Quantum Mechanical And Molecular Mechanical Research Articles

QM/MM study of the catalytic reaction of aphid myrosinase

Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.

Level-Shifted Embedded Cluster Method for Modeling the Chemistry of Metal Oxides.

The embedded cluster method has been used extensively in the study of the chemical and physical properties of metal oxides. This method has been a popular tool due to its relatively high accuracy and low computational cost. An even more promising option may entail integrating the embedded cluster method with the combined quantum mechanical and molecular mechanical (QM/MM) approach, thereby enabling further consideration of interactions within the entire system for superior results. We aim to accurately model the chemistry of metal oxides using this combined scheme. Here, using the prototypical MgO(100) surface as a test system, with Mg9O14 as the cluster in the quantum mechanical region, we show that the embedded cluster with untailored boundary effective core potentials (ECPs) can have frontier orbital energy levels that substantially deviate from the quantum mechanical reference results. This occurs even when Mg9O9, which retains the stoichiometry of MgO, is used as the cluster in the quantum mechanical region. As a result, the chemical properties of the embedded cluster models differ from those of the quantum mechanical reference model. To address this issue, we propose a new variant of the embedded cluster method called the level-shifted embedded cluster (LSEC) method, which allows the energy levels to be shifted to match the reference levels by tuning the boundary ECPs. Our validation calculations on the adsorption of various adsorbates with different properties on the MgO(100) surface show that the overall performance of QM/MM with the LSEC method is excellent for the adsorption energies, geometries, and charge properties. The excellent performance holds for both the nonstoichiometric and stoichiometric clusters (i.e., Mg9O14 and Mg9O9, respectively), demonstrating the robustness of the LSEC method. We expect that the LSEC method can be combined with QM/MM or used separately for future chemical studies of metal oxides and other ionically bonded systems.

Solid-state effect on the luminescence mechanism of thermally activated delayed fluorescence with aggregation induced emission: A theoretical perspective

An investigation of high-performance organic green thermally activated delayed fluorescence (TADF) material, PyB-DPAC, with aggregation-induced luminescence (AIE) characteristics was theoretically conducted by the first principle calculations method in this work. The polarizable continuum mode (PCM) and the combination of quantum mechanics and molecular mechanics (QM/MM) method were employed to consider the liquid-phase and solid-phase environments, respectively. Results show that TADF mechanism of the molecule is mainly due to the occurrence of efficient intersystem crossing (ISC) and reverse intersystem crossing (RISC) processes between S1 and T2, which benefits from the small energy gap, large SOC and the limited changes of molecular geometry structures in solid-phase environment. The increase of radiative transition rate (Kr) and significant decrease of non-radiative transition rate (Knr) is responsible for the AIE property. Our calculations reasonably explained the experimental results and showed that PyB-DPAC is an excellent TADF material with AIE characteristics, this may help to better understand the influence of solid-state effect and the luminescence mechanism of AIE-TADF molecules.

H2 formation from the E2-E4 states of nitrogenase.

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological lifeforms. The active site is a MoFe7S9C cluster (the FeMo cluster) that binds eight electrons and protons during one catalytic cycle, giving rise to eight intermediate states E0-E7. It is experimentally known that N2 binds to the E4 state and that H2 is a compulsory byproduct of the reaction. However, formation of H2 is also an unproductive side reaction that should be avoided, especially in the early steps of the reaction mechanism (E2 and E3). Here, we study the formation of H2 for various structural interpretations of the E2-E4 states using combined quantum mechanical and molecular mechanical (QM/MM) calculations and four different density-functional theory methods. We find large differences in the predictions of the different methods. B3LYP strongly favours protonation of the central carbide ion and H2 cannot form from such structures. On the other hand, with TPSS, r2SCAN and TPSSh, H2 formation is strongly exothermic for all structures and En and therefore need strict kinetic control to be avoided. For the E2 state, the kinetic barriers for the low-energy structures are high enough to avoid H2 formation. However, for both the E3 and E4 states, all three methods predict that the best structure has two hydride ions bridging the same pair of Fe ions (Fe2 and Fe6) and these two ions can combine to form H2 with an activation barrier of only 29-57 kJ mol-1, corresponding to rates of 7 ×102 to 5 × 107 s-1, i.e. much faster than the turnover rate of the enzyme (1-5 s-1). We have also studied H-atom movements within the FeMo cluster, showing that the various protonation states can quite freely be interconverted (activation barriers of 12-69 kJ mol-1).

Protonation of Homocitrate and the E1 State of Fe-Nitrogenase Studied by QM/MM Calculations.

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E0 state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E1 state, we find that protonation of the S2B μ2 belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E1 state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E1 state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. The adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems. Program SummaryProgram Title: QMMM 2023.CPC Library link to program files:https://doi.org/10.17632/zmkc9db4zj.1.Licensing provisions: Apache-2.0 for the program and CC-BY-4.0 for the manual.Programming languages: Fortran90, Perl, and shell scripting.Nature of problem: Multiscale modeling and simulations by the combined quantum mechanical and molecular mechanical (QM/MM) method.Solution method: The program performs single-point calculations, geometry optimizations, transition state optimizations, and molecular dynamics (MD) by the QM/MM method by interfacing calls to binary executables in a QM package (GAMESS-US, Gaussian, or ORCA) and an MM package (TINKER) for the required calculations. QMMM 2023 supports various types of embedding schemes and multiple ways of treating a QM-MM boundary passing through a covalent bond.Additional comments including restrictions and unusual features: (1) QMMM 2023 supports polarizable-embedding and flexible-embedding schemes based on the electronegativity equalization principle and allowing charge transfer between the QM and MM regions. (2) For a QM-MM boundary passing through covalent bonds, all link-atom-based treatments preserve the charge of the MM region (and MM bond dipoles if desired) while effectively avoiding the over-polarization of the QM region. Further tuning is available to account for the charge penetration effects at the QM-MM boundary. (3) For dynamics simulations, Hamiltonian-based adaptive-partitioning algorithms allow on-the-fly reclassification of atoms or groups into the QM or MM regions without abrupt changes in the energy of the entire system or in the forces on all atoms.

Structural insights in the permeation mechanism of an activated GIRK2 channel

G protein-gated inwardly rectifying potassium (GIRK) channels play a significant role in physiopathology by the regulation of cell excitability. This regulation depends on the K+ ion conduction induced by structural constrictions: the selectivity filters (SFs), helix bundle crossings (HBCs), and G-loop gates. To explore why no permeation occurred when the constrictions were kept in the open state, a 4-K+-related occupancy mechanism was proposed. Unfortunately, this hypothesis was neither assessed, nor was the energetic characteristics presented. To identify the permeation mechanism on an atomic level, all-atom molecular dynamic (MD) simulations and a coupled quantum mechanics and molecular mechanics (QM/MM) method were used for the GIRK2 mutant R201A. It was found that the R201A had a moderate conductive capability in the presence of PIP2. Furthermore, the 4-K+ group of ions was found to dominate the conduction through the activated HBC gate. This shielding-like mechanism was assessed by the potential energy barrier along the conduction pathway. Mutation studies did further support the assumption that E152 was responsible for the mechanism. Moreover, E152 was most probably facilitating the inflow of ions from the SF to the cavity. On the contrary, N184 had no remarkable effect on this mechanism, except for the conduction efficiency. These findings highlighted the necessity of a multi-ion distribution for the conduction to take place, and indicated that the K+ migration was not only determined by the channel conductive state in the GIRK channel. The here presented multi-ion permeation mechanism may help to provide an effective way to regulate the channelopathies.

Bridging semiempirical and abinitio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation.

Free energy simulations that employ combined quantum mechanical and molecular mechanical (QM/MM) potentials at abinitio QM (AI) levels are computationally highly demanding. Here, we present a machine-learning-facilitated approach for obtaining AI/MM-quality free energy profiles at the cost of efficient semiempirical QM/MM (SE/MM) methods. Specifically, we use Gaussian process regression (GPR) to learn the potential energy corrections needed for an SE/MM level to match an AI/MM target along the minimum free energy path (MFEP). Force modification using gradients of the GPR potential allows us to improve configurational sampling and update the MFEP. To adaptively train our model, we further employ the sparse variational GP (SVGP) and streaming sparse GPR (SSGPR) methods, which efficiently incorporate previous sample information without significantly increasing the training data size. We applied the QM-(SS)GPR/MM method to the solution-phase SN2 Menshutkin reaction, NH3+CH3Cl→CH3NH3++Cl-, using AM1/MM and B3LYP/6-31+G(d,p)/MM as the base and target levels, respectively. For 4000 configurations sampled along the MFEP, the iteratively optimized AM1-SSGPR-4/MM model reduces the energy error in AM1/MM from 18.2 to 4.4 kcal/mol. Although not explicitly fitting forces, our method also reduces the key internal force errors from 25.5 to 11.1 kcal/mol/Å and from 30.2 to 10.3 kcal/mol/Å for the N-C and C-Cl bonds, respectively. Compared to the uncorrected simulations, the AM1-SSGPR-4/MM method lowers the predicted free energy barrier from 28.7 to 11.7 kcal/mol and decreases the reaction free energy from -12.4 to -41.9 kcal/mol, bringing these results into closer agreement with their AI/MM and experimental benchmarks.

Two local minima for structures of [4Fe–4S] clusters obtained with density functional theory methods

[4Fe–4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe–Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe–4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.

Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6).

Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG‡ ≈ 21 kcal·mol-1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF3 or -CHF2 substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.

Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM

Since the design of metal complexes with better biological activities is important, herein a new palladium(II) complex bearing en and acac (en and acac stand for ethylenediamine and acetylacetonato, respectively) as its ligands, [Pd(en)(acac)]NO3 complex, was synthesized and fully characterized. Quantum chemical computations of the palladium(II) complex were done via DFT/B3LYP method. Cytotoxicity activity of the new compound on leukemia cell line (K562) was assessed via MTT method. The findings indicated that the metal complex has remarkable cytotoxic effect than cisplatin. OSIRIS DataWarrior software was employed to calculate in-silico physicochemical and toxicity parameters of the synthesized complex which rendered significant results. To comprehend the interaction type of new metal compound with macromolecules, the in depth investigation of interaction of mentioned complex with CT-DNA and BSA was accomplished by fluorescence, UV-Visible absorption spectroscopy, viscosity measurement, gel electrophoresis, FRET analysis and circular dichroism (CD) spectroscopy. On the other hand, computational molecular docking was carried out and the obtained data demonstrated that H-bond and van der Waals forces are the dominant forces for the binding of the compound to the mentioned biomolecules. Molecular dynamics simulation was also done and confirmed the stability of best docked pose of palladium(II) complex inside DNA or BSA over the time and in presence of water solvent. Also, Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) methodology based on the hybridization of quantum mechanics and molecular mechanics (QM/MM) methodology was accomplished to inquire about binding of Pd(II) complex with DNA or BSA. Communicated by Ramaswamy H. Sarma

Catalytic Mechanism of Human T-Cell Leukemia Virus Type 1 Protease Investigated by Combined QM/MM Molecular Dynamics Simulations.

Combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the catalytic mechanism of human T-cell leukemia virus type 1 (HTLV-1) protease, a retroviral aspartic protease that is a potential therapeutic target for curing HTLV-1-associated diseases. To elucidate the proteolytic cleavage mechanism, we determined the two-dimensional free energy surfaces of the HTLV-1 protease-catalyzed reactions through various possible pathways. The free energy simulations suggest that the catalytic reactions of the HTLV-1 protease occur in the following sequential steps: (1) a proton is transferred from the lytic water to Asp32', followed by the nucleophilic addition of the resulting hydroxyl to the carbonyl carbon of the scissile bond, forming a tetrahedral oxyanion intermediate, and (2) a proton is transferred from Asp32 to the peptide nitrogen of the scissile bond, leading to the spontaneous breakage of the scissile bond. The rate-limiting step of this catalytic process is the proton transfer from Asp32 to the peptide nitrogen of the scissile bond, with a free energy of activation of 21.1 kcal/mol. This free energy barrier is close to the experimentally determined free energy of activation (16.3 kcal/mol) calculated from the measured catalytic rate constant (kcat). This mechanistic study provides detailed dynamic and structural information that will facilitate the design of mechanism-based inhibitors for the treatment of HTLV-1-associated diseases.

Demystifying Solvent Effects on Diels–Alder Reactions in Pure and Mixed Solvents: A Combined Electronic DFT and QM/MM Study

Although solvent effects on chemical reactions in pure solvents are well elucidated, both reaction mechanisms and solvent effects in mixed solvents remain poorly understood. Herein, the free energy profiles and the solute–solvent energy pair distribution of the Diels–Alder reaction in pure water, acetonitrile (ACN), carbon tetrachloride (CTC), and their mixtures ACN-water and ACN-CTC are calculated using the quantum and molecular mechanical (QM/MM) Monte Carlo method. The results show that the presence of solvent can significantly reduce the reaction free energy barrier, and the barrier in the mixed solvent is intermediate between the two pure solvents. Additionally, the free energy decomposition analysis demonstrated that the QM region dominates the reaction free energy. Electronic DFT calculations are employed to delineate the interactions between reactants and solvent molecules in pure and mixed solvents, with a particular focus on the role of electrostatic potential characteristics and an independent gradient model based on Hirshfeld partition. By rigorously analyzing these interactions, this study demystifies the mechanism underlying the phenomenon of preferential solvation and competition for reacting sites in mixed solvents, which alters the microenvironment of the solute.

Histidine oxidation in lytic polysaccharide monooxygenase

The lytic polysaccharide monooxygenases (LPMOs) comprise a super-family of copper enzymes that boost the depolymerisation of polysaccharides by oxidatively disrupting the glycosidic bonds connecting the sugar units. Industrial use of LPMOs for cellulose depolymerisation has already begun but is still far from reaching its full potential. One issue is that the LPMOs self-oxidise and thereby deactivate. The mechanism of this self-oxidation is unknown, but histidine residues coordinating to the copper atom are the most susceptible. An unusual methyl modification of the NE2 atom in one of the coordinating histidine residues has been proposed to have a protective role. Furthermore, substrate binding is also known to reduce oxidative damage. We here for the first time investigate the mechanism of histidine oxidation with combined quantum and molecular mechanical (QM/MM) calculations, with outset in intermediates previously shown to form from a reaction with peroxide and a reduced LPMO. We show that an intermediate with a [Cu–O]+ moiety is sufficiently potent to oxidise the nearest C–H bond on both histidine residues, but methylation of the NE2 atom of His-1 increases the reaction barrier of this reaction. The substrate further increases the activation barrier. We also investigate a [Cu–OH]2+ intermediate with a deprotonated tyrosine radical. This intermediate was previously proposed to have a protective role, and we also find it to have higher barriers than the corresponding a [Cu–O]+ intermediate.Graphical abstract

Effect of aggregation on thermally activated delayed fluorescence and ultralong organic phosphorescence: QM/MM study

Aggregation-induced thermally activated delayed fluorescence (TADF) phenomena have attracted extensive attention recently. In this paper, several theoretical models including monomer, dimer, and complex are used for the explanation of the luminescent properties of (R)-5-(9H-carbazol-9-yl)-2-(1,2,3,4-tetrahydronaphthalen-1-yl)isoindoline-1,3-dione ((R)-ImNCz), which was recently reported [Chemical Engineering Journal 418 129167 (2021)]. The polarizable continuum model (PCM) and the combined quantum mechanics and molecular mechanics (QM/MM) method are adopted in simulation of the property of the molecule in the gas phase, solvated in acetonitrile and in aggregation states. It is found that large spin–orbit coupling (SOC) constants and a smaller energy gap between the first singlet excited state and the first triplet excited state (ΔE st) in prism-like single crystals (SCp-form) are responsible for the TADF of (R)-lmNCz, while no TADF is found in block-like single crystals (SCb-form) with a larger ΔE st. The multiple ultralong phosphorescence (UOP) peaks in the spectrum are of complex origins, and they are related not only to ImNCz but also to a minor amount of impurities (ImNBd) in the crystal prepared in the laboratory. The dimer has similar phosphorescence emission wavelengths to the (R)-lmNCz-SCp monomers. The complex composed of (R)-lmNCz and (R)-lmNBd contributes to the phosphorescent emission peak at about 600 nm, and the phosphorescent emission peak at about 650 nm is generated by (R)-lmNBd. This indicates that the impurity could also contribute to emission in molecular crystals. The present calculations clarify the relationship between the molecular aggregation and the light-emitting properties of the TADF emitters and will therefore be helpful for the design of potentially more useful TADF emitters.

Theoretical exploration of the bromine substitution effect and hydrostatic pressure responsive mechanism for room temperature phosphorescence.

Stimulus-responsive organic room temperature phosphorescence (RTP) materials with long lifetimes, high efficiencies and tunable emission properties have broad applications. However, the amounts and species of efficient RTP materials are far from meeting the requirements and the inner stimulus-responsive mechanisms are unclear. Therefore, developing efficient stimulus-responsive RTP materials is highly desired and the relationship between the molecular structures and luminescent properties of RTP materials needs to be clarified. Based on this point, the influences of different substitution sites of Br on the luminescent properties of RTP molecules are studied by the combined quantum mechanics and molecular mechanics (QM/MM) coupled with thermal vibration correlation function (TVCF) theory. Moreover, the hydrostatic pressure effect on the efficiencies and lifetimes is explored and the inner mechanism is illustrated. The results show that, for the exciton conversion process, the o-substitution molecule possesses the largest spin-orbit coupling (SOC) value (〈S1|Ĥso|T1〉) in the intersystem crossing (ISC) process and this is conducive to the accumulation of triplet excitons. However, for the energy consumption process, the large SOC value (〈S0|Ĥso|T1〉) for the p-substitution molecule brings a fast non-radiative decay rate, and the small SOC value for the m-substitution molecule generates a decreased non-radiative decay rate which is helpful for realizing long lifetime emission. Keeping with this perspective, the conflict between high exciton utilization and long RTP emission needs to be balanced rather than enhancing the SOC effect by simply adding heavy atoms in RTP systems. Through regulating the molecular stacking modes by the hydrostatic pressure effect, the inner stimulus-responsive mechanism is revealed. The data of 〈S1|Ĥso|T1〉 in the ISC process remain almost unchanged, while 〈S0|Ĥso|T1〉 values and transition dipole moments are sensitive to the hydrostatic pressure. Under 1 GPa, the RTP molecule achieves a maximum efficiency (81.17%) and long lifetime (2.72 ms) with the smallest SOC and decreased non-radiative decay rate. To our knowledge, this is the first time that the hydrostatic pressure responsive mechanism for RTP molecules is revealed from a theoretical perspective, and the relationships between molecular structures and luminescent properties are detected. Our work could facilitate the development of high performance RTP molecules and expand their applications in multilevel information encryption.

Theoretical insights on the luminescent mechanism of a highly efficient green-activated delayed fluorescence emitter using the QM/MM method

The solid-state effect plays an important role in excited-state dynamics and luminescence properties of thermally activated delayed fluorescence (TADF) materials. Here, the luminescent mechanism of two novel TADF emitters, PPZTPI and PPZPPI, with aggregation-induced emission (AIE) features are theoretically studied based on the first-principles calculations. The polarisable continuum model (PCM) and the combined quantum mechanics and molecular mechanics (QM/MM) method are used to simulate the solvent environments in toluene and the solid-state effects, respectively. Our results show that both PPZTPI and PPZPPI exhibit excellent TADF and AIE properties with similar but not identical luminescence mechanisms. In the solid state, the delayed fluorescence emission of the two molecules mainly depends on the two-step reverse intersystem crossing process. The molecular radiation rates increase by 1–2 orders of magnitude due to the enhancement of intermolecular interactions in the aggregation. For PPZTPI, the solid-state environment exerts a greater influence on the molecular geometry and electronic structure, non-radiative transitions, excited state dynamics, and emission mechanism due to the substitution of tert-butyl groups and their induced steric hindrance effects. Our theoretical study reasonably elucidates the experimental results and provides valuable information for designing high-efficient AIE-TADF emitters.

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron-sulfur clusters with 1-4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400-500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P1+/PN redox potential is nearly the same independently of whether P1+ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E0 state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E0-E4 states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E4-E8) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E0/E1 couple.

Exploration on dual emission mechanism of CPzP and CPzPO with thermally activated delayed fluorescence

ABSTRACT Thermally activated delayed fluorescence (TADF) molecules with dual emission have attracted extensive attention recently. However, the dual emission mechanism is complex and difficult to be studied especially in solid state. In this paper, asymmetrical diphenylketone derivatives CPzP and CPzPO are investigated in both benzene and in aggregation state with polarisable continuum model (PCM) and combined quantum mechanics and molecular mechanics (QM/MM) method respectively. It is found that there are both quasi-axial (ax) and quasi-equatorial (eq) conformations for CPzP and CPzPO in benzene. The ax conformation is responsible for the high energy band emission, while the low energy band emission is contributed by eq conformations. The dimers with intermolecular hydrogen bond have similar emission wavelengths with monomers. The small energy gap between the first singlet excited state and the first triplet excited state as well as large reverse intersystem crossing rate in eq conformations confirms  the generation of TADF in eq conformation, which agree with experimental results that the low energy band emission is TADF. Our calculation results revealed the dual emission mechanism of two TADF molecules, which would favor the understanding of light emitting properties and the design of new type dual emission TADF emitters.

Theoretical study on the origin of the dual phosphorescence emission from organic aggregates at room temperature

Purely organic materials with dual room temperature phosphorescence (RTP) phenomenon were reported recently, but the underlying mechanism was still ambiguous. Herein, we revealed the source of dual RTP emission, taking CzDPS crystal as prototype, by using hybrid quantum mechanics and molecular mechanics (QM/MM) coupled with the thermal vibration correlation function rate theory. Theoretical calculations verified that the emission lifetimes are prolonged from 70 ms in the higher triplet state T2 to 216 ms in the lowest triplet state T1, which is well consistent with the increase of RTP lifetimes from 74 ms for the peak at 465 nm to 627 ms for the band at 565 nm. This is because the radiative and nonradiative decay rates are larger for T2 → S0 than that of T1 → S0, which was mainly contributed by the synergistic effect of the increase of spin–orbit coupling and excitation energy, as well as the decrease of reorganization energy. Moreover, the simulated RTP spectra agree well with the experimental ones, including the emission position and profiles. Therefore, the upper-lying triplet excited states are responsible for the dual RTP in CzDPS crystal. This work could contribute to further understanding on the multiple luminescence of organic aggregates.