Energy transfer from two luteins to chlorophylls in light-harvesting complex II study by using exciton models with phase correction.

In light-harvesting complex II of plants, the two lutein pigments (LUT1 and LUT2) are always paired and an energy transfer pathway between them is believed to exist. However, it remains unclear whether this pathway is essential for the energy transfer between carotenoids and chlorophylls. In this work, we performed hybrid quantum mechanics/molecular mechanics simulations with Frenkel exciton models to investigate this energy transfer. The results show that the energy transfer pathways between the S2 state of LUT1 and CLAs are not affected by LUT2 S2. The energy transfer between LUT and chlorophyll-a (CLA) also follows a resonance mechanism. The two LUTs have different energy transfer pathways according to their energy gaps and coupling strengths with each CLA. The present work sheds light on the energy transfer pathways involved in the two LUTs.

Importance of Spin Channels from Radical-Radical Reactions in Hydrogen-Oxygen Combustion Mechanisms at High Temperatures.

Radical-radical reactions can generate two channels with high and low spins. In this work, ten radical-radical reactions with different spin channels and four radical-molecule reactions in hydrogen-oxygen combustion were systematically investigated from a theoretical perspective. The potential energy surface (PES) of radical-radical reactions reveals that the high- and low-spin states of the reactant are energetically degenerate and the two channels are energetically feasible. The difference in rate constants between the high- and low-spin channels gradually decreases as the temperature increases. Then, the kinetic parameters of the 14 bimolecular reactions in the hydrogen-oxygen mechanism of the University of California, San Diego (UCSD), were replaced to simulate the ignition delay time and laminar flame speed. The simulation results agree well with the available experimental findings, indicating the necessity of considering both high- and low-spin channels for kinetic simulation.

Ultrafast vibrational energy redistribution in cyclotrimethylene trinitramine (RDX).

The microscopic mechanism of the energy transfer in cyclotrimethylene trinitramine (RDX) is of particular importance for the study of the energy release process in high-energy materials. In this work, an effective vibrational Hamiltonian based on normal modes (NMs) has been introduced to study the energy transfer process of RDX. The results suggest that the energy redistribution in RDX can be characterized as an ultrafast process with a time scale of 25 fs, during which the energy can be rapidly localized to the -NNO2 twisting mode (vNNO2), the N-N stretching mode (vN-N), and the C-H stretching mode (vC-H). Here, the vNNO2 and vN-N modes are directly related to the cleavage and dissociation of the N-N bond in RDX and, therefore, can be referred to as "active modes." More importantly, we found that the energy can be rapidly transferred from the vC-H mode to the vNNO2 mode due to their strong coupling. From this perspective, the vC-H mode can be regarded as an "energy collector" that plays a pivotal role in supplying energy to the "active modes." In addition, the bond order analysis shows that the dissociation of the N-N bonds of RDX follows a combined twisting and stretching path along the N-N bond. This could be an illustration of the further exothermic decomposition triggered by the accumulation of vibrational energy. The present study reveals the microscopic mechanism for the vibrational energy redistribution process of RDX, which is important for further investigation of the energy transfer process in high-energy materials.

Enabling Carbonized Polymer Dots with Color-tunable Time-dependent Room Temperature Phosphorescence through Confining Carboxyl Dimer Association.

Developing a facile strategy to realize fine-tuning of phosphorescence color in time-dependent room temperature phosphorescence (RTP) materials is essential but both theoretically and practically rarely exploited. Through simultaneously confining carboxyl dimer association and isolated carboxyl into the particle via a simple hydrothermal treatment of polyacrylic acid, a dual-peak emission of red phosphorescence (645 nm) and green phosphorescence (550 nm) was observed from carbonized polymer dots (CPDs). The ratio of the two luminescent species can be well regulated by hydrochloric acid inhibiting the dissociation of carboxyl to promote hydrogen bond. Due to comparable but different lifetimes, color-tunable time-dependent RTP with color changing from yellow to green or orange to green were obtained. Based on the crosslinking enhanced emission effect, the phosphorescence visible time was even extended to 7 s through introducing polyethylenimide. This study not only proposes a novel and facile method for developing CPDs with color-tunable time-dependent RTP, but also provides a bran-new non-conjugated red phosphorescence unit and its definite structure.

Controlling the repair mechanisms of oxetanes through functional group substitution.

Intersystem crossing (ISC) plays a key role in the photolysis processes of oxetanes formed by benzophenone (BP)-like and thymine structures. In this work, we systematically explored the photophysical processes of oxetanes and ring-splitting products and investigated the effect of substituents on the repair mechanisms of oxetanes. The regioselectivity of oxetanes (head-to-head, HH and head-to-tail, HT) and the electron-donating and electron-withdrawing substituents, including CH3, OCH3 and NO2, were considered. It was found that the substituents influence the ISC rates of these compounds more by changing their spin-orbit coupling (SOC) coefficients rather than energy gaps. The SOC coefficients of HH-oxetanes are more affected by these groups than HT-oxetanes and products, and they have greater ISC rates on the whole. Besides, the insertion of substituents can alter the radiative and nonradiative decay rates, thereby transforming the photoinduced cycloreversion mechanisms of oxetanes. The ring-splitting reactions of non-substituted oxetanes could occur via two pathways of singlet and triplet manifolds. Furthermore, oxetanes with NO2 at the X site have the largest ISC rates but hardly undergo repair processes, while the introduction of electron-donating substituents can effectively promote the repair of oxetanes. The singlet ring-splitting reactions of HH-oxetanes are more inclined to occur after introducing CH3 and OCH3 at two sites. However, HT-oxeatnes with CH3 are more likely to undergo triplet repair processes and OCH3-substituted structures tend to originate cycloreversion in the singlet manifolds. Moreover, the introduction of CH3 and OCH3 at the Y site rather than the X site can more significantly accelerate the repair processes of HH-oxetanes. Contrarily, HT-oxetanes with electron-donating groups at the X site exhibit faster repair rates than those at the Y site. We hope this work can provide valuable insights into BP-like drugs and photosensitive DNA repair.

Intermolecular resonance energy transfer between two lutein pigments in light-harvesting complex II studied by frenkel exciton models.

The energy transfer pathways in light-harvesting complex II are complicated and the discovery of the energy transfer between the two luteins revealed an unelucidated important role of carotenoids in the energy flow. This energy transfer between the two S2 states of luteins was for the first time investigated using Frenkel exciton models, using a hybrid scheme of molecular mechanics and quantum mechanics. The results show the energy flow between the two luteins under the Förster resonance energy transfer mechanism. The energy transfer caused by energy level resonance occurs in configurations with small energy gaps. This energy transfer pathway is particularly sensitive to conformation. Moreover, according to the statistical characteristics of the data of the energy gaps and coupling values between LUTs, we proposed stochastic exciton Hamiltonian models to facilitate clarification of the energy transfer among pigments in antenna complexes.

Benchmark Study on Phosphorescence Energies of Anthraquinone Compounds: Comparison between TDDFT and UDFT.

Phosphorescent material is widely used in light-emitting devices and in the monitoring of cell phenomena. Anthraquinone compounds (AQs), as important phosphorescent materials, have potential applications as emitters for highly efficient organic light-emitting diodes (OLEDs). Therefore, the accurate calculation of the phosphorescence energy of anthraquinone compounds is particularly important. This study mainly analyzes the phosphorescence energy calculation method of anthraquinone compounds. The time-dependent density functional theory (TDDFT) and the unrestricted density functional theory (UDFT) with seven functionals are selected to calculate the phosphorescence of AQs, taking the high-precision coupled-cluster singles and doubles (CC2) method as a reference. The results showed that the mean unsigned error (MUE) of UDFT was 0.14 eV, which was much smaller than that of TDDFT at 0.29 eV. Therefore, UDFT was more suitable for calculating the phosphorescence energy of AQs. The results obtained by different functionals indicate that the minimum MUE obtained by M06-2X was 0.14 eV. More importantly, the diffuse function in the basis set played an important role in calculating the phosphorescence energy in the M06-HF functional. In the BDBT, FBDBT, and BrBDBT, when M06-HF selected the basis set containing a diffuse function, the differences with CC2 was 0.02 eV, which is much smaller than the one obtained without a diffuse function at 0.80 eV. These findings might be of great significance for the future study of the phosphorescence energy of organic molecules.

Top-Down Rational Engineering of Heteroatom-Doped Graphene Quantum Dots for Laser Desorption/Ionization Mass Spectrometry Detection and Imaging of Small Biomolecules.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is widely applied in mapping macrobiomolecules in tissues, but it is still limited in profiling low-molecular-weight (MW) compounds (typically metabolites) due to ion interference and suppression by organic matrices. Here, we present a versatile "top-down" strategy for rational engineering of carbon material-based matrices, by which heteroatom-doped graphene quantum dots (HGQDs) were manufactured for LDI MS detection and imaging of small biomolecules. The HGQDs derived from parent materials inherited the π-conjugated networks and doping sites for promoting energy transfer and negative ion generation, while their extremely small size guaranteed the matrix uniformity and signal reproducibility in LDI MSI. Compared to other HGQDs, nitrogen-doped graphene quantum dots (NGQDs) exhibited superior capability of assisting LDI of various small molecules, including amino acids, fatty acids, saccharides, small peptides, nucleobases, anticancer drugs, and bisphenol pollutants. Density functional theory simulations also corroborated that the LDI efficiency was markedly raised by the proton-capturing pyridinic nitrogen species and compromised by the electron-deficient boron dopants. NGQDs-assisted LDI MS further enabled label-free investigation on enzyme kinetics using an ordinary short peptide as the substrate. Moreover, due to the high salt tolerance and signal reproducibility, the proposed negative-ion NGQDs-assisted LDI MSI was able to reveal the abundance and distribution of low-MW species in rat brain tissue and achieved the imaging of low-MW lipids in coronally sectioned rat brains subjected to traumatic brain injury. Our work offers a new route for customizing nanomaterial matrices toward LDI MSI of small biomolecules in biomedical and pathological research.

Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms.

A community-reaction network reduction (CNR) approach is presented for mechanism reduction on the basis of a network-based community detection technique, a concept related to pre-equilibrium in chemical kinetics. In this method, the detailed combustion mechanism is first transformed into a weighted network, in which communities of species that have dense inner connections under the critical ignition conditions are identified. By analyzing the community partitions in different regions, we determine the effective functional groups and driving processes. Then, a skeletal model for the overall mechanism is deduced according to the network centrality data, including transition pathway identification and reaction-path flux. The CNR method is illustrated on the hydrogen autoignition system which has been extensively investigated, and a new reduced mechanism involving seven processes is proposed. Dynamics simulations employing the present CNR model show that the computed ignition time and distribution of major species on a wide range of temperature and pressure conditions are in accord with the experiments and results from other methods.

Generation of singlet oxygen catalyzed by the room-temperature-stable anthraquinone anion radical.

The chemical nature and the catalytic selectivity of the complex of anthraquinone and potassium tert-butoxide, AQ-KOtBu, in generating singlet oxygen (1O2) have been studied using a high-level ab initio method and density functional theory (DFT). The results suggest that the stable catalytic center of the AQ anion radical (semiquinone, [AQ˙]-) can be produced at room temperature, which is due to the strong delocalization characteristics of electrons in potassium atoms. Two experimentally observed complexes, the ground state AQ-KOtBu, i.e., C(1), and the photoexcited AQ-KOtBu, i.e., C(2), can be distinguished via the two different electronic states (π-type and σ-type) of the tert-butoxide group. More interestingly, the catalytic selectivity of AQ-KOtBu to generate 1O2 was investigated using multistate density functional theory (MSDFT), and the results suggest that only open-shell 1O2 rather than the closed-shell component can be generated. This work explores the electronic structure and the catalytic nature of AQ-KOtBu, which is of great importance for the application of AQ and its derivatives.

Lack of the ESIPT band of aromatic ortho-aminoaldehyde derivatives triggered by N-H vibration.

The excited state intramolecular proton transfer (ESIPT) reactions and the fluorescence emission spectra of o-aminoaldehyde and o-aminoketone derivatives were systematically studied with density functional theory (DFT) and time-dependent density functional theory (TDDFT). The results suggest that the ESIPT process can be characterized as an ultra-fast process and that N-H vibration plays an important role in fluorescence emissions. The minimum energy pathways (MEP) on the excited states along the proton transfer coordinates (N-H vibration) were constructed for both o-aminoaldehyde and o-aminoketone derivatives, respectively, which showed a small barrier between the normal and tautomer (ESIPT) structures. By comparing the proton transfer barriers (Eb) and the N-H reorganization energies (λeleNH), we find that λeleNH is less than Eb in o-aminoketone derivatives, while λeleNH is greater than Eb in o-aminoaldehyde derivatives. It is clear that protons could move freely in o-aminoaldehyde derivatives, and thus only one normal emission band could be observed. Subsequently, the fluorescence emission spectra upon introduction of the N-H vibration effect can further confirm this mechanism, and the simulated spectra are in good agreement with the experimental observations, in which the o-aminoaldehyde derivatives have only one normal emission band while the o-aminoketone derivatives have two emission bands corresponding to the normal and tautomer structures. Consequently, this work can elucidate the lack of the ESIPT band in o-aminoaldehyde derivatives and also offer new insight into ESIPT by considering the vibronic effect.

Dearomatization of Benzenoid Arenes Triggered by Triplet Excited State Intramolecular Proton Transfer.

The detailed mechanism of photoinduced dearomatization of benzenoid arenes is investigated using both the high-level ab initio method and density functional theory. The results suggest that the optically allowed singlet excited state (S2) can quickly decay to the lowest triplet excited state (T1) through a barrierless internal conversion and intersystem crossing. Importantly, we find a triplet excited state intramolecular proton transfer (T-ESIPT) pathway to produce a diradical triplet intermediate (3MO-H), which can trigger the subsequent [4 + 2] dearomatization reaction. Furthermore, the diastereoselectivity of the reaction was illustrated by the rotation of the O-H group of 3MO-H, which could be effectively modulated by the solvent effect (arising from the strength of the intermolecular hydrogen bond) and the substituted effect (arising from the strength of the electron-donation group). This photochemical mechanism can explain well the experimental observations, and the novel T-ESIPT process can open a new door in studying the photoinduced proton transfer reactions.

Minimal Active Space for Diradicals Using Multistate Density Functional Theory.

This work explores the electronic structure as well as the reactivity of singlet diradicals, making use of multistate density functional theory (MSDFT). In particular, we show that a minimal active space of two electrons in two orbitals is adequate to treat the relative energies of the singlet and triplet adiabatic ground state as well as the first singlet excited state in many cases. This is plausible because dynamic correlation is included in the first place in the optimization of orbitals in each determinant state via block-localized Kohn-Sham density functional theory. In addition, molecular fragment, i.e., block-localized Kohn-Sham orbitals, are optimized separately for each determinant, providing a variational diabatic representation of valence bond-like states, which are subsequently used in nonorthogonal state interactions (NOSIs). The computational procedure and its performance are illustrated on some prototypical diradical species. It is shown that NOSI calculations in MSDFT can be used to model bond dissociation and hydrogen-atom transfer reactions, employing a minimal number of configuration state functions as the basis states. For p- and s-types of diradicals, the closed-shell diradicals are found to be more reactive than the open-shell ones due to a larger diabatic coupling with the final product state. Such a diabatic representation may be useful to define reaction coordinates for electron transfer, proton transfer and coupled electron and proton transfer reactions in condensed-phase simulations.

Theoretical Study of a Two-Photon Fluorescent Probe Based on Nile Red Derivatives with Controllable Fluorescence Wavelength and Water Solubility.

Hypochloric acid (HOCl) plays a vital role in the natural defense system, but abnormal levels of it can cause cell damage, accelerated human aging, and various diseases. It is of great significance to develop new probes for detecting HOCl in biosystems nondestructively and noninvasively. The purpose of this work is to explore new chemical modification strategies of two-photon excitation fluorescence (TPEF) probes to improve the poor water solubility and low efficiency in imaging applications. Nil-OH-6 has a two-photon absorption cross-section value as high as 243 GM and attains a good quantum yield of 0.49. In addition, the modification of terminal groups with different azetidine-heterospirocycles or N,N-dialkyl fused amino groups to Nile Red can effectively improve the fluorescence efficiency as well as increase the solubility to some extent. This study provides some strategies to simultaneously improve the fluorescence performance and solubility of these two-photon probes and, hence, reliable guidance and a foundation for the subsequent synthesis of TPEF probes based on Nile Red.

A new permutation-symmetry-adapted machine learning diabatization procedure and its application in MgH2 system.

This work introduces a new permutation-symmetry-adapted machine learning diabatization procedure, termed the diabatization by equivariant neural network (DENN). In this approach, the permutation symmetric and anti-symmetric elements in diabatic potential energy metrics (DPEMs) were simultaneously simulated by the equivariant neural network. The diabatization by deep neural network scheme was adopted for machine learning diabatization, and non-zero diabatic coupling was included to increase accuracy in the near degenerate region. Based on DENN, the global DPEMs for 11A' and 21A' states of MgH2 have been constructed. To the best of our knowledge, these are the first global DPEMs for the MgH2 system. The root-mean-square-errors (RMSEs) for diagonal elements (H11 and H22) and the off-diagonal element (H12) around the conical intersection region were 5.824, 5.307, and 5.796 meV, respectively. The RMSEs of global adiabatic energies for two adiabatic states were 4.613 and 12.755 meV, respectively. The spectroscopic calculations of the 11A' state in the linear HMgH region are in good agreement with the experiment and previous theoretical results. The differences between calculated frequencies and corresponding experiment values are 1.38 and 1.08 cm-1 for anti-symmetric stretching fundamental vibrational frequency and first overtone. The global DPEMs obtained in this work should be useful for further quantum mechanics dynamic simulations on the MgH2 system.

Allosteric Impact of the Variable Insert Loop in Vaccinia H1-Related (VHR) Phosphatase.

Dynamics and conformational motions are important to the activity of enzymes, including protein tyrosine phosphatases. These motions often extend to regions outside the active site, called allosteric regions. In the tyrosine phosphatase Vaccinia H1-related (VHR) enzyme, we demonstrate the importance of the allosteric interaction between the variable insert region and the active-site loops in VHR. These studies include solution nuclear magnetic resonance, computation, steady-state, and rapid kinetic measurements. Overall, the data indicate concerted millisecond motions exist between the variable insert and the catalytic acid loop in wild-type (WT) VHR. The 150 ns computation studies show a flexible acid loop in WT VHR that opens during the simulation from its initial closed structure. Mutation of the variable insert residue, asparagine 74, to alanine results in a rigidification of the acid loop as observed by molecular dynamics simulations and a disruption of crucial active-site hydrogen bonds. Moreover, enzyme kinetic analysis shows a weakening of substrate affinity in the N74A mutant and a >2-fold decrease in substrate cleavage and hydrolysis rates. These data show that despite being nearly 20 Å from the active site, the variable insert region is linked to the acid loop by coupled millisecond motions, and that disruption of the communication between the variable insert and active site alters the normal catalytic function of VHR and perturbs the active-site environment.

A self-consistent coulomb bath model using density fitting.

A self-consistent Coulomb bath model is presented to provide an accurate and efficient way of performing calculations for interfragment electrostatic and polarization interactions. In this method, a condensed-phase system is partitioned into molecular fragment blocks. Each fragment is embedded in the Coulomb bath due to other fragments. Importantly, the present Coulomb bath is represented using a density fitting method in which the electron densities of molecular fragments are fitted using an atom-centered auxiliary basis set of Gaussian type. The Coulomb bath is incorporated into an effective Hamiltonian for each fragment, with which the electron density is optimized through an iterative double self-consistent field (DSCF) procedure to realize the mutual many-body polarization effects. In this work, the accuracy of interfragment interaction energies enumerated using the Coulomb bath is tested, showing a good agreement with the exact results from an energy decomposition analysis. The qualitative features of many-body polarization effects are visualized by electron density difference plots. It is also shown that the present DSCF method can yield fast and robust convergence with near-linear scaling in performance with increase in system size.

Reactivities of singlet oxygen: open-shell or closed-shell?

This work explores the reactivity of singlet oxygen with respect to two typical reactions: cycloaddition to anthracene and excitation energy transfer (EET) to a carotenoid using diabatic states with multistate density functional theory (MSDFT). Noticeably, the degenerate state 1Δg has distinct open-shell (OS) and closed-shell (CS) components, and the closed-shell component showed more reactivity than the open-shell one due to the strong diabatic couplings to the product diabatic states. The diabatic perspective presented in this work could also apply to general singlet fission processes.

Photoisomerization of silyl-substituted cyclobutadiene induced by σ → π* excitation: a computational study.

Photoinduced chemical processes upon Franck-Condon (FC) excitation in tetrakis(trimethylsilyl)-cyclobutadiene (TMS-CBD) have been investigated through the exploration of potential energy surface crossings among several low-lying excited states using the complete active space self-consistent field (CASSCF) method. Vertical excitation energies are also computed with the equation-of-motion coupled-cluster model with single and double excitations (EOM-CCSD) as well as the multireference Møller-Plesset (MRMP) methods. Upon finding an excellent coincidence between the computational results and experimental observations, it is suggested that the Franck-Condon excited state does not correspond to the first π-π* single excitation state (S1, 1(1)B1 state in terms of D2 symmetry), but to the second (1)B1 state (S3), which is characterized as a σ-π* single excitation state. Starting from the Franck-Condon region, a series of conical intersections (CIs) are located along one isomerization channel and one dissociation channel. Through the isomerization channel, TMS-CBD is transformed to tetrakis(trimethylsilyl)-tetrahedrane (TMS-THD), and this isomerization process could take place by passing through a "tetra form" conical intersection. On the other hand, the dissociation channel yielding two bis(trimethylsilyl)-acetylene (TMS-Ac) molecules through further stretching of the longer C-C bonds might be more competitive than the isomerization channel after excitation into S3 state. This mechanistic picture is in good agreement with recently reported experimental observations.

Diradical-Based Strategy in Designing Narrowband Thermally Activated Delayed Fluorescence Molecules with Tunable Emission Wavelengths.

In the design of thermally activated delayed fluorescence (TADF) materials, narrow-band emission is of particular importance for the development of organic light-emitting diodes (OLEDs). In this work, we proposed a new strategy for designing TADF molecules utilizing degenerate nonbonding (NB) orbitals of diradical parent molecules, and these designed molecules are termed NB-TADF molecules. Based on this strategy, a series of NB-TADF molecules is finely designed and systematically studied by theoretical calculations. Taking advantage of the nonbonding properties, these NB-TADF molecules exhibit desirable narrowband emissions and high quantum yields. More importantly, the emission bands can be easily tuned from blue to near-infrared by changing the conjugate length of the parent group in the NB-TADF molecules. We hope that this new strategy can open a new door for the design of novel TADF materials.