Mixed Aggregates of 1-Methoxyallenyllithium with Lithium Chloride

A combined computational and ¹³C NMR study was used to investigate the formation of mixed aggregates of 1-methoxyallenyllithium and lithium chloride in tetrahydrofuran (THF) solution. The observed and calculated chemical shifts, as well as the calculated free energies of mixed aggregate formation (MP2/6-31+G(d)), are consistent with the formation of a mixed dimer as the major species in solution. Free energies of mixed dimer, trimer, and tetramer formation were calculated by using the B3LYP and MP2 methods and the 6-31+G(d) basis set. The two methods generated different predictions of which mixed aggregates will be formed, with B3LYP/6-31+G(d) favoring mixed trimers and tetramers in THF solution, and MP2/6-31+G(d) favoring mixed dimers. Formation of the sterically unhindered mixed dimers is also consistent with the enhanced reactivity of these compounds in the presence of lithium chloride. The spectra are also consistent with some residual 1-methoxyallenyllithium tetramer, as well as small amounts of higher mixed aggregates. Although neither computational method is perfect, for this particular system, the calculated free energies derived using the MP2 method are in better agreement with experimental data than those derived using the B3LYP method.     

双一流背景下有机化学精准教学的探究实践*

有机化学课程是本校化学师范和高分子材料与工程2个国家级一流本科专业以及应用化学、制药工程等专业基础必修课程。由于化学师范和非师范专业的培养目标不同,有机化学的精准教学方面也有所差异。主要从理论教学、实验教学和多媒体教学等3个方面对化学师范专业和非师范专业有机化学差异化精准教学进行了探究实践,化学师范专业有机化学的精准教学侧重于培养学生的教学能力,非师范专业有机化学的精准教学侧重于培养学生的应用能力。     

计算化学在正丁醚制备实验教学中的应用*

正丁醚的制备是重要的大学有机化学实验,为提高学生对该实验所涉及的反应机理和关键操作要点的深入了解,采用Gaussian计算软件对正丁醇在酸催化下和无催化剂下的反应体系进行了研究,重点考察了酸催化下反应的主、副反应方向的反应机理。结果表明无催化剂下,正丁醇在常压液相下几乎不能发生反应;在酸催化下,正丁醇发生取代反应生成醚的反应路径是优势反应通道;酸催化下正丁醇的取代和消除反应速率常数均随温度增加而迅速增大,但消除反应的反应速率随温度增加更快,温度超过420 K消除反应将变得很明显,综合考虑,制备正丁醚的反应温度应控制在130~140 ℃之间较为合适。利用计算化学以图、表和动图等形式直观、动态、量化地解释了正丁醇成醚和成烯反应的竞争,该结果有助于更好地控制该反应体系,可用作实验教材的补充内容。     

Exploring the Influence of Intermolecular Interactions in Prebiotic Chemistry Using Laser Spectroscopy and Calculations

One of the most fascinating questions in chemistry is why nature chose CGAT as the alphabet of life. Very likely, such selection was the result of multiple factors and a long period of refinement. Here, we explore how the intermolecular interactions influenced such process, by characterizing the formation of dimers between adenine, theobromine and 4-aminopyrimidine. Using a combination of mass-resolved excitation spectroscopy and DFT calculations, we determined the structure of adenine-theobromine and 4-aminopyrimidine-theobromine dimers. The binding energy of these dimers is very close to the canonical adenine-thymine nucleobases. Likewise, the dimers are able to adopt Watson-Crick conformations. These findings seem to indicate that there were many options available to build the first versions of the informational polymers, which also had to compete with other molecules, such as 4-aminopyrimidine, which does not have a valid attaching point for a saccharide. For some reason, nature did not select the most strongly-bonded partners or if it did, such proto-bases were later replaced by the nowadays canonical CGAT.     

Acyl Group Migration in Pyranosides as Studied by Experimental and Computational Methods

Acyl group migration affects the synthesis, isolation, manipulation and purification of all acylated organic compounds containing free hydroxyl groups, in particular carbohydrates. While several isolated studies on the migration phenomenon in different buffers have been reported, comprehensive insights into the overall migration process in different monosaccharides under similar conditions have been lacking. Here, we have studied the acyl migration in different monosaccharides using five different acyl groups by a combination of experimental, kinetic and theoretical tools. The results show that the anomeric configuration in the monosaccharide has a major influence on the migration rate, together with the relative configurations of the other hydroxyl groups and the nature of the migrating acyl group. Full mechanistic model, based on computations, demonstrates that the acyl migration proceeds through an anionic stepwise mechanism with linear dependence on the [OH⁻] and the pK_a of the hydroxyl group toward which the acyl group is migrating.     

Combined in Silico and in Vitro Approaches To Uncover the Oxidation and Schiff Base Reaction of Baicalein as an Inhibitor of Amyloid Protein Aggregation

The oxidized form of baicalein ( BA ) leads to covalent binding with human amyloid proteins. Such adducts hamper the aggregation and deposition of fibrils. A novel reaction of BA with pentylamine ( PA ) as a model for the lysine side chain is described. This is the first study addressing the atomistic details of a Schiff base reaction with the trihydroxylated moiety of BA . Nuclear magnetic resonance and mass spectrometry approaches clearly indicate the formation of dehydrobaicalein in solution as well as its condensation with PA under aerobic conditions, yielding regioselectively C6-substituted products. The combined results suggest initial ion pair formation between BA and PA , followed by a redox chain reaction: the initiation by oxygen/air; an o-quinone-based chain involving oxidation and reduction steps; and extra off-chain formation of a doubly oxidized product. These mechanistic details support the anti-amyloid activity of BA and endorse its trihydroxyphenyl moiety as a pharmacophore for drug-design studies.     

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.     

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.