Single molecule kinetics of bacteriorhodopsin by HS-AFM

Bacteriorhodopsin is a seven-helix light-driven proton-pump that was structurally and functionally extensively studied. Despite a wealth of data, the single molecule kinetics of the reaction cycle remain unknown. Here, we use high-speed atomic force microscopy methods to characterize the single molecule kinetics of wild-type bR exposed to continuous light and short pulses. Monitoring bR conformational changes with millisecond temporal resolution, we determine that the cytoplasmic gate opens 2.9 ms after photon absorption, and stays open for proton capture for 13.2 ms. Surprisingly, a previously active protomer cannot be reactivated for another 37.6 ms, even under excess continuous light, giving a single molecule reaction cycle of ~20 s−1. The reaction cycle slows at low light where the closed state is prolonged, and at basic or acidic pH where the open state is extended.

Intracluster Sulphur Dioxide Oxidation by Sodium Chlorite Anions: A Mass Spectrometric Study

The reactivity of [NaL·ClO2]− cluster anions (L = ClOx−; x = 0–3) with sulphur dioxide has been investigated in the gas phase by ion–molecule reaction experiments (IMR) performed in an in-house modified Ion Trap mass spectrometer (IT-MS). The kinetic analysis revealed that SO2 is efficiently oxidised by oxygen-atom (OAT), oxygen-ion (OIT) and double oxygen transfer (DOT) reactions. The main difference from the previously investigated free reactive ClO2− is the occurrence of intracluster OIT and DOT processes, which are mediated by the different ligands of the chlorite anion. This gas-phase study highlights the importance of studying the intrinsic properties of simple reacting species, with the aim of elucidating the elementary steps of complex processes occurring in solution, such as the oxidation of sulphur dioxide.

Profiling single-molecule reaction kinetics under nanopore confinement

The development of single-molecule reaction inside nanoconfinement is benefit to study the intrinsic molecular mechanism of a complex chemical reaction. However, the reaction kinetics model of single-molecule reaction inside confinement remains elusive. Herein we engineered the Aerolysin nanopore reactor to elaborate the single-molecule reaction kinetics inside nanoconfinement. By identifying bond forming and non-forming events directly, a four-state kinetics model is proposed for the first time. Our results demonstrated that the single-molecule reaction kinetics inside a nanopore depends on the voltage-dependent frequency of captured individual reactant and the fraction of effective collision inside nanopore confined space. This new insight will guide the design of nanoconfinement for resolving the single-molecule chemistry, and shed light on the mechanistic understanding of dynamic covalent chemistry in-side a nanopore

Photocatalytic nitrogen reduction to ammonia: Insights into the role of defect engineering in photocatalysts

Engineering of defects in semiconductors provides an effective protocol for improving photocatalytic N2 conversion efficiency. This review focuses on the state-of-the-art progress in defect engineering of photocatalysts for the N2 reduction toward ammonia. The basic principles and mechanisms of thermal catalyzed and photon-induced N2 reduction are first concisely recapped, including relevant properties of the N2 molecule, reaction pathways, and NH3 quantification methods. Subsequently, defect classification, synthesis strategies, and identification techniques are compendiously summarized. Advances of in situ characterization techniques for monitoring defect state during the N2 reduction process are also described. Especially, various surface defect strategies and their critical roles in improving the N2 photoreduction performance are highlighted, including surface vacancies (i.e., anionic vacancies and cationic vacancies), heteroatom doping (i.e., metal element doping and nonmetal element doping), and atomically defined surface sites. Finally, future opportunities and challenges as well as perspectives on further development of defect-engineered photocatalysts for the nitrogen reduction to ammonia are presented. It is expected that this review can provide a profound guidance for more specialized design of defect-engineered catalysts with high activity and stability for nitrogen photochemical fixation.

Mechanism of the improvement of the energy of host–guest explosives by incorporation of small guest molecules: HNO3 and H2O2 promoted C–N bond cleavage of the ring of ICM-102

Host–guest materials exhibit great potential applications as an insensitive high-energy–density explosive and low characteristic signal solid propellant. To investigate the mechanism of the improvement of the energy of host–guest explosives by guest molecules, ReaxFF-lg reactive molecular dynamics simulations were performed to calculate the thermal decomposition reactions of the host–guest explosives systems ICM-102/HNO3, ICM-102/H2O2, and pure ICM-102 under different constant high temperatures and different heating rates. Incorporation of guest molecules significantly increased the energy level of the host–guest system. However, the initial reaction path of the ICM-102 molecule was not changed by the guest molecules. The guest molecules did not initially participate in the host molecule reaction. After a period of time, the H2O2 and HNO3 guest molecules promoted cleavage of the C–N bond of the ICM-102 ring. Stronger oxidation and higher oxygen content resulted in the guest molecules more obviously accelerating destruction of the ICM-102 ring structure. The guest molecules accelerated the initial endothermic reaction of ICM-102, but they played a more important role in the intermediate exothermic reaction stage: incorporation of guest molecules (HNO3 and H2O2) greatly improved the heat release and exothermic reaction rate. Although the energies of the host–guest systems were clearly improved by incorporation of guest molecules, the guest molecules had little effect on the thermal stabilities of the systems.

Mechanism of the Improvement of the Energy of Host–Guest Explosives by Incorporation of Small Guest Molecules: HNO3 and H2 O2 Promoted C–N Bond Cleavage of the Ring of ICM-102

Host–guest materials exhibit great potential applications as an insensitive high-energy-density explosive and low characteristic signal solid propellant. To investigate the mechanism of the improvement of the energy of host–guest explosives by guest molecules, ReaxFF-lg reactive molecular dynamics simulations were performed to calculate the thermal decomposition reactions of the host–guest explosives systems ICM-102/HNO3, ICM-102/H2O2, and pure ICM-102 under different constant high temperatures and different heating rates. Incorporation of guest molecules significantly increased the energy level of the host–guest system. However, the initial reaction path of the ICM-102 molecule was not changed by the guest molecules. The guest molecules did not initially participate in the host molecule reaction. After a period of time, the H2O2 and HNO3 guest molecules promoted cleavage of the C–N bond of the ICM-102 ring. Stronger oxidation and higher oxygen content resulted in the guest molecules more obviously accelerating destruction of the ICM-102 ring structure. The guest molecules accelerated the initial endothermic reaction of ICM-102, but they played a more important role in the intermediate exothermic reaction stage: incorporation of guest molecules (HNO3 and H2O2) greatly improved the heat release and exothermic reaction rate. Although the energies of the host–guest systems were clearly improved by incorporation of guest molecules, the guest molecules had little effect on the thermal stabilities of the systems.

Mechanism Dictates Mechanics: A Molecular Substituent Effect in the Macroscopic Fracture of a Covalent Polymer Network

<div><p>Here, we report covalent polymer gels in which the macroscopic fracture “reaction” is controlled by mechanophores embedded within mechanically active network strands. We synthesized poly(ethylene glycol) (PEG) gels through the end-linking of azide-terminated tetra-arm PEG (M_n= 5 kDa) with bis-alkyne linkers. Networks were formed under identical conditions, except that the bis-alkyne was varied to include either a <i>cis</i>-diaryl (<b>1</b>) or <i>cis</i>-dialkyl (<b>2</b>) linked cyclobutane mechanophore that acts as a mechanochemical “weak link” through a force-coupled cycloreversion. A control network featuring a bis-alkyne without cyclobutane (<b>3</b>) was also synthesized. The networks show the same linear elasticity (G' = 23~24 kPa, 0.1 – 100 Hz) and equilibrium mass swelling ratios (Q = 10~11 in tetrahydrofuran), but they exhibit tearing energies that span a factor of 8 (3.4 J∙m^-2, 10.5 J∙m^-2, and 27.1 J∙m^-2 for networks with <b>1</b>, <b>2</b>, and <b>3</b>, respectively). The difference in fracture energy is well aligned with the force-coupled scission kinetics of the mechanophores observed in single-molecule force spectroscopy experiments, implicating local resonance stabilization of a diradical transition state in the cycloreversion of <b>1 </b>as a key determinant of the relative ease with which its network is torn. The connection between macroscopic fracture and small molecule reaction mechanism suggests opportunities for molecular understanding and optimization of polymer network behavior. </p></div>

Mechanism Dictates Mechanics: A Molecular Substituent Effect in the Macroscopic Fracture of a Covalent Polymer Network

<div><p>Here, we report covalent polymer gels in which the macroscopic fracture “reaction” is controlled by mechanophores embedded within mechanically active network strands. We synthesized poly(ethylene glycol) (PEG) gels through the end-linking of azide-terminated tetra-arm PEG (M_n= 5 kDa) with bis-alkyne linkers. Networks were formed under identical conditions, except that the bis-alkyne was varied to include either a <i>cis</i>-diaryl (<b>1</b>) or <i>cis</i>-dialkyl (<b>2</b>) linked cyclobutane mechanophore that acts as a mechanochemical “weak link” through a force-coupled cycloreversion. A control network featuring a bis-alkyne without cyclobutane (<b>3</b>) was also synthesized. The networks show the same linear elasticity (G' = 23~24 kPa, 0.1 – 100 Hz) and equilibrium mass swelling ratios (Q = 10~11 in tetrahydrofuran), but they exhibit tearing energies that span a factor of 8 (3.4 J∙m^-2, 10.5 J∙m^-2, and 27.1 J∙m^-2 for networks with <b>1</b>, <b>2</b>, and <b>3</b>, respectively). The difference in fracture energy is well aligned with the force-coupled scission kinetics of the mechanophores observed in single-molecule force spectroscopy experiments, implicating local resonance stabilization of a diradical transition state in the cycloreversion of <b>1 </b>as a key determinant of the relative ease with which its network is torn. The connection between macroscopic fracture and small molecule reaction mechanism suggests opportunities for molecular understanding and optimization of polymer network behavior. </p></div>