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.     

The Activation and Carbonylation of the C-Cl Bond Catalyzed by Transition-Metal Complexes

Thecarbonylationoforganichalides,catalyzedbytransition-metalcomPlexes,isareactionofindustrialinterestleadingtoawiderange0fproductslilieesters,aldehydes,awhdesandacids.Formanyyears,catalyticactivationandfunctionalisationofthecarbonthalogenbondsinorganichalideshavebeenoneofthemostchallengingproblemsanddesirablegoalsforchendsts.Oforganichalides,0rgancchlorideisthemodrmaforeundiDexPdrieerefD1thepeDfu3efulboinboLalindusny.However,because0ftheinertness0ftheirC-Clbonds,organicchloridesexhibitl0wre…     

Mild and Efficient Nitration of Aromatic Compounds Mediated by Transition-Metal Complexes

Aromatic compounds were efficiently nitrated under facile reaction conditions by employing 69% nitric acid catalyzed by transition-metal complexes such as [Co(NH₃)₅Cl]Cl₂, [Cu(NH₃)₄]SO₄, Mn(acac)₃, [Ni(NH₃)₆]Cl₂, [Ni(en)₃]S₂O₃, and Hg[Co(SCN)₄]. The reaction was completed smoothly at room temperature and afforded corresponding mono-nitro derivatives in quantitative yield. This new method offers efficient and facile regioselective mononitration of aromatic compounds.

Light on the Structural Evolution of Photoresponsive Molecular Switches in Electronically Excited States

Stimuli-responsive materials are attracting extensive interest as they offer the opportunity to transform external inputs such as light into a functionality by control at the molecular level. As a result, a large number of molecular building units have been developed that enable switching between two or more states. Since the trajectory describing the transition between the various states defines the efficiency of the usually immobilized unit and the resulting functionality, it does not suffice to merely consider the initial and final states of the switching process. A key challenge is in fact to decipher at the atomic scale the actual motion that takes place after photoexcitation. Understanding and being able to manipulate this trajectory is crucial for an efficient implementation of photoactive molecular switches into functional materials, as well as to rationally develop novel tailor-made materials. In this Concept article, we highlight the potential to characterize in detail photoinitiated switching mechanisms by combining quantum chemical calculations with advanced laser spectroscopic techniques that probe the vibrational manifold of electronically excited states and its evolution.     

Electronic Transitions in Different Redox States of Trinuclear 5,6,11,12,17,18-Hexaazatrinaphthylene-Bridged Titanium Complexes: Spectroelectrochemistry and Quantum Chemistry

Multinuclear transition metal complexes bridged by ligands with extended π-electronic systems show a variety of complex electronic transitions and electron transfer reactions. While a systematic understanding of the photochemistry and electrochemistry has been attained for binuclear complexes, much less is known about trinuclear complexes such as hexaphenyl-5,6,11,12,17,18-hexaazatrinaphthylene-tristitanocene [(Cp₂Ti)₃HATN(Ph)₆]. The voltammogram of [(Cp₂Ti)₃HATN(Ph)₆] shows six oxidation and three reduction waves. Solution spectra of [(Cp₂Ti)₃HATN(Ph)₆] and of the electrochemically formed oxidation products show electronic transitions in the UV, visible and the NIR ranges. Density functional theory (DFT) and linear response time-dependent DFT show that the three formally titanium(II) centers transfer an electron to the HATN ligand in the ground state. The optically excited transitions occur exclusively between ligand-centered orbitals. The charged titanium centers only provide an electrostatic frame to the extended π-electronic system. Complete active self-consistent field (CASSCF) calculation on a structurally simplified model compound, which considers the multi-reference character imposed by the three titanium centers, can provide an interpretation of the experimentally observed temperature-dependent magnetic behavior of the different redox states of the title compound in full consistency with the interpretation of the electronic spectra.     

过渡金属配合物催化乙腈碳碳单键断裂的研究进展

有机化合物中的碳碳单键断裂反应是一类非常重要而且具有挑战性的反应,过去的几十年中,关于有机腈类化合物中碳碳单键的催化断裂反应研究受到了很多的关注。而乙腈作为常用的有机溶剂之一,其分子是有机腈类中的最小分子。本文结合最近几年国内外及本课题组关于乙腈分子的碳碳单键活化断裂的研究,综述了各类过渡金属配合物催化乙腈分子碳碳单键断裂的研究进展,分析了当前存在的问题,提出了对今后研究的展望。     

过渡金属配合物催化乙腈碳碳单键断裂的研究进展

有机化合物中的碳碳单键断裂反应是一类非常重要而且具有挑战性的反应,过去的几十年中,关于有机腈类化合物中碳碳单键的催化断裂反应研究受到了很多的关注。而乙腈作为常用的有机溶剂之一,其分子是有机腈类中的最小分子。本文结合最近几年国内外及本课题组关于乙腈分子的碳碳单键活化断裂的研究,综述了各类过渡金属配合物催化乙腈分子碳碳单键断裂的研究进展,分析了当前存在的问题,提出了对今后研究的展望。     

Modern Theoretical Approaches to Modeling the Excited-State Intramolecular Proton Transfer: An Overview

The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, a rich manifold of theoretical approaches at different levels is nowadays available to support and guide experimental investigations. In this perspective, we summarize the state-of-the-art quantum-chemical methods, as well as molecular- and quantum-dynamics tools successfully applied in ESIPT process studies, focusing on a critical comparison of their specific properties.     

Strain Release Chemistry of Photogenerated Small-Ring Intermediates

Photochemical processes, such as isomerizations and cycloadditions, have proven to be very useful in the construction of highly strained molecular frameworks. Photoinduced ring strain enables subsequent exergonic reactions which do not require the input of additional chemical energy and provides a variety of attractive synthetic options leading to complex structures. This review covers the progress achieved in the application of sequences combining excitation by ultraviolet light to form strained intermediates, which are further transformed to lower energy products in strain-release reactions. As ring strain is considerable in small ring systems, photogenerated three- and four-membered rings will be covered, mainly focusing on examples from 2000 to May 2020.     

Quantum Chemical Modeling of Pressure-Induced Spin Crossover in Octahedral Metal-Ligand Complexes

Spin state switching on external stimuli is a phenomenon with wide applicability, ranging from molecular electronics to gas activation in nanoporous frameworks. Here, we model the spin crossover as a function of the hydrostatic pressure in octahedrally coordinated transition metal centers by applying a field of effective nuclear forces that compress the molecule towards its centroid. For spin crossover in first-row transition metals coordinated by hydrogen, nitrogen, and carbon monoxide, we find the pressure required for spin transition to be a function of the ligand position in the spectrochemical sequence. While pressures on the order of 1 GPa are required to flip spins in homogeneously ligated octahedral sites, we demonstrate a fivefold decrease in spin transition pressure for the archetypal strong field ligand carbon monoxide in octahedrally coordinated Fe²⁺ in [Fe(II)(NH₃)₅CO]²⁺.     

Fluorescence Quenching of Benzaldehyde in Water by Hydrogen Atom Abstraction

We computed the mechanism of fluorescence quenching of benzaldehyde in water through relaxed potential energy surface scans. Time‐dependent density functional theory calculations along the protonation coordinate from water to benzaldehyde reveal that photoexcitation to the bright ππ* (S₃) state is immediately followed by ultrafast decay to the nπ* (S₁) state. Evolving along this state, benzaldehyde (BA) abstracts a hydrogen atom, resulting in a BAH^. and OH^. radical pair. Benzaldehyde does not act as photobase in water, but abstracts a hydrogen atom from a nearby solvent molecule. The system finally decays back to the ground state by non‐radiative decay and an electron transfers back to the OH^. radical. Proton transfer from BAH⁺ to OH^? restores the initial situation, BA in water.     

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid‐Complex Tauto‐Conformers

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism‐driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe^II₄ L ₄]⁸⁺ complexes were determined by X‐ray diffraction, and the distinctness of the products was confirmed by ion‐mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe^II spin crossover vs. a blocked Fe^II high‐spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology.     

Spin Crossover and Long-Lived Excited States in a Reduced Molecular Ruby

The chromium(III) complex [Cr^III(ddpd)₂]³⁺ (molecular ruby; ddpd=N,N′-dimethyl-N,N′-dipyridine-2-yl-pyridine-2,6-diamine) is reduced to the genuine chromium(II) complex [Cr^II(ddpd)₂]²⁺ with d⁴ electron configuration. This reduced molecular ruby represents one of the very few chromium(II) complexes showing spin crossover (SCO). The reversible SCO is gradual with T_1/2 around room temperature. The low-spin and high-spin chromium(II) isomers exhibit distinct spectroscopic and structural properties (UV/Vis/NIR, IR, EPR spectroscopies, single-crystal XRD). Excitation of [Cr^II(ddpd)₂]²⁺ with UV light at 20 and 290 K generates electronically excited states with microsecond lifetimes. This initial study on the unique reduced molecular ruby paves the way for thermally and photochemically switchable magnetic systems based on chromium complexes complementing the well-established iron(II) SCO systems.     

可蒸镀自旋交叉配合物的薄膜与器件

自旋交叉配合物在温度、压力、光照和磁场等刺激下可以发生高低自旋态之间的可逆转变,通常还伴随着颜色、体积和电导率变化以及热滞等效应,因此这类材料在光热开关、传感器、显示和存储等领域具有潜在的应用.由于可以获得高质量的超洁净薄膜,高真空蒸镀工艺常用于分子电子学与分子磁学等的器件制备,目前报道的可蒸镀自旋交叉配合物种类较少,大大限制了自旋交叉配合物的器件应用.针对可蒸镀自旋交叉配合物的薄膜与器件进行了系统的综述,介绍了几种主要的适于高真空蒸镀的自旋交叉配合物,结合不同的表征手段分析了衬底对分子薄膜自旋转变特性的影响,并针对相关的概念性器件进行了讨论,最后对自旋交叉配合物在器件应用中存在的难点和未来的发展趋势进行了展望和评述,希望能够为自旋交叉领域的器件应用提供一些借鉴.     

Spin crossover in polyaniline

Solutions of the basic form of polyaniline in m-cresol were studied by ESR and optical spectroscopy in the visible region. m-Cresol can slowly (during one month) protonate polyaniline. For the first time characteristic features of spin crossover were found: sharp changes in the magnetic susceptibility and the ESR line width of polyaniline at ∼200 and 250 K, a smooth decrease in the susceptibility and absorption with the temperature increase from 293 to 423 K, and the temperature hysteresis. The temperature-induced structural rearrangements of polyaniline are caused, most likely, by singlet-triplet transitions in relatively short sections of the polymer chain. The model of short sections permits to explain the origin of the temperature-independent part of susceptibility. Quantum-chemical calculations for the aniline dimers and tetramers describe correctly the singlet-triplet splitting value, thermochromism, and HFS constants in the spectrum of polyaniline. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1959–1966, October, 2007.     

Molecular Photochemistry: Recent Developments in Theory

Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light‐induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non‐adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.     

GPU引发的计算化学革命

综述了图形处理器(GPU)在计算化学中的应用和进展.首先简单介绍了GPU在科学计算中应用的发展,然后分别详细讲述了迄今几个使用GPU和CUDA(compute unified device architecture,显卡厂商Nvidia推出的计算平台)开发工具设计的量子化学计算和分子动力学(MD)模拟的算法和程序,尤其对目前唯一完全使用GPU技术开发的量子化学计算软件TeraChem做了完备的介绍,包括算法、实现的细节和程序目前的功能.此外,本文还对GPU在计算化学上将会发挥的作用做出了极为乐观的展望.