On the Dissociation of Aromatic Radical Anions in Solution

A new theoretical formulation is given for the reaction rate and path for the important reaction class of aromatic radical anion dissociation in solution [Ar? X]^?.→Ar^.+X^?, and is illustrated for the case of the cyanochlorobenzene radical anion [CN? Φ? Cl]^?. in dimethylformamide. Among the theory's novel features is the inclusion of the conical intersection aspect of this ground electronic state problem, which is key in allowing the reaction to occur and which has a significant impact on the reaction barrier height. Reasonable agreement with the experimental rate is found.     

Coherent Vibrational and Dissociation Dynamics of Polyatomic Radical Cations

The ultrafast dynamics of polyatomic radical cations contribute to important processes including energy transfer in photovoltaics, electron transfer in photocatalysis, radiation-induced DNA damage, and chemical reactions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of polyatomic radical cations following electron removal, which arises from excess electronic excitation of the molecule during the ionization process. This Concept article introduces the reader to how the pump-probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can overcome this challenge to capture coherent vibrational dynamics on the femtosecond timescale in polyatomic radical cations and enable the analysis of their dissociation pathways. Examples of FTRMS applied to three families of polyatomic radical cations are discussed.     

Micro-Solvated DMABN: Excited State Quantum Dynamics and Dual Fluorescence Spectra

In this work, we report a complete analysis by theoretical and spectroscopic methods of the short-time behaviour of 4-(dimethylamino)benzonitrile (DMABN) in the gas phase as well as in cyclohexane, tetrahydrofuran, acetonitrile, and water solution, after excitation to the La state. The spectroscopic properties of DMABN were investigated experimentally using UV absorption and fluorescence emission spectroscopy. The computational study was developed at different electronic structure levels and using the Polarisable Continuum Model (PCM) and explicit solvent molecules to reproduce the solvent environment. Additionally, excited state quantum dynamics simulations in the diabatic picture using the direct dynamics variational multiconfigurational Gaussian (DD-vMCG) method were performed, the largest quantum dynamics “on-the-fly” simulations performed with this method until now. The comparison with fully converged multilayer multiconfigurational time-dependent Hartree (ML-MCTDH) dynamics on parametrised linear vibronic coupling (LVC) potentials show very similar population decays and evolution of the nuclear wavepacket. The ring C=C stretching and three methyl tilting modes are identified as the responsible motions for the internal conversion from the La to the Lb states. No major differences are observed in the ultrafast initial decay in different solvents, but we show that this effect depends strongly on the level of electronic structure used.     

How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations

Photoswitchable azobenzene cross‐linkers can control the folding and unfolding of peptides by photoisomerization and can thus regulate peptide affinities and enzyme activities. Using quantum mechanics/molecular mechanics (QM/MM) methods and classical MM force fields, we report the first molecular dynamics simulations of the photoinduced folding and unfolding processes in the azobenzene cross‐linked FK‐11 peptide. We find that the interactions between the peptide and the azobenzene cross‐linker are crucial for controlling the evolution of the secondary structure of the peptide and responsible for accelerating the folding and unfolding events. They also modify the photoisomerization mechanism of the azobenzene cross‐linker compared with the situation in vacuo or in solution.     

分子间自由基正离子反应研究进展

自由基正离子含有一个正电荷和一对未成对电子,是很多有机化学反应的重要的活性中间体。文章综述了近几年自由基正离子反应研究进展,主要包括化学氧化剂诱导的自由基正离子反应、可见光诱导的自由基正离子反应、电诱导的自由基正离子反应等方面的研究。     

Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective

This work provides a novel interpretation of elementary processes of photophysical relevance from the standpoint of the electron density using simple model reactions. These include excited states of H₂ taken as a prototype for a covalent bond, excimer formation of He₂ to analyze non‐covalent interactions, charge transfer by an avoided crossing of electronic states in LiF and conical interesections involved in the intramolecular scrambling in C₂H₄. The changes of the atomic and interaction energy components along the potential energy profiles are described by the interacting quantum atoms approach and the quantum theory of atoms in molecules. Additionally, the topological analysis of one‐ and two‐electron density functions is used to explore basic reaction mechanisms involving excited and degenerate states in connection with the virial theorem. This real space approach allows to describe these processes in a unified way, showing its versatility and utility in the study of chemical systems in excited states. © 2017 Wiley Periodicals, Inc.     

Hierarchical equations of motion in the Libra software package

We report the implementation of a hierarchical equations of motion (HEOM) module within the open-source Libra software. It includes the standard and scaled HEOM algorithms for computing the dynamics of open quantum systems interacting with a harmonic bath. The module allows the computing of the evolution of the reduced density matrix, as well as spectral lineshapes. The truncation, filtering, and “update list” schemes, as well as OpenMP parallelization, allow for further computational saving. The package is written in a mix of C++ and Python languages, delivering the best compromise between user friendliness and efficiency. The Python layer of the package takes advantage of standard Python libraries, such as h5py, which allows efficient storage and retrieval of the generated results. The package can be seamlessly used within Jupyter notebooks; its careful design shall provide the maximal convenience and intuitiveness to its users.     

Radical Cation of Pyrazine-di-N-oxide as a Mediator in Electrocatalytic Oxidation of Organic Compounds

The mechanism of oxidation of cyclohexanol, methanol, diethyl ether, triethyl orthoformate, and cyclohexane in the presence of a mediator—electrochemically generated radical cation of pyrazine-di-N-oxide (PyrDNO)—is studied on glassy carbon and platinum in a 0.1 M LiClO₄ solution in acetonitrile employing cyclic voltammetry, ESR electrolysis, and gas chromatography. Effect of temperature, additives of acid and water, oxygen, and the nature of the substrate and solvent on the shape of cyclic voltammograms and intensity of ESR signal of PyrDNO is examined. ESR spectra for radical cations and anions of PyrDNO with g factors equal to, respectively, 2.0090 and 2.0031 are recorded. A mechanism for the overall two-electron catalytic oxidation of an organic substance, which involves a stage in which it complexes with the radical cation of PyrDNO, is suggested.     

Channel-Resolved Ultrafast Dissociation Dynamics of NO2 Molecules Studied via Femtosecond Time-Resolved Ion Imaging

The ultrafast dissociation dynamics of NO₂ molecules was investigated by femtosecond laser pump-probe mass spectra and ion images. The results show that the kinetic energy release of NO⁺ ions has two components, 0.05 eV and 0.25 eV, and the possible dissociation channels have been assigned. The channel resolved transient measurement of NO⁺ provides a method to disentangle the contribution of ultrafast dissociation pathways, and the transient curvesof NO⁺ ions at different kinetic energy release are fitted by a biexponential function. The fast component with a decay time of 0.25 ps is generated from the evolution of Rydberg states. The slow component is generated from two competitive channels, one of the channel is absorbing one 400 nm photon to the excited state A²B2, which has a decay time of 30.0 ps, and the other slow channel is absorbing three 400 nm photons to valence type Rydberg states which have a decay time less than 7.2 ps. The channel and time resolved experiment present the potential of sorting out the complex ultrafast dissociation dynamics of molecules.     

实验与理论研究G-四链体中鸟嘌呤自由基阳离子脱质子反应

G-四链体传输空穴的特殊性质使其有望应用于发展分子电子器件.由于鸟嘌呤自由基阳离子（G^·+）脱质子反应会中断空穴传递,影响传递效率,我们对G-四链体AG₃（T₂AG₃）₃中G^·+脱质子过程展开了理论与实验的研究.根据瞬态紫外可见吸收光谱,确定了脱质子产物是G（N（2）-H）^·;通过测量不同温度下G^·+脱N（2）-H质子的速率常数,得到脱质子活化能为20.0±1.0 kJ/mol.进而,采用显性水和连续溶剂化模型相结合的方法模拟G-四链体中G^·+脱质子环境,在M062X/6-31G（d）水平上得到了脱质子势垒（26.4 kJ/mol）.结合实验值,理论计算的势能面描述了G-四链体中G^·+脱N2-H的过程.这些结果为G-四链体在电子器件方面的应用提供了重要依据和指导.     

The Jahn-Teller and pseudo-Jahn-Teller effects in the anion photoelectron spectroscopy of B3 cluster

The photodetachment spectroscopy of B3- anion is theoretically studied with the aid of a quantum dynamical approach. The theoretical results are compared with the available experimental photoelectron spectra of B3-. Both B3- and B3 possess D(3h) symmetry at the equilibrium configuration of their electronic ground state. Distortion of B3 along its degenerate vibrational mode nu2 splits the degeneracy of its excited C2E' electronic manifold and exhibits (E [symbol: see text] e)-Jahn-Teller (JT) activity. The components of the JT split potential energy surface form conical intersections, and they can also undergo pseudo-Jahn-Teller (PJT) crossings with the X2A1' electronic ground state of B3 via the degenerate nu2 vibrational mode. The impact of the JT and PJT interactions on the nuclear dynamics of B3 in its X2A1'-C2E' electronic states is examined here by establishing a diabatic model Hamiltonian. The parameters of the electronic part of this Hamiltonian are calculated by performing electronic structure calculations and the nuclear dynamics on it is simulated by solving quantum eigenvalue equation. The theoretical results are in good accord with the experimental data.     

电子转移的外电场效应──苯分子与苯正离子自由基间电子转移的从头算研究

基于半经典电子转移理论,结合量子化学计算,在HF/DZP水平上,研究外电场作用下平行的苯分子-苯正离子自由基体系(C₆H₄)₂⁺的分子内电子转移问题.在给体和受体几何构型优化的基础上,用线性反应坐标确定电子转移过渡态,分别用两态变分方法和基于Koopmans定理的分子轨道跃迁能方法计算电子转移矩阵元V_AB,讨论了V_AB对给体和受体中心距d的指数衰减关系.取中心距为0.6nm,研究了外电场对反应热的影响,计算得到在不同外电场强度下分子内气相电子转移的速率常数k.     

On the Dynamics of the Carbon–Bromine Bond Dissociation in the 1-Bromo-2-Methylnaphthalene Radical Anion

This paper studies the mechanism of electrochemically induced carbon–bromine dissociation in 1-Br-2-methylnaphalene in the reduction regime. In particular, the bond dissociation of the relevant radical anion is disassembled at a molecular level, exploiting quantum mechanical calculations including steady-state, equilibrium and dissociation dynamics via dynamic reaction coordinate (DRC) calculations. DRC is a molecular-dynamic-based calculation relying on an ab initio potential surface. This is to achieve a detailed picture of the dissociation process in an elementary molecular detail. From a thermodynamic point of view, all the reaction paths examined are energetically feasible. The obtained results suggest that the carbon halogen bond dissociates following the first electron uptake follow a stepwise mechanism. Indeed, the formation of the bromide anion and an organic radical occurs. The latter reacts to form a binaphthalene intrinsically chiral dimer. This paper is respectfully dedicated to Professors Anny Jutand and Christian Amatore for their outstanding contribution in the field of electrochemical catalysis and electrosynthesis.     

非绝热分子动力学模拟A位阳离子对钙钛矿热载流子弛豫的影响

钙钛矿具有优异的光学和电学性质,近年来成为太阳能电池领域的研究热点.大量实验报道钙钛矿热载流子弛豫时间变化顺序为CsPbBr₃>MAPbBr₃(MA=CH₃NH₃)>FAPbBr₃[FA=HC(NH₂)₂],但A位阳离子(Cs⁺,MA⁺,FA⁺)对弛豫快慢的影响机制仍不明确.采用基于含时密度泛函理论的非绝热动力学方法研究了上述3种钙钛矿热电子和热空穴的能量弛豫动力学,计算得到的热载流子弛豫时间与实验结果吻合.结果表明,A位阳离子通过静电和氢键作用影响其与无机Pb—Br骨架的电子-振动耦合,使非绝热耦合强度遵从FAPbBr₃>MAPbBr₃>CsPbBr₃的变化趋势,进而使热载流子弛豫时间尺度变化趋势与之相同,表明合理选择A位阳离子可以优化钙钛矿太阳能电池的性能.     

Radical Desorption Kinetics in Emulsion Polymerization, 2 – Brownian Dynamics Simulation of Radical Desorption in Non‐Homogeneous Particles

One of the most important events in free‐radical emulsion polymerization is desorption of radicals from the polymer particles to the aqueous phase. Desorption takes place by diffusion of radicals inside the particle toward the surface and transfer to the aqueous phase. The rate of desorption can be determined theoretically for homogeneous spherical particles. For more complex cases, analytical solutions become difficult or impossible to obtain and a numerical approach is better suited for estimating desorption rate coefficients. In this paper, Brownian dynamics simulation is used for the estimation of desorption rate coefficients in emulsion polymerization systems of increased complexity, in particular for non‐homogeneous polymer particles.

     

Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics

Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.     

The Role of Hydrogen‐Bonding Interactions in the Ultrafast Relaxation Dynamics of the Excited States of 3‐ and 4‐Aminofluoren‐9‐ones

The dynamics of the excited states of 3‐ and 4‐aminofluoren‐9‐ones (3AF and 4AF, respectively) are investigated in different kinds of solvents by using a subpicosecond time‐resolved absorption spectroscopic technique. They undergo hydrogen‐bonding interaction with protic solvents in both the ground and excited states. However, this interaction is more significant in the lowest excited singlet (S₁) state because of its substantial intramolecular charge‐transfer character. Significant differences in the spectroscopic characteristics and temporal dynamics of the S₁ states of 3AF and 4AF in aprotic and protic solvents reveal that the intermolecular hydrogen‐bonding interaction between the S₁ state and protic solvents plays an important role in its relaxation process. Perfect linear correlation between the relaxation times of the S₁ state and the longitudinal relaxation times (τ_L) of alcoholic solvents confirms the prediction regarding the solvation process via hydrogen‐bond reorganization. In the case of weakly interacting systems, the relaxation process can be well described by a dipolar solvation‐like process involving rotation of the OH groups of the alcoholic solvents, whereas in solvents having a strong hydrogen‐bond‐donating ability, for example, methanol and trifluoroethanol, it involves the conversion of the non‐hydrogen‐bonded form to the hydrogen‐bonded complex of the S₁ state. Efficient radiationless deactivation of the S₁ state of the aminofluorenones by protic solvents is successfully explained by the energy‐gap law, by using the energy of the fully solvated S₁ state determined from the time‐resolved spectroscopic data.     

Radical cation formation in characterization of novel C3-symmetric disks and their precursors by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Four C3-symmetrical tris(dipeptide) disks and their precursors were characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). The C3-symmetrical disks were based on a benzene-1,3,5-triscarboxamide core extended by oligopeptides with trialkoxyanilide tails. The results indicate that MALDI TOF MS is a powerful and straightforward analytical technique for characterizing C3-symmetrical disks and their precursors. Clear (pseudo)-molecular ion peaks could readily be identified. It is remarkable that strong radical ion signals were observed for all the compounds, including the anilines that were expected to be protonated prior to laser irradiation using acidic MALDI matrixes. Possible mechanisms for radical ion formation were investigated with the employment of radical scavengers, with various matrixes and with direct laser desorption/ionization (LDI). Most likely the radicals are formed by losing one electron from the aniline nitrogen and stabilized by conjugation through the phenyl ring. It appears that direct photo/thermal ionization of analytes is an important route for the radical ion formation of the compounds with trialkoxy aniline/anilide groups.     

An Exploration of the Transformation of the 8-Oxo-7,8-Dihydroguanine Radical Cation to Protonated 2-Amino-5-Hydroxy-7,9-Dihydropurine-6,8-Dione in a Base Pair

A theoretical investigation was performed to disclose the transformation mechanism of 8-oxo-7,8-dihydroguanine radical cation (8-oxoG⋅⁺) to protonated 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-8-oxoG) in base pair. The energy profiles for three possible pathways of the events were mapped. It is shown that direct loss of H7 from base paired 8-oxoG⋅⁺ is the only energetically favorable pathway to generate neutral radical, 8-oxoG(-H7)⋅. Further oxidation of 8-oxoG(-H7)⋅ : C to 8-oxoG(-H7)⁺ : C is exothermic. However, the 8-oxoG(-H7)⁺ : C deprotonation from all possible active sites is infeasible, indicating the inaccessible second proton loss and the lack of essential intermediate 2-amino-7,9-dihydropurine-6,8-dione (8-oxoG^OX). This makes 8-oxoG(-H7)⁺ act as the precursor of hydration leading to the generation of protonated 5-HO-8-oxoG by stepwise fashion in base pair, which would initiate the step down guanidinohydantoin (Gh) pathway. These results clearly specify the structure-dependent transformation for 8-oxoG⋅⁺ and verify the emergence of protonated 5-HO-8-oxoG in base pair.