Controlling the Conformational Changes in Donor–Acceptor [4]‐Dendralenes through Intramolecular Charge‐Transfer Processes

The synthesis of two [4]‐dendralene compounds incorporating thiophene‐(p‐nitrophenyl) donor–acceptor units is presented. The dendralenes adopt two different conformers in solution and solid state and the transformation between the structures can be controlled by light and heat. The electron‐donating components of the dendralenes are represented by bromothienyl (in 13 ) and ethylenedioxythiophene(EDOT)‐thienyl (in 15 ) end‐groups. The most facile transformation involves the isomerisation of donor–acceptor conjugated systems ( a conformers) into structures in which only the thiophenes are conjugated ( b conformers), and this process is driven by ambient light. The structures of the two conformers of compound 13 are confirmed by single‐crystal X‐ray diffraction studies and the structural changes in both compounds have been monitored by ¹H NMR spectroscopy and absorption studies. The transformations were found to be first‐order processes with rate constants of k=0.0027 s^?1 and k=0.00022 s^?1 for 13 and 15 , respectively. Density functional theory calculations at the B3LYP/6‐31G* level give credence to the proposed mechanism for the a → b conversion, which involves photoinduced intramolecular charge transfer (ICT) as the key step. The EDOT derivative ( 15 ) can be polymerised by electrochemical oxidation and a combination of cyclic voltammetry and UV/Vis spectroelectrochemical experiments indicate that the a conformer can be trapped and stabilised in the solid state.     

苯基在联苯亲电取代反应中的定位作用

运用G03程序,在HF/6-31G基组水平,分析了苯基（RPh）在联苯类化合物（RPh-Ph,R：NH2,CH3,OH,Br,H,CHO,CN,COOH,NO2）亲电取代反应中的定位作用。联苯和取代联苯的构象分析表明,联苯和间、对位取代联苯的碳-碳单键旋转的能垒很小,约12 kJ/mol,邻取代联苯的碳-碳单键旋转能垒△E（R）较大,且△E（COOH） > △E（NO2） > △E（CHO） > △E（CH3） > △E（NH2） > △E（OH） > △E（Br） > △E（CN）,因此,邻位取代基的空间效应较大,碳-碳单键旋转受阻。联苯和取代联苯的原子电荷分布随它们的构象改变而变化,在同一联苯或取代联苯化合物的最低能稳定结构中,无论取代基R为第一类还是第二类定位基,未取代苯环的碳原子总电荷密度比取代苯环碳原子的总电荷密度大,亲电取代反应将选择在未取代的苯环上发生;未取代苯环的邻位碳原子电荷密度较低、空间效应较大,而对位碳原子的电荷密度较大,亲电取代反应难以在该环的2,6-位（邻位）发生,将选择在该苯环的对位发生。因此,取代苯基（RPh-）在联苯的亲电取代反应中主要表现为对位定位基。     

Toward ab initio potential energy surface for paclitaxel: a baccatin III conformational study

The ab initio conformational energy profile of baccatin III, the diterpene part of paclitaxel, a natural, taxoid anticancer agent, has been investigated using medium‐size basis sets including an electron correlation method (MP2/DFT). By exploiting the internal coordinates using random search methods, 39 conformers of baccatin III were found. The most stable conformer, competing with its 13‐C rotamers, was shown to have three intramolecular hydrogen bonds of 1, 7 and 13 hydroxyls to the carbonyl oxygen atoms of 2‐benzoate and 10‐ and 4‐acetate ester groups, respectively. The results of the polarizable continuum model (PCM) used to account for the dielectric effect of the environment show that in water, the delicate balances between intramolecular hydrogen bridges and general conformational preferences are conserved, at least in the absence of explicit solvent molecules. Copyright © 2016 John Wiley & Sons, Ltd.     

Trans‐2‐Aminocyclohexanol derivatives as pH‐triggered conformational switches

A series of trans‐2‐aminocyclohexanol derivatives have been explored as powerful conformational pH triggers. On protonation of the amino group, a conformer with equatorial position of ammonio and hydroxy groups becomes predominant because of an intramolecular hydrogen bond and electrostatic interactions. The energy of these interactions was estimated to be above 10 kJ/mol and in some models exceeded 20 kJ/mol (strong enough to twist a ring in tert‐butyl derivatives). As a result of this conformational flip, all other substituents are forced to change their orientation. If the substituents are designed to perform certain geometry‐dependent functions, for example, as cation chelators or as lipid tails, such acid‐induced transition may be used to control the corresponding molecular properties. The pH sensitivity of conformational equilibria was explored by ¹H nuclear magnetic resonance spectroscopy (NMR), and the titration curves were used for estimation of the pK_a values of protonated compounds that varied from 2.6 to 8.5 (in d₄‐methanol) depending on the structure of amino group. Thus, trans‐2‐aminocyclohexanols can be also used as conformational pH indicators in organic solvents.     

The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex

Roughly three quarters of eucaryotic DNA are tightly wrapped onto protein cylinders organized in so-called nucleosomes. Despite this fact, the wrapped DNA cannot be inert since DNA is at the heart of many crucial life processes. We focus here on physical mechanisms that might allow nucleosomes to perform a great deal of such processes, specifically 1) on unwrapping fluctuations that give DNA-binding proteins access to the wrapped DNA portions without disrupting the nucleosome as a whole, 2) on corkscrew sliding along DNA and some implications and on 3) tail-bridging-induced attraction between nucleosomes as a means of controlling higher-order folding.     

Probing DNA and RNA single molecules with a double optical tweezer

A double-tweezer setup is used to induce mechanical stress in systems of molecular biology. A double strand of DNA is first stretched and the data is compared to precedent experiments to check the experimental setup. Then a short foldable fragment of RNA is probed; the typical unfolding/refolding hysteresis behaviour of this kind of construction is shown and followed by a study of its elasticity and a comparison to a worm-like chain model. Eventually, we describe the unfolding of a larger RNA structure, which unfolds by multiple steps. We show that this unfolding is not reversible and that it presents numerous unfolding pathways.     

Exploiting Coordination Isomerism for Controlled Self‐Assembly

We exploited the inherent geometrical isomerism of a Pt^II complex as a new tool to control supramolecular assembly processes. UV irradiation and careful selection of solvent, temperature, and concentration leads to tunable coordination isomerism, which in turn allows fully reversible switching between two distinct aggregate species (1D fibers?2D lamellae) with different photoresponsive behavior. Our findings not only broaden the scope of coordination isomerism, but also open up exciting possibilities for the development of novel stimuli‐responsive nanomaterials.     

Tailored Peptide Phenyl Esters Block ClpXP Proteolysis by an Unusual Breakdown into a Heptamer–Hexamer Assembly

The proteolytic complex ClpXP is fundamental to bacterial homeostasis and pathogenesis. Because of its conformational flexibility, the development of potent ClpXP inhibitors is challenging, and novel tools to decipher its intricate regulation are urgently needed. Herein, we present amino acid based phenyl esters as molecular probes to study the activity and oligomerization of the ClpXP complex of S. aureus. Systematic screening of (R)‐ and (S)‐amino acids led to compounds showing potent inhibition, as well as stimulation of ClpXP‐mediated proteolysis. Substoichiometric binding of probes arrested ClpXP in an unprecedented heptamer–hexamer assembly, in which the two heptameric ClpP rings are dissociated from each other. At the same time, the affinity between ClpX and ClpP increased, leading to inhibition of both enzymes. This conformational arrest is beneficial for the consolidated shutdown of ClpXP, as well as for the study of the oligomeric state during its catalytic cycle.     

Isomer Structural Transformation in Au–Cu Alloy Nanoclusters: Water Ripple‐Like Transfer of Thiol Ligands

Structure isomerism is observed in noble metal nanoclusters; however, the mechanism study of this process is rarely reported. Herein, by using the biphosphine ligands instead of phosphine ligands, the high symmetry of the Au₂Cu₆(PPh₃)₂(SAdm)₆ nanocluster is successfully broken and [Au₄Cu₄(L₁)₂(SAdm)₅]Br (where, L₁ is bis(diphenylphosphine)methane, DPPM) nanocluster is obtained with chiral arrangement. This newly obtained nanocluster contains a total of four isomers in crystal unit cell. Interestingly, these isomers undergo rapid isomorphism in solution, which is confirmed by ¹H‐¹H COSY spectrum. Density functional theory calculations demonstrate that the water ripple–like transfer of the thiol ligands results from the isomorphism of nanoclusters.     

Vibrational spectroscopic studies,conformations and ab initio calculations of 1,2‐bis(trifluorosilyl)ethane (SiF3CH2CH2SiF3)

Infrared spectra of 1,2‐bis(trifluorosilyl)ethane (SiF₃CH₂CH₂SiF₃) were obtained in the vapour and liquid phases, in argon matrices and in the solid phase. Raman spectra of the compound as a liquid were recorded at various temperatures between 293 and 270 K and spectra of an apparently crystalline solid were observed. The spectra revealed the existence of two conformers (anti and gauche) in the vapour, liquid and in the matrix. When the vapour was chock‐frozen on a cold finger at 78 K and annealed to 150 K, certain weak Raman bands vanished in the crystal. The vibrational spectra of the crystal demonstrated mutual exclusion between IR and Raman bands in accordance with C_2h symmetry. Intensity variations between 293 and 270 K of pairs of various Raman bands gave ΔH(gauche—anti) = 5.6 ± 0.5 kJ mol⁻¹ in the liquid, suggesting 85% anti and 15% gauche in equilibrium at room temperature. Annealing experiments indicate that the anti conformer also has a lower energy in the argon matrices, is the low‐energy conformer in the liquid and is also present in the crystal. The spectra of both conformers have been interpreted, and 34 anti and 17 gauche bands were tentatively identified. Ab initio and density functional theory (DFT) calculations were performed giving optimized geometries, infrared and Raman intensities and anharmonic vibrational frequencies for both conformers. The conformational energy difference derived in CBS‐QB3 and in G3 calculations was 5 kJ mol⁻¹. Copyright © 2009 John Wiley & Sons, Ltd.