved anisotropy studies. In the asymmetric 9‐amino‐2,7,12,17‐tetraphenylporphycene, tautomerization occurs with a similar rate in the ground state. In the S₁ state, the reaction is hindered in its vibrationally relaxed form, but the excitation spectra suggest that it may occur for an unrelaxed molecule. Unlike all porphycenes that have been studied so far, 9‐amino‐2,7,12,17‐tetraphenylporphycene does not reveal significant changes in anisotropy owing to intramolecular double hydrogen transfer; rather, the transition‐moment directions are similar in the two tautomeric forms. Analysis of the molecular orbitals allows for an explanation of the “locking” of the transition moments: it is due to a large splitting of the two HOMO orbitals, which retain the order of their energies in the two tautomers.     

Synthesis and 1H and 13C NMR structural analysis of cis‐ and trans‐2‐imino‐1,3‐ and ‐3,1‐perhydrobenzoxazines and their 3‐ and 1‐N‐methyl derivatives

cis‐ and trans‐2‐imino‐1,3‐ and ‐3,1‐perhydrobenzoxazines and the N‐methyl derivatives of the latter were synthesized from the corresponding cyclic 1,3‐amino alcohol with cyanogen bromide. The configurations of the studied compounds were confirmed by ¹H and ¹³C NMR spectra. All trans‐fused compounds exist in biased chair–chair conformations as expected, whereas the cis‐fused 1,3‐benzoxazines attain exclusively the O‐in conformations. The cis‐fused 3,1‐benzoxazines, especially the 1‐methyl‐substituted derivatives, tend to favor the N‐out form, obviously owing to the favorable axial orientation of this N‐methyl. Copyright © 2003 John Wiley & Sons, Ltd.     

Conformational Selection in Glycomimetics: Human Galectin‐1 Only Recognizes syn‐Ψ‐Type Conformations of β‐1,3‐Linked Lactose and Its C‐Glycosyl Derivative

The human lectin galectin‐1 (hGal‐1) translates sugar signals, that is, β‐galactosides, into effects on the level of cells, for example, growth regulation, and has become a model for studying binding of biopharmaceutically relevant derivatives. Bound‐state conformations of Galβ‐C‐(1→3)‐Glcβ‐OMe ( 1 ) and its βGal‐(1→3)‐βGlc‐OMe disaccharide parent compound were studied by using NMR spectroscopy (transferred (TR)‐NOESY data), assisted by docking experiments and molecular dynamics (MD) simulations. The molecular recognition process involves a conformational selection event. Although free C‐glycoside access four distinct conformers in solution, hGal‐1 recognizes shape of a local minimum of compound 1 , the syn‐Φ/syn‐Ψ conformer, not the structure at global minimum. MD simulations were run to explain, in structural terms, the observed geometry of the complex.     

Synthesis and NMR studies of novel chromone‐2‐carboxamide derivatives

Chromones are heterocyclic compounds of natural or synthetic origin that possess relevant pharmacological activities. Versatile functionalization of the chromone nucleus allows attaining of a chemical diversity suitable to perform structure–activity relationships in drug discovery and development programs. Accordingly, the synthesis and identification of novel chromone carboxamide derivatives with electron‐donating and electron‐withdrawing substituents in different positions of the exocyclic ring are reported in this work. Their complete structural characterization was performed using one‐dimensional and two‐dimensional resonance techniques. The data acquired are useful for a prompt analysis of related compounds that encompass our integrated medicinal chemistry sketch. Copyright © 2013 John Wiley & Sons, Ltd.     

Conformational dynamics of bis(BF2)‐2,2′‐bidipyrrins revealed by through‐space 13C?19F and 19F?19F couplings

The conformation of [bis‐(N,N′‐difluoroboryl)]‐3,3′‐diethyl‐4,4′,8,8′,9,9′,10,10′‐octamethyl‐2,2′‐bidipyrrin (1) in solution was studied by analyzing the ¹³C? ¹⁹F and ¹⁹F? ¹⁹F through‐space spin–spin couplings. The ¹H and ¹³C NMR spectra were assigned on the basis of nuclear Overhauser effect spectroscopy (NOESY), heteronuclear single‐quantum correlation (HSQC), and heteronuclear multiple‐bond correlation (HMBC) experiments. The ¹⁹F spectrum of 1 was compared with that of 2‐ethyl‐1,3,5,6,7‐pentamethyl‐4,4‐difluoro‐4‐bor‐3a,4a‐diaza‐s‐indacen (2). The ¹⁹F? ¹⁹F through‐space spin? spin coupling in 1 was thus assigned and the coupling constant was obtained by simulating the coupling patterns. The obtained conformation of 1 was compared with those of the known complexes [bis‐(N,N′‐difluoroboryl)]‐3,3′,8,8′,9,9′‐hexaethyl‐4,4′,10,10′‐tetramethyl‐6,6′‐(4‐methylphenyl)‐2,2′‐bidipyrrin (3)and [bis‐(N,N′‐difluoroboryl)]‐9,9′‐diethyl‐4,4′,8,8′,10,10′‐hexamethyl‐3,3′‐bis(methoxycarbonylethyl)‐2,2′‐bidipyrrin (4). The conformational dynamics of 1, 3, and 4 was surveyed by observing the temperature dependence of the through‐space coupling constants between 253 and 333 K. The ¹³C? ¹⁹F and ¹⁹F? ¹⁹F through‐space spin–spin couplings thus confirm similar conformations of different BisBODIPYs in solution in contrast to earlier findings in the solid state. Copyright © 2009 John Wiley & Sons, Ltd.     

Formation of Periodic γ‐Turns in α/β‐Hybrid Peptides: DFT and NMR Experimental Evidence

Hybrid peptidic oligomers comprising natural and unnatural amino acid residues that can exhibit biomolecular folding and hydrogen‐bonding mimicry have attracted considerable interest in recent years. While a variety of hybrid peptidic helices have been reported in the literature, other secondary structural patterns such as γ‐turns and ribbons have not been well explored so far. The present work reports the design of novel periodic γ‐turns in the oligomers of 1:1 natural‐α/unnatural trans‐β‐norborenene (TNAA) amino acid residues. Through DFT, NMR, and MD studies, it is convincingly shown that, in the mixed conformational pool, the heterogeneous backbone of the hybrid peptides preferentially adopt periodic 8‐membered (pseudo γ‐turn)/7‐membered (inverse γ‐turn) hydrogen bonds in both polar and non‐polar solvent media. It is observed that the stereochemistry and local conformational preference of the β‐amino acid building blocks have a profound influence on accessing the specific secondary fold. These findings may be of significant relevance for the development of molecular scaffolds that facilitate desired positioning of functional side‐chains.     

Molecular Reorientational Dynamics of the Neat Ionic Liquid 1‐Butyl‐3‐methylimidazolium Hexafluorophosphate by Measurement of 13C Nuclear Magnetic Relaxation Data

The reorientational dynamics of the ionic liquid 1butyl‐3‐methylimidazolium hexafluorophosphate ([BMIM]PF₆) were studied over a wide range of temperatures by measurement of ¹³C spin–lattice relaxation rates and NOE factors. The reorientational dynamics were evaluated by performing fits to the experimental relaxation data. Thus, the overall reorientational motion was described by a Cole–Davidson spectral density with a Vogel–Fulcher–Tammann temperature dependence of the correlation times. The reorientational motion of the butyl chain was modelled by a combination of the latter model for the overall motion with a Bloembergen–Purcell–Pound spectral density and an Arrhenius temperature dependence for the internal motion. Except for C2 in the aromatic ring, an additional reduction of the spectral density by the Lipari–Szabo model had to be employed. This reduction is a consequence of fast molecular motions before the rotational diffusion process becomes effective. The C2 atom did not exhibit this reduction, because the librational motion of the corresponding C2? H vector is severely hindered due to hydrogen bonding with the hexafluorophosphate anion. The observed dynamic features of the [BMIM]⁺ cation confirm quantum‐chemical structures obtained in a former study.     

Structure Determination of a Flexible Cyclic Peptide Based on NMR and MD Simulation 3J‐Coupling

Molecular dynamics (MD) simulations, in which experimental values such as nuclear Overhauser effects (NOEs), dipolar couplings, ³J‐coupling constants or crystallographic structure factors are used to bias the values of specific molecular properties towards experimental ones, are often carried out to study the structure refinement of peptides and proteins. However, ³J‐coupling constants are usually not employed because of the multiplicity of torsional angle values (φ) corresponding to each ³J‐coupling constant value. Here, we apply the method of adaptively enforced restraining using a local‐elevation (LE) biasing potential energy function in which a memory function penalizes conformations in case both the average <³J> and the current ³J‐values deviate from the experimental target value. Then, the molecule is forced to sample other parts of the conformational space, thereby being able to cross high energy barriers and to bring the simulated average <³J> close to the measured <³J> value. Herein, we show the applicability of this method in structure refinement of a cyclo‐β‐tetrapeptide by enforcing the ³J‐value restraining with LE on twelve backbone torsional angles. The resulting structural ensemble satisfies the experimental ³J‐coupling data better than the NMR model structure derived using conventional single‐structure refinement based on these data. Thus, application of local‐elevation search MD simulation in combination with biasing towards ³J‐coupling makes it possible to use ³J‐couplings quantitatively in structure determination of peptides.     

Short Syntheses of some ‘Decalin‐1,8‐diones’ and their Derivatives: Breaking the Pretended Symmetry

A cheap synthesis of the so‐called ‘decalin‐1,8‐diones’ started with the conjugate (1,4‐) addition of cyclohex‐2‐en‐1‐one derivatives to the γ‐position of the dilithium derivative (buta‐1,3‐diene‐1,1‐bis(olate)) of crotonic acid. Hydrogenation of these ‘1,4‐γ’ adducts and final cyclization afforded the enol tautomers of decalin‐1,8‐diones. Nucleophilic substitutions at these 3‐oxoenols by NH₃ or primary amines created only monoamino products (namely, 3‐oxoenamines) whose reactions with OPCl₃ yielded dihydro(1,3,2)oxazaphosphinin‐2‐one derivatives. The two regioisomers of a trimethyl‐3‐oxoenamine served as models for the constitutional assignments of the two rapidly interconverting (hence, individually NMR‐invisible), tautomeric trimethyl‐3‐oxoenols. Such methyl substitutions served to break the ‘pretended’ symmetry of ‘decalin‐1,8‐dione’. Hydrazine and 3‐oxoenols furnished oxygen‐free indazole derivatives whose N?H bonds exchanged with t_1/2=ca. 0.00035 s at ca. ?58(9) °C.