Theoretical Perspectives in Organocatalysis

It is clear that the field of organocatalysis is continuously expanding during the last decades. With increasing computational capacity and new techniques, computational methods have provided a more economic approach to explore different chemical systems. This review offers a broad yet concise overview of current state-of-the-art studies that have employed novel strategies for catalyst design. The evolution of the all different theoretical approaches most commonly used within organocatalysis is discussed, from the traditional approach, manual-driven, to the most recent one, machine-driven.     

The Mechanism of Biochemical NO-Sensing: Insights from Computational Chemistry

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO-receptor in humans is soluble guanylyl cyclase (sGC) – a histidine-ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO-signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high-level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H-NOX protein from Shewanella oneidensis (So H-NOX) homologous to the NO-binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six-coordinate intermediate heme-NO complex, followed by relatively facile His decoordination yielding a five-coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.     

Modeling of the Simultaneous Hydrogen Evolution and Cobalt Electrodeposition

A mathematical model of simultaneous cobalt deposition and hydrogen evolution was developed and applied to the electroreduction process of 5 mM Co²⁺ ions investigated by cyclic voltammetry (CV) technique at different hydrogen ion concentrations (pH=2, 3, 4). The kinetic parameters of such a complex process were determined, and the validity of the model and its sensitivity to changes in individual parameters were verified. The relative value of the approximate standard deviation (ASD_%) was used to determine the degree of fit of the model to the experimental data. The catalytic effect of cobalt on the hydrogen evolution process was comprehensively confirmed.     

Delocalized \begin{document}$\pi_3^6$\end{document} Bond in OX\begin{document}$_2$\end{document} (X=Halogen) Molecules

OX\begin{document}$_2$\end{document} (X=halogen) molecules was studied theoretically. Calculation results show that delocalized \begin{document}$\pi_3^6$\end{document} bonds exist in their electronic structures and O atoms adopt the sp\begin{document}$^2$\end{document} type of hybridization, which violates the prediction of the valence shell electron pair repulsion theory of sp\begin{document}$^3$\end{document} type. Delocalization stabilization energy is proposed to measure the contribution of delocalized \begin{document}$\pi_3^6$\end{document} bond to energy decrease and proves to bring extra-stability to the molecule. These phenomena can be summarized as a kind of coordinating effect.     

Methoxy-Substituted Tyramine Derivatives Synthesis,Computational Studies and Tyrosinase Inhibitory Kinetics

Targeting tyrosinase for melanogenesis disorders is an established strategy. Hydroxyl-substituted benzoic and cinnamic acid scaffolds were incorporated into new chemotypes that displayed in vitro inhibitory effects against mushroom and human tyrosinase for the purpose of identifying anti-melanogenic ingredients. The most active compound 2-((4-methoxyphenethyl)amino)-2-oxoethyl (E)-3-(2,4-dihydroxyphenyl) acrylate (Ph9), inhibited mushroom tyrosinase with an IC₅₀ of 0.059 nM, while 2-((4-methoxyphenethyl)amino)-2-oxoethyl cinnamate (Ph6) had an IC₅₀ of 2.1 nM compared to the positive control, kojic acid IC₅₀ 16700 nM. Results of human tyrosinase inhibitory activity in A375 human melanoma cells showed that compound (Ph9) and Ph6 exhibited 94.6% and 92.2% inhibitory activity respectively while the positive control kojic acid showed 72.9% inhibition. Enzyme kinetics reflected a mixed type of inhibition for inhibitor Ph9 (K_i 0.093 nM) and non-competitive inhibition for Ph6 (K_i 2.3 nM) revealed from Lineweaver–Burk plots. In silico docking studies with mushroom tyrosinase (PDB ID:2Y9X) predicted possible binding modes in the catalytic site for these active compounds. Ph9 displayed no PAINS (pan-assay interference compounds) alerts. Our results showed that compound Ph9 is a potential candidate for further development of tyrosinase inhibitors.     

Novel nonperipheral octa-3-hydroxypropylthio substituted metallo-phthalocyanines: synthesis,characterization, and investigation of their electrochemical,photochemical and computational properties

The current study describes the synthesis, electrochemical, computational, and photochemical properties of octa (3-hydroxypropylthio) substituted cobalt (II) ( 4 ), copper (II) ( 5 ), nickel (II) ( 6 ) and zinc(II) ( 7 ) phthalocyanine derivatives. These novel compounds were characterized by elemental analysis,¹H,¹³C NMR, FT-IR, UV-Vis, and MS. The redox behaviors of these metallo-phthalocyanines were investigated by the cyclic voltammetric method. The optimized molecular structure and gauge-including atomic orbital (GIAO)¹H and¹³C NMR chemical shift values of these phthalocyanines in the ground state had been calculated by using B3LYP/6–31G(d,p) basis set. The outcomes of the optimized molecular structure were given and compared with the experimental NMR values. The photochemical properties including photodegradation and singlet oxygen generation of zinc(II) phthalocyanine were studied in DMSO solution for the determination of its photosensitizer behaviors.     

Modulating Protein–Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples

Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein–protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.     

用于气象观测的阵列式温度传感器流体动力学分析与实验研究

传统百叶箱和防辐射罩内部的温度传感器受到太阳辐射会导致其温度高于大气真实温度, 升温量可达0.8 K甚至更高. 为提高大气温度观测精度, 本文设计了一种阵列式温度传感器. 利用计算流体动力学方法分析计算该传感器在不同环境条件下的辐射升温量, 采用遗传算法对计算结果进行拟合, 获得辐射升温量修正方程. 为验证阵列式温度传感器的实际性能, 研制了强制通风温度测量平台. 将阵列式温度传感器、配有传统防辐射罩的温度传感器和强制通风温度测量平台置于相同环境下, 进行大气温度观测比对实验. 配有传统防辐射罩的温度传感器辐射升温量平均值为0.409 K; 与前者相比, 阵列式温度传感器的辐射升温量仅为0.027 K. 这种阵列式温度传感器可将辐射升温引起的误差降低约93%. 辐射升温量实验测量值与修正方程修正值之间的平均偏移量为0.0174 K, 均方根误差为0.0215 K, 该结果验证了计算流体动力学方法与遗传算法的准确性. 如果配合计算流体动力学方法与遗传算法, 温度测量精度有进一步提高的潜力.     

Sensory Perception of Non-Deuterated and Deuterated Organic Compounds

The chemical background of olfactory perception has been subject of intensive research, but no available model can fully explain the sense of smell. There are also inconsistent results on the role of the isotopology of molecules. In experiments with human subjects it was found that the isotope effect is weak with acetone and D₆-acetone. In contrast, clear differences were observed in the perception of octanoic acid and D₁₅-octanoic acid. Furthermore, a trained sniffer dog was initially able to distinguish between these isotopologues of octanoic acid. In chromatographic measurements, the respective deuterated molecule showed weaker interaction with a non-polar liquid phase. Quantum chemical calculations give evidence that deuterated octanoic acid binds more strongly to a model receptor than non-deuterated. In contrast, the binding of the non-deuterated molecule is stronger with acetone. The isotope effect is calculated in the framework of statistical mechanics. It results from a complicated interplay between various thermostatistical contributions to the non-covalent free binding energies and it turns out to be very molecule-specific. The vibrational terms including non-classical zero-point energies play about the same role as rotational/translational contributions and are larger than bond length effects for the differential isotope perception of odor for which general rules cannot be derived.