含BN旋转轴的光驱动分子马达的理论设计和机理研究

依据B=N键与C=C键的电子结构相似性,以Feringa型二苯乙烯型光驱动分子马达（CC-stilbene）为母体,设计了含极性旋转轴的模型马达BN-stilbene.CASPT2//CASSCF计算结果表明,优化所得的BN-stilbene分子的基态存在四个与CC-stilbene马达结构相似、相对能量一致的螺旋异构体;B=N极性共价双键对BN-stilbene的基态和激发态电子结构有显著影响.对BN-stilbene模型马达的工作机理研究表明,极性旋转轴的引入使得BN-stilbene中S₁/S₀-CI与激发态中间体构型更加相似且能量更低,同时可增加旋转的驱动力,起到改进分子马达光异构化过程的单向性的目的.     

Operations and Thermodynamics of an Artificial Rotary Molecular Motor in Solution

A general framework is provided that makes possible the estimation of time‐dependent properties of a stochastic system moving far from equilibrium. The process is investigated and discussed in general terms of nonequilibrium thermodynamics. The approach is simple and can be exploited to gain insight into the dynamics of any molecular‐level machine. As a case study, the dynamics of an artificial molecular rotary motor, similar to the inversion of a helix, which drives the motor from a metastable state to equilibrium, are examined. The energy path that the motor walks was obtained from the results of atomistic calculations. The motor undergoes unidirectional rotation and its entropy, internal energy, free energy, and net exerted force are given as a function of time, starting from the solution of Smoluchowski’s equation. The rather low value of the organization index, that is, the ratio of the work done by the particle against friction during the unidirectional motion per available free energy, reveals that the motion is mainly subject to randomness, and the amount of energy converted to heat due to the directional motion is very small.     

Are Conical Intersections Responsible for the Ultrafast Processes of Adenine,Protonated Adenine,and the Corresponding Nucleosides?

Excited-state potential energy surfaces of adenine, protonated adenine, and their N9-methylated analogs are explored by means of a complete active space (CAS) and time-dependent density functional theory (TD-DFT) study to understand the dynamics associated with internal conversion. After photoexcitation of the ground-state molecules to the S(1) state, the nuclear motions that are responsible for taking the wavepacket out of the Franck-Condon region are either an H--N9/C--N9 stretch or a ring-puckering motion that leads to pyramidalization. These motions lead to accessible conical intersections with the ground-state surface. The results are used to successfully interpret previous measurements on the photodissociation of adenosine 5'-monophosphate nucleotide anions and cations, where the latter react in a highly nonstatistical manner.     

Functional and Basis Set Dependence for Time-Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis-Azobenzene Photoisomerization

Within three functionals (TD-B3LYP, TD-BHandHLYP, and TD-CAM-B3LYP) in combination with four basis sets (3-21g, 6-31g, 6-31g(d), and cc-pvdz), global switching (GS) trajectory surface hopping molecular dynamics has been performed for cis-to-trans azobenzene photoisomerization up to the S₁(nπ*) excitation. Although all the combinations show artificial double-cone structure of conical intersection between ground and first excited states, simulated quantum yields and lifetimes are in good agreement with one another; 0.6 (±5%) and 40.5 fs (±10%) by TD-B3LYP, 0.5 (±10%) and 35.5 fs (±4%) by TD-BHandHLYP, and 0.44 (±9%) and 35.2 fs (±10%) by TD-CAM-B3LYP. By analyzing distributions of excited-state population decays, hopping spots, and typical trajectories with performance of 12 functional/basis set combinations, it has been concluded that functional dependence for given basis set is slightly more sensitive than basis set dependence for given functional. The present GS on-the-fly time-dependent density functional theory (TDDFT) trajectory surface hopping simulation can provide practical benchmark guidelines for conical intersection driven excited-state molecular dynamics simulation involving in large complex system within ordinary TDDFT framework. © 2019 Wiley Periodicals, Inc.     

Synthetic Molecular Motors: Thermal N Inversion and Directional Photoinduced CN Bond Rotation of Camphorquinone Imines

The thermal and photochemical E/Z isomerization of camphorquinone‐derived imines was studied by a combination of kinetic, structural, and computational methods. The thermal isomerization proceeds by linear N inversion, whereas the photoinduced process occurs through C?N bond rotation with preferred directionality as a result of diastereoisomerism. Thereby, these imines are arguably the simplest example of synthetic molecular motors. The generality of the orthogonal trajectories of the thermal and photochemical pathways allows for the postulation that every suitable chiral imine qualifies, in principle, as a molecular motor driven by light or heat.     

Insights into the Mechanism of Reaction of [(C5Me5)2SmII(thf)2] with CO2 and COS by DFT Studies

Reaction mechanisms for the oxidative reactions of CO₂ and COS with [(C₅Me₅)₂Sm] have been investigated by means of DFT methods. The experimental formation of oxalate and dithiocarbonate complexes is explained. Their formation involve the samarium(III) bimetallic complexes [(C₅Me₅)₂Sm‐CO₂‐Sm(C₅Me₅)₂] and [(C₅Me₅)₂Sm‐COS‐Sm(C₅Me₅)₂] as intermediates, respectively, ruling out radical coupling for the formation of the oxalate complex.     

Trianglimine-Mediated Selective Sieving of Cis Isomer from the Mixture of Dihaloethenes: A Combined Molecular Dynamics and DFT Investigation

The manufacture of alkenyl halides on a larger scale often results in the formation of a mixture of isomers, each having individual significant applications while their separation from each other is a strenuous task. Since most of the conventional distillation techniques are known to be intricate, energy consuming and expensive, the quest for an alternative separation strategies is still continuing. In this context, the recently reported trianglimine macrocycle - a new class of intrinsically porous material, is promising in discerning cis isomer from a mixture of cis and trans dichloroethene. Herein, an attempt has been made to apprehend the host-guest inclusion phenomenon accountable for the selectivity of cis over the trans isomers of 1,2-dihaloethene (F, Cl and Br) using molecular dynamics simulation and density functional calculations at ω-B97xd/6-311G+(d,p) level of theory. The average binding energy of selected snapshots has been calculated at different loadings, temperatures and pressures from molecular dynamics simulation. Our results show that trianglimine can stabilise the cis isomers of the dihaloethenes inside its cavity forming complexes with high interaction energies and the rationale behind the recyclability of the host molecule has been clarified. The outcomes of the calculations bring out the potential utility of this new host architecture to produce highly pure value added chemicals in industries.     

The Molecular Mechanism of the Formation of Four-Membered Cyclic Nitronates and Their Retro (3 + 2) Cycloaddition: A DFT Mechanistic Study

In the present work, the formation of the four-membered cyclic nitronates and the retro (3 + 2) cycloaddition (retro-32CA) reaction of the 4H-[1,2]oxazete 2-oxide were studied using the density functional theory method at the MPWB1K/6-311G(d,p) theoretical level. The electronic structure of 3-tert-butyl-4,4-dimethyl-1,2-dinitro-pent-2-ene was known through electron localization function analysis, natural population analysis, and molecular electrostatic potential analysis. The formation of 4,4-di-tert-butyl-3-nitromethyl-4H-[1,2]oxazete 2-oxide proceeds through a one-step mechanism. The mechanism of the retro-32CA leading to di-tert-butyl ketone and nitrile oxide derivative should be described as an asynchronous two-stage one-step process. The bonding evolution theory study was carried out to clarify the mechanisms of the formation of 4H-[1,2]oxazete 2-oxide and their retro-32CA.     

Molecular structure, barriers to internal rotation, and the enthalpy of formation of cumene hydroperoxide PhCMe2OOH: a DFT study

Conformational analysis of cumene hydroperoxide PhCMe₂OOH (1) has been carried out using the density functional methods B3LYP/6-31G(d,p) and B3LYP/6-311+G(3df,2p). Ignoring rotation of methyl groups, molecule 1 has seven conformers differing in orientation of the — CMe₂OOH fragment relative to the benzene ring and in mutual position of atoms in this fragment. The molecular structures, relative energies, and statistical distribution of the conformers were determined, and intramolecular rotational barriers were estimated. The enthalpies of formation of all conformers of molecule 1 were calculated using two approximations with inclusion of zero-point vibrational energy and temperature correction. Calculations using the isodesmic reaction (IDR) scheme made it possible to reduce the systematic error of the determination of the enthalpy of reactions. The total enthalpy of formation of compound 1 calculated with inclusion of statistical distribution of rotamers equals −19.7±3.6 kcal mol⁻¹. The combination of the B3LYP/6-31G(d,p) approximation and the IDR scheme gives fairly accurate results (relative error is ±0.4 kcal mol⁻¹) as compared to those obtained with the extended basis set 6-311+G(3df,2p). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1157–1164, June, 2008.     

Molecular Modeling of Bioorganometallic Compounds: Thermodynamic Properties of Molybdocene–Glutathione Complexes and Mechanism of Peptide Hydrolysis

The computational study of bioinorganic complexes between transition metals and flexible ligands is still challenging, given that, besides requiring extensive conformational searches, the treatment of metal–ligand bonds demands the application of quantum chemical methods. Herein, the adducts formed between molybdocene, which exhibits antitumor activity and reacts with thiol groups to give stable water‐soluble complexes, and the tripeptide glutathione, which is a major source of biological thiols, are studied. Conformational searches are performed using the semiempirical PM6 method followed by geometry optimizations and single‐point calculations using density functional theory methods. In addition, molecular dynamics simulations of the molybdocene–glutathione complex involved in the regioselective hydrolysis of the Cys–Gly linkage are performed in explicit solvent. The reactive process is also studied theoretically on cluster models of both the molybdocene‐bound and the free peptide.     

Computational Insight to Improve the Thermal Isomerisation Performance of Overcrowded Alkene‐Based Molecular Motors through Structural Redesign

Synthetic overcrowded alkene‐based molecular motors achieve 360° unidirectional rotary motion of one motor half (rotator) relative to the other (stator) through sequential photochemical and thermal isomerisation steps. In order to facilitate and expand the use of these motors for various applications, it is important to investigate ways to increase the rates and efficiencies of the reactions governing the rotary motion. Here, we use computational methods to explore whether the thermal isomerisation performance of some of the fastest available motors of this type can be further improved by reducing the sizes of the motor halves. Presenting three new redesigned motors that combine an indanylidene rotator with a cyclohexadiene, pyran or thiopyran stator, we first use multiconfigurational quantum chemical methods to verify that the photoisomerisations of these motors sustain unidirectional rotary motion. Then, by performing density functional calculations, we identify both stepwise and concerted mechanisms for the thermal isomerisations of the motors and show that the rate‐determining free‐energy barriers of these processes are up to 25 kJ mol^?1 smaller than those of the original motors. Furthermore, the thermal isomerisations of the redesigned motors proceed in fewer steps. Altogether, the results suggest that the redesigned motors are useful templates for improving the thermal isomerisation performance of existing overcrowded alkene‐based motors.     

A DFT Study on the Molecular Mechanism of Additions of Electrophilic and Nucleophilic Carbenes to Non-Enolizable Cycloaliphatic Thioketones

The molecular mechanisms of addition of dihalocarbenes and dimethoxycarbene to thioketones derived from 2,2,4,4-tetrmethylcyclobutane-1,3-dione were examined on the basis of the DFT wb97xd/6-311g(d,p)(PCM) calculations. Obtained results demonstrated that the examined processes exhibit polar nature and in the case of electrophilic dichloro-, and dibromocarbenes are initiated by the attack of carbene species onto the sulfur atom of the C=S group. Remarkably, reactions involving more electrophilic carbenes (dichloro-, and dibromocarbene) proceeds via stepwise mechanism involving thiocarbonyl ylide as a transient intermediate. In contrast, analogous reactions with nucleophilic dimethoxycarbene occur via a single step reaction, which can be considered as the [2 + 1] cycloaddition reaction initiated by the attack onto the C=S bond. A computational study showed that difluorocarbene tends to react as a nucleophilic species and resembles rather dimethoxycarbene and not typical dihalocarbene species. Significantly higher reactivity of the thioketone unit in comparison to the ketone group, both present in 3-thioxo-2,2,4,4-tetramthylcyclobutanone molecule, was rationalized in the light of DFT computational study.     

On the Catalytic Mechanism of (S)‐2‐Hydroxypropylphosphonic Acid Epoxidase (HppE): A Hybrid DFT Study

The mechanism of oxidative epoxidation catalyzed by HppE, which is the ultimate step in the biosynthesis of fosfomycin, was studied by using hybrid DFT quantum chemistry methods. An active site model used in the computations was based on the available crystal structure for the HppE‐Fe^II‐(S)‐HPP complex and it comprised first‐shell ligands of iron as well as second‐shell polar groups interacting with the substrates. The reaction energy profiles were constructed for three a priori plausible mechanisms proposed in the literature, and it was found that the most likely scenario for the native substrate, that is, (S)‐HPP, involves generation of the reactive Fe^III? O ^. /Fe^IV?O species, which is responsible for the C? H bond‐cleavage. At the subsequent reaction stage, the OH‐rebound, which would lead to a hydroxylated product, is prevented by a fast protonation of the OH ligand and, as a result, ring closure is the energetically preferred step. For the R enantiomer of the substrate ((R)‐HPP), which is oxidized to a keto product, comparable barrier heights were found for the C? H bond activation by both the Fe^III? O₂ ^. and Fe^IV?O species.     

A DFT Study on the Mechanism of the Cycloaddition Reaction of CO2 to Epoxides Catalyzed by Zn(Salphen) Complexes

The reaction mechanism for the Zn(salphen)/NBu₄X (X=Br, I) mediated cycloaddition of CO₂ to a series of epoxides, affording five‐membered cyclic carbonate products has been investigated in detail by using DFT methods. The ring‐opening step of the process was examined and the preference for opening at the methylene (C_β) or methine carbon (C_α) was established. Furthermore, calculations were performed to clarify the reasons for the lethargic behavior of internal epoxides in the presence of the binary catalyst. Also, the CO₂ insertion and the ring‐closing steps have been explored for six differently substituted epoxides and proved to be significantly more challenging compared with the ring‐opening step. The computational findings should allow the design and application of more efficient catalysts for organic carbonate formation.     

Understanding the Regioselectivity and the Molecular Mechanism of [3 + 2] Cycloaddition Reactions between Nitrous Oxide and Conjugated Nitroalkenes: A DFT Computational Study

Regiochemical aspects and the molecular mechanism of the [3 + 2] cycloaddition between nitrous oxide and conjugated nitroalkenes were evaluated on the basis of the wb97xd/6-311 + G(d) (PCM) computational study. It was found that, independently of the nature of the nitroalkene, all considered processes are realized via polar, single-step mechanisms. All attempts at the localization of hypothetical zwitterionic intermediates were unsuccessful. Additionally, the DFT computational study suggested that, in the course of the reaction, the formation of respective Δ²-4-nitro-4-R₁-5-R₂-1-oxa-2,3-diazolines was preferred from the kinetic point of view.     

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.     

Photoinduced oxygen transfer and double-linkage isomerism in a cis-(NO)(NO2) transition-metal complex by photocrystallography, FT-IR spectroscopy and DFT calculations

Photocrystallographic experiments show that laser exposure of crystals of [Ru(bpy)2(NO)(NO2)](PF6)2 at 90 K produces a double isonitrosyl-nitrito linkage isomer and provide the detailed geometry of the metastable species generated. The analysis indicates that the isomerization is accomplished through an intramolecular redox reaction involving oxygen transfer from the nitro to the nitrosyl group. At 200 K only a single (nitrito) linkage isomer is formed with a U-shaped conformation of the nitrito group rather than the Z conformation observed at 90 K. A mechanism for the isomerization is proposed based on the crystallographic results and FTIR data collected at low temperatures during the isomerization process. The study presents the first structural evidence for double linkage isomerization in transition-metal complexes.