Exploring the Conformational Space of Bridge‐Substituted Dithienylcyclopentenes

Stimuli responsive compounds and materials are of high interest in synthetic chemistry and materials science, with light being the most intriguing stimulus due to the possibility to remote control the physicochemical properties of a molecule or a material. There is a constant quest to design photoswitches with improved switching efficiency and especially diarylethene‐type switches promise photo cyclization quantum yields up to unity. However, only limited attention has been paid towards the influence of the solution conformation on the switching efficiency. Here, we describe a detailed NMR spectroscopic investigation on the conformational distribution of bridge‐substituted dithienylcyclopentenes in solution. We could discriminate between several photoactive and photoinactive as well as two diastereomorphous conformations and show that the trends observed in the switching efficiency match the conformer populations obtained from state of the art NMR parameters in solution.     

Unusual inversion phenomenon of β-cyclodextrin dimers in water

A conformational analysis of three triazole-containing bridged bis-β- cyclodextrins (CD) has been carried out to evaluate their recognition ability. NMR spectroscopy and ITC measurements clearly demonstrate that one of the CD glucopyranose units undergoes a 360° rotation in water so that the spacer linking the two CDs is deeply included into one of the CD cavities. The amplitude of this inversion phenomenon depends on the nature of the spacer and results in a limited accessibility to the CD cavities in line with previous catalytic results.     

Using Lateral Substitution to Control Conformational Preference and Phase Behaviour of Benzanilide-based Liquid Crystal Dimers

The inclusion of secondary and tertiary benzanilide-based mesogenic groups into liquid crystal dimers is reported as a means to develop new materials. Furthermore, substitution at the nitrogen atom is shown to introduce an additional synthetic ‘handle’ to modify the molecular structure of the tertiary materials. The design of these materials has proved challenging due to the strong preferences of 3° benzanilides for the E amide conformation. In this work, lateral substitution is used to modify the conformational preferences of the amide linkage and promote liquid crystallinity for a series of N-methyl benzanilide dimers. As the proportion of the E conformer decreases, the nematic-isotropic transition temperatures increase, and enantiotropic nematic behaviour is observed. We also report the synthesis and characterisation of the analogous 2° benzanilide-based materials, which show nematic and twist-bend nematic behaviour. This approach highlights the effects that seemingly small structural modifications, such as the inclusion and position of a methyl group, can have on molecular shape and hence, liquid crystalline behaviour.     

A Computational Study of Vicinal Fluorination in 2,3‐Difluorobutane: Implications for Conformational Control in Alkane Chains

A comprehensive conformational analysis of both 2,3‐difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2‐difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3‐difluorobutane there is a complex interplay of several effects, which are of similar magnitude but often of opposite sign. As a result, unexpected deviations in dihedral angles, relative conformational energies and populations are observed which cannot be rationalised only by chemical intuition. Furthermore, it was found that it is important to consider the free energies of the various conformers, as these lead to qualitatively different results both in vacuum and in solvent, when compared to calculations based only on the electronic energies. In contrast to expectations, it was found that vicinal syn‐difluoride introduction in the butane and by extension, longer hydrocarbon chains, is not expected to lead to an effective stabilisation of the linear conformation. Our findings have implications for the use of the vicinal difluoride motif for conformational control.     

Enhancing the Sensitivity of CPMG Relaxation Dispersion to Conformational Exchange Processes by Multiple‐Quantum Spectroscopy

A triple‐quantum ¹H Carr–Purcell–Meiboom–Gill NMR relaxation dispersion experiment is presented that uses methyl group probes as reporters of conformational exchange in highly deuterated, methyl‐protonated proteins. Significantly larger dispersion profiles, by as much as a factor of nine, can be obtained relative to single‐quantum approaches, thus offering very significant advantages in applications involving interconverting conformers with only small changes in structure or in studies of rare states that are at very low populations. Applications to a number of protein systems are presented where the utility of the method, including its improved sensitivity to chemical exchange processes, is established.     

Bis antennae amphiphilic cyclodextrins: the first examples

Methylated 6A,6D-diamino 6A,6D-dideoxy β-cyclodextrin 4 was coupled with three cholesterol substituted glutaric or succinic acids 5-7 to give amphiphilic cyclodextrins 1-3 with good yields. The succinic acid derivative 1, a typical member of this new family, has shown good compatibility with phosphatidyl choline monolayer and bilayer as confirmed by deuterium magnetic nuclear resonance (²H NMR).     

Conformational Dynamics of apo‐GlnBP Revealed by Experimental and Computational Analysis

The glutamine binding protein (GlnBP) binds l ‐glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo‐ and holo‐GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single‐molecule FRET techniques to decipher the conformational dynamics of apo‐GlnBP. The NMR residual dipolar couplings of apo‐GlnBP were in good agreement with a MD‐derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four‐state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP.     

Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

The internal motions of integral membrane proteins have largely eluded comprehensive experimental characterization. Here the fast side‐chain dynamics of the α‐helical sensory rhodopsin II and the β‐barrel outer membrane protein W have been investigated in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Despite their differing topologies, both proteins have a similar distribution of methyl‐bearing side‐chain motion that is largely independent of membrane mimetic. The methyl‐bearing side chains of both proteins are, on average, more dynamic in the ps–ns timescale than any soluble protein characterized to date. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect. Furthermore, the high conformational entropy could greatly influence the thermodynamics underlying membrane‐protein functions, including ligand binding, allostery, and signaling.     

Conformational Plasticity in Glycomimetics: Fluorocarbamethyl‐L‐idopyranosides Mimic the Intrinsic Dynamic Behaviour of Natural Idose Rings

Sugar function, structure and dynamics are intricately correlated. Ring flexibility is intrinsically related to biological activity; actually plasticity in L ‐iduronic rings modulates their interactions with biological receptors. However, the access to the experimental values of the energy barriers and free‐energy difference for conformer interconversion in water solution has been elusive. Here, a new generation of fluorine‐containing glycomimetics is presented. We have applied a combination of organic synthesis, NMR spectroscopy and computational methods to investigate the conformational behaviour of idose‐ and glucose‐like rings. We have used low‐temperature NMR spectroscopic experiments to slow down the conformational exchange of the idose‐like rings. Under these conditions, the exchange rate becomes slow in the ¹⁹F NMR spectroscopic chemical shift timescale and allows shedding light on the thermodynamic and kinetic features of the equilibrium. Despite the minimal structural differences between these compounds, a remarkable difference in their dynamic behaviour indeed occurs. The importance of introducing fluorine atoms in these sugars mimics is also highlighted. Only the use of ¹⁹F NMR spectroscopic experiments has permitted the unveiling of key features of the conformational equilibrium that would have otherwise remained unobserved.     

Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction

States along the phosphoryl transfer reaction catalyzed by the nucleoside monophosphate kinase UmpK were captured and changes in the conformational heterogeneity of conserved active site arginine side‐chains were quantified by NMR spin‐relaxation methods. In addition to apo and ligand‐bound UmpK, a transition state analog (TSA) complex was utilized to evaluate the extent to which active site conformational entropy contributes to the transition state free energy. The catalytically essential arginine side‐chain guanidino groups were found to be remarkably rigid in the TSA complex, indicating that the enzyme has evolved to restrict the conformational freedom along its reaction path over the energy landscape, which in turn allows the phosphoryl transfer to occur selectively by avoiding side reactions.     

Conformational mobility of the six-membered ring in 5-oxo-1,3-cyclohexadiene and its derivatives

Molecular mechanics and MNDO calculations showed that the six-membered ring in the molecule of 5-oxo-1,3-cyclohexadiene possesses high conformational mobility. The transition from a planar equilibrium conformation to a distorted sofa conformation in which the C(sp²)-C(=O)-C(sp³)-C(sp²) torsion angle is equal to ±30° increases the energy of the molecule by less than 1 kcal mol^–1. The influence of steric (R = Me, Et, Prⁱ, Bu^t) and electronic (R = NH₂, NO₂) effects of substituents R on the equilibrium conformation and mobility of the carbocycle has been analyzed. Both types of substituents at unsaturated C atoms do not change the equlibrium conformation or flexibility of the six-membered ring. Substituents at saturated C atoms cause the transition of the carbocycle to the distorted sofa conformation and significantly restrict its mobility. The electronic structures of 5-oxo-1,3-cyclohexadiene and its amino and nitro derivatives have been analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 849–854, May, 1995.     

Deciphering the Conformational Choreography of Zinc Coordination Complexes with Standard and Novel Proton NMR Techniques Combined with DFT Methods

The presence of water has been shown to deeply impact the stability and geometry of Zn complexes in solution. Evidence for tetra‐ and penta‐coordinated species in a pyridylmethylamine–Zn^II model complex is presented. Novel ¹H NMR tools such as T₁‐filtered selective exchange spectroscopy and pure shifted gradient‐encoded selective refocusing as well as classical 2D (¹H–¹H) exchange spectroscopy, diffusion‐ordered spectroscopy and T₁(¹H) measurements, in combination with density functional theory methods allow the full conformational dynamics of a pyridylmethylamine–Zn^II complex to be revealed. Four conformers and two families of complexes depending on the hydration states are elucidated.     

环丙沙星与环糊精超分子体系的研究

利用荧光光谱法研究了环丙沙星与母体β-环糊精(β-CD)及其2种修饰衍生物羟丙基-β-环糊精(Hp-β-CD)、甲基-β-环糊精(Me-β-CD)形成的超分子体系,同时测定了3种超分子体系的猝灭常数和热力学参数.结果表明:环丙沙星与3种环糊精之间常温下均形成稳定的包合物;环丙沙星与3种环糊精包结过程中△G＜0和△H＜0,这说明环丙沙星与3种环糊精的包结能够自发进行而形成超分子体系,且反应为放热过程.通过对3种环糊精与环丙沙星的热力学数包结能力进行了比较,初步探讨了作用机理和影响包结能力大小的可能因素.     

Targeting the Rich Conformational Landscape of N-Allylmethylamine Using Rotational Spectroscopy and Quantum Mechanical Calculations

The highly variable conformational landscape of N-allylmethylamine (AMA) was investigated using Fourier transform microwave spectroscopy aided by high-level theoretical calculations to understand the energy relationship governing the interconversion between nine stable conformers. Spectroscopically, transitions belonging to four low energy conformers were identified and their hyperfine patterns owing to the ¹⁴N quadrupolar nucleus were unambiguously resolved. The rotational spectrum of the global minimum geometry, conformer I, shows an additional splitting associated with a tunneling motion through an energy barrier interconnecting its enantiomeric forms. A two-step tunneling trajectory is proposed by finding transition state structures corresponding to the allyl torsion and NH inversion. Natural bond orbital and non-covalent interaction analyses reveal that an interplay between steric and hyperconjugative effects rules the conformational preferences of AMA.     

Between Two Chairs: Combination of Theory and Experiment for the Determination of the Conformational Dynamics of Xylosides

The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d -xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.