Molecular and crystal structures of six poly(arylsulfinyl)- and poly(arylsulfanyl)ferrocenes.

Starting from (p-tolylsulfinyl)ferrocene (1), a mixture of the complete series [CpFe{C5H5-n(SOTol-p)n}] (n = 2-4) (2-4) in all regioisomers was obtained. After chromatographic separation, crystals of 1,2-bis[(4-methylbenzene)sulfinyl]ferrocene, 2a, and 1,3-bis[(4-methylbenzene)sulfinyl]ferrocene, 2b, both [Fe(C5H5)(C19H17O2S2)], as well as of 1,2,3-tris[(4-methylbenzene)sulfinyl]ferrocene, [Fe(C5H5)(C26H23O3S3)], 3a, and 1,2,3,4-tetrakis[(4-methylbenzene)sulfinyl]ferrocene ethyl acetate 0.75-solvate, [Fe(C5H5)(C33H29O4S4)]·0.75C4H8O2, 4, could be isolated. Their molecular and crystal structures are compared with each other and also with the so far unreported structures of related 1,2-bis(phenylsulfanyl)ferrocene, [Fe(C5H5)(C17H13S2)], 5, and 1,2,3,4-tetrakis(phenylsulfanyl)ferrocene, [Fe(C5H5)(C29H21S4)], 6. In all the sulfinyl structures, the O atoms of the S=O groups are in equatorial positions, except for that in tetrasubstituted 4. All the arene rings of these compounds (except for one ring in 4) are in axial positions directed away from the Fe atom, mostly in a near perpendicular orientation with respect to the plane of the cyclopentadienyl ring. The main intermolecular interactions in the crystals are C-H...H-C, C-H...π and C-H...O, while C-H...S interactions are much less important, except for tetrasulfanyl compound 6. π-π interactions (intramolecular) are only important in compound 3a. Hirshfeld analysis shows that dispersion terms are dominant for the interaction energies of all six compounds. In general, the calculated total interaction energies increase with increasing number of substituents and are higher for the sulfinyl than for the sulfanyl groups.

Crystal structure-mechanical property relationship in succinic acid and L- alanine probed by nanoindentation.

Establishing structure-mechanical property relationships is crucial for understanding and engineering the performance of pharmaceutical molecular crystals. In this study, we employed nanoindentation, a powerful technique that can probe mechanical properties at the nanoscale, to investigate the hardness and elastic modulus of single crystals of succinic acid and L-alanine. Nanoindentation results reveal distinct mechanical behaviors between the two compounds, with L-alanine exhibiting significantly higher hardness and elastic modulus compared to succinic acid. These differences are attributed to the underlying variations in molecular crystal structures - the three-dimensional bonding network and high intermolecular interaction energies of L-alanine molecules leads to its stiffness compared to the layered and weakly bonded crystal structure of succinic acid. Furthermore, the anisotropic nature of succinic acid is reflected in the directional dependence of the mechanical responses where it has been found that the (111) plane is more resistant to indentation than (100). By directly correlating the nanomechanical properties obtained from nanoindentation with the detailed crystal structures, this study provides important insights into how differences in molecular arrangements can translate into different macroscopic mechanical performance. These findings have implications on the selection of molecular crystals for optimized drug manufacturability.

Control ultrafiltration membrane fouling in Chlorella-laden water treatment by integrated heat-activated peroxydisulfate pre-oxidation and coagulation treatment.

The membrane fouling induced by algal extracellular organic matter (EOM) remain a bottleneck in restricting ultrafiltration (UF) application during harmful algal-water treatment. In current study, the application of heat-activated peroxydisulfate (PMS) and coagulation (Aluminum chlorohydrate, PACI) on membrane fouling behavior during Chlorella-laden water treatment was investigated. The membrane fouling mechanism was analyzed using the extended Derjaguin-Landau-Verwey-Over-beek (XDLVO) theory. The results revealed that separated heat-activated PMS could enhance the filtration flux of EOM at high PMS does >0.2 mM, whereas the membrane fouling was further alleviated by combined heat-activated PMS (0.2-1.0 mM) and PACI (20 mg/L) treatment, especially at low PMS dose. Combined heat-activated PMS and PACI pretreatment could effectively increase the adhesive repulsion between membrane and foulants and reduce the cohesion free energies between organic foulants than those by separated heat-activated PMS treatment, making the initial filtration flux reduced and the cake layer looser. Moreover, the organic foulants of proteins, polysaccharides, and humic-like organics were removed. Cake formation was the major fouling mechanism when EOM was treated with/without separated heat-activated PMS treatment, whereas the membrane fouling mechanism was changed from cake layer formation to pore blocking after combined heat-activated PMS and PACI treatment. Overall, this research provided a feasible method in membrane fouling control during Chlorella -laden water treatment.

Revisiting the Most Stable Structures of the Benzene Dimer.

The benzene dimer (BD) is an archetypal model of π∙∙∙π and C-H∙∙∙π noncovalent interactions as they occur in its cofacial and perpendicular arrangements, respectively. The enthalpic stabilization of the related BD structures has been debated for a long time and is revisited here. The revisit is based on results of computations that apply the coupled-cluster theory with singles, doubles and perturbative triples [CCSD(T)] together with large basis sets and extrapolate results to the complete basis set (CBS) limit in order to accurately characterize the three most important stationary points of the intermolecular interaction energy (ΔE) surface of the BD, which correspond to the tilted T-shaped (TT), fully symmetric T-shaped (FT) and slipped-parallel (SP) structures. In the optimal geometries obtained by searching extensive sets of the CCSD(T)/CBS ΔE data of the TT, FT and SP arrangements, the resulting ΔE values were -11.84, -11.34 and -11.21 kJ/mol, respectively. The intrinsic strength of the intermolecular bonding in these configurations was evaluated by analyzing the distance dependence of the CCSD(T)/CBS ΔE data over wide ranges of intermonomer separations. In this way, regions of the relative distances that favor BD structures with either π∙∙∙π or C-H∙∙∙π interactions were found and discussed in a broader context.

Theoretical Insight into Complexation Between Cyclocarbons and C60 Fullerene.

This work conducts a comprehensive theoretical study on the non-covalent complexation between cyclocarbons and C60 fullerene for the first time. The binding energy between cyclocarbons and C60 fullerene is significantly stronger than that between two C18 or two C60 fullerenes, indicating a particularly strong affinity. The cyclocarbons and C60 fullerene can spontaneously assemble into complexes in the gas phase at room temperature, and the hydrophobic effect caused by the solvent environment can promote this binding. The binding strength with C60 fullerene increases almost linearly with the increase of cyclocarbon size, and the C34@C60 dimer exhibits a perfect nano-Saturn structure. As the ring size increases, the angle between the two cyclocarbons of the 2 : 1 trimers formed by cyclocarbons and C60 fullerene gradually decreases. In C60@2 C34 trimer, the fullerene is symmetrically surrounded by two cyclocarbons. The results on the trimers formed by cyclocarbon and C60 fullerenes in a 1 : 2 ratio showed when the cyclocarbon sandwiched between two fullerenes is not quite large, the trimers exhibit an ideal dumbbell-like structure, and the presence of the first fullerene has a significant synergistic effect on the binding of the second one. The cyclocarbon greatly promotes the dimerization of fullerenes, which acted as a "molecular glue".

The packing fraction of the oxygen sublattice: its impact on the heat of mixing.

The heat of mixing of some petrological relevant substitutions (i.e., Mg-Al, Si-Al, Mg-Ti, Mg-Ca, and Mg-Fe) was investigated systematically in silicates, titanates, tungstates, carbonates, oxides, hydroxides, and sulphates by density functional theory calculations (e.g., melilite, chlorite, biotite, brucite, cordierite, amphibole, talc, pseudobrookite, pyroxene, olivine, wadsleyite, ilmenite, MgWO4, ringwoodite (spinel), perovskite, pyrope-grossular, magnesite-calcite, MgO-CaO, anhydrous and different hydrated MgSO4). A specific substitution is characterised by different microscopic interaction energies in different minerals, e.g., the octahedral Mg-Al exchange on a single crystallographic site in pyroxene has a microscopic interaction energy that is more than twice compared to that in biotite. A comparative investigation of the heat of mixing using microscopic interaction energies on a single crystallographic site has the advantage that they are not influenced by cation ordering. They could be successfully correlated with the stiffnesses of the minerals, which in turn were scaled to the oxygen packing fraction, a parameter that is easily available for poorly investigated minerals. With this information, the interaction energies of a certain substitution can be transferred from minerals where they are well-known to mineral groups where they are less- or unknown. Using the cross-site terms and the microscopic interaction energies, the macroscopic interaction energies of the coupled substitution, e.g., Mg + Si = Al + Al, of biotite and pyroxene were calculated, which are, however, affected by cation ordering and different degrees of local charge balance, for which appropriate models are necessary. Supplementary Information: The online version contains supplementary material available at 10.1007/s00269-024-01277-6.

Comparison of Phosphogypsum-Steel Slag-Based cement and Portland cement for stabilization of heavy metals in oil-based drillings cuttings.

This research compared Portland cement and Phosphogypsum-Steel Slag-Based (PSSB) cement in terms of their capabilities to stabilize heavy metals (specifically lead and nickel) in Oil-Based Drill Cuttings (OBDC). In the experimental section, the qualitative analysis of heavy metal constituents in OBDC was captured by X-ray Photoelectron Spectroscopy (XPS). Additionally, an acetic acid leaching test was implemented for the heavy metal leaching concentration to evaluate the ceramsite stabilization effect on OBDC. In the simulation phase, cement models, heavy metal ion models, and stabilization models were constructed to explore the stabilization mechanism of heavy metals. Results demonstrated that PSSB cement exhibits superior stabilization effects on OBDC compared to Portland cement. Flame Atomic Absorption Spectrophotometry (FAAS) tests showed that PSSB cement reduced Ni and Pb leaching by 21.87 % and 47.32 %, respectively, compared to Portland cement. In PSSB cement, the diffusion coefficients for Ni and Pb ions were observed to decrease by 42.92 % and 79.63 %, respectively, as revealed through Mean Square Displacement (MSD) analysis. The cohesive energy of PSSB cement was 76.73 % lower than that of Portland cement, and its interaction energies for stabilizing Ni and Pb ions were 59.43 % and 76.22 % lower, respectively, demonstrating greater stability and efficiency in metal stabilization. PSSB cement exhibited lower heavy metal concentration and better structural stability than Portland cement.

Interaction energy flow paths analysis of PMSG-based wind power integrated systems during LVRT and its parameter adjustment strategy.

To solve the problem of oscillation instability in permanent magnetic synchronous generator (PMSG)-based wind power connected systems during low-voltage ride through (LVRT) process, a parameter adjustment strategy based on interaction energy path optimization is proposed in this paper. Firstly, a modular state-space model of PMSG under fault transient conditions is constructed, and the system is divided into five subsystems. Then, the dynamic energy function of subsystems reflecting the oscillation stability of the system is derived. Based on that, the dynamic energy flow path is described considering the introduction of LVRT control. On this basis, the interaction energy between LVRT control links and subsystems is analyzed, and the coupling mechanism of voltage support and damping characteristics in the LVRT process is explained. Further, aiming at the optimal change rate of the total interaction energy in the LVRT process, the adjustment strategy of LVRT control parameters is constructed to meet voltage and damping requirements. Finally, a PMSG-connected system model is built on the MATLAB/Simulink platform to verify the effectiveness of the adjustment strategy. The results show that the proposed method can effectively improve the damping level under the fault transient condition, as well as supporting system voltage.

ProBAN: Neural network algorithm for predicting binding affinity in protein-protein complexes.

Determining binding affinities in protein-protein and protein-peptide complexes is a challenging task that directly impacts the development of peptide and protein pharmaceuticals. Although several models have been proposed to predict the value of the dissociation constant and the Gibbs free energy, they are currently not capable of making stable predictions with high accuracy, in particular for complexes consisting of more than two molecules. In this work, we present ProBAN, a new method for predicting binding affinity in protein-protein complexes based on a deep convolutional neural network. Prediction is carried out for the spatial structures of complexes, presented in the format of a 4D tensor, which includes information about the location of atoms and their abilities to participate in various types of interactions realized in protein-protein and protein-peptide complexes. The effectiveness of the model was assessed both on an internal test data set containing complexes consisting of three or more molecules, as well as on an external test for the PPI-Affinity service. As a result, we managed to achieve the best prediction quality on these data sets among all the analyzed models: on the internal test, Pearson correlation R = 0.6, MAE = 1.60, on the external test, R = 0.55, MAE = 1.75. The open-source code, the trained ProBAN model, and the collected dataset are freely available at the following link https://github.com/EABogdanova/ProBAN.

Study of Cellulose Dissolution in ZnO/NaOH/Water Solvent Solution and Its Temperature-Dependent Effect Using Molecular Dynamics Simulation.

Cellulose is a biopolymer with numerous advantages that make it an ecological, economical, and high-performing choice for various applications. To fully exploit the potential of cellulose, it is often necessary to dissolve it, which poses a current challenge. The aqueous zinc oxide/sodium hydroxide (ZnO/NaOH/Water) system is a preferred solvent for its rapid dissolution, non-toxicity, low cost, and environmentally friendly nature. In this context, the behavior of cellulose chains in the aqueous solution of ZnO/NaOH and the impact of temperature on the solubility of this polymer were examined through a molecular dynamics simulation. The analysis of the root means square deviation (RMSD), interaction energy, hydrogen bond curves, and radial distribution function revealed that cellulose is insoluble in the ZnO/NaOH solvent at room temperature (T = 298 K). Decreasing the temperature in the range of 273 K to 268 K led to a geometric deformation of cellulose chains, accompanied by a decrease in the number of interchain hydrogen bonds over the simulation time, thus confirming the solubility of cellulose in this system between T = 273 K and T = 268 K.

The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation.

The enhancement of the peptide bond order by a resonance in the lone pair of N and the π-bond of CO is analyzed. A decomposition of the bond order in terms of localized molecular orbitals is developed and applied to the peptide bond. A combination of two rotations of hybrid orbitals is proposed to improve the boundary treatment in the fragment molecular orbital method. The developed approach is applied to peptide bonds, and it is found crucial to retain the π orbital in the variational space of both fragments across the boundary. The interaction energies between conventional amino acid residues in Trp-cage (1L2Y) are discussed.

Hydrocarbon Transportation in Heterogeneous Shale Pores by Molecular Dynamic Simulation.

Shale oil in China is widely distributed and has enormous resource potential. The pores of shale are at the nanoscale, and traditional research methods encounter difficulty in accurately describing the fluid flow mechanism, which has become a bottleneck restricting the industrial development of shale oil in China. To clarify the distribution and migration laws of fluid microstructure in shale nanopores, we constructed a heterogeneous inorganic composite shale model and explored the fluid behavior in different regions of heterogeneous surfaces. The results revealed the adsorption capacity for alkanes in the quartz region was stronger than that in the illite region. When the aperture was small, solid-liquid interactions dominated; as the aperture increased, the bulk fluid achieved a more uniform and higher flow rate. Under conditions of small aperture/low temperature/low pressure gradient, the quartz region maintained a negative slip boundary. Illite was more hydrophilic than quartz; when the water content was low, water molecules formed a "liquid film" on the illite surface, and the oil flux percentages in the illite and quartz regions were 87% and 99%, respectively. At 50% water content, the adsorbed water in the illite region reached saturation, the quartz region remained unsaturated, and the difference in the oil flux percentage of the two regions decreased. At 70% water content, the adsorbed water in the two regions reached a fully saturated state, and a layered structure of "water-two-phase region-water" was formed in the heterogeneous nanopore. This study is of great significance for understanding the occurrence characteristics and flow mechanism of shale oil within inorganic nanopores.

Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro.

Here, we introduce the use of ANI-ML potentials as a rescoring function in the host-guest interaction in molecular docking. Our results show that the "docking power" of ANI potentials can compete with the current scoring functions at the same level of computational cost. Benchmarking studies on CASF-2016 dataset showed that ANI is ranked in the top 5 scoring functions among the other 34 tested. In particular, the ANI predicted interaction energies when used in conjunction with GOLD-PLP scoring function can boost the top ranked solution to be the closest to the x-ray structure. Rapid and accurate calculation of interaction energies between ligand and protein also enables screening of millions of drug candidates/docking poses. Using a unique protocol in which docking by GOLD-PLP, rescoring by ANI-ML potentials and extensive MD simulations along with end state free energy methods are combined, we have screened FDA approved drugs against the SARS-CoV-2 main protease (Mpro). The top six drug molecules suggested by the consensus of these free energy methods have already been in clinical trials or proposed as potential drug molecules in previous theoretical and experimental studies, approving the validity and the power of accuracy in our screening method.

The Pivotal Distinction between Antagonists' and Agonists' Binding into Dopamine D4 Receptor-MD and FMO/PIEDA Studies.

The dopamine D4 receptor (D4R) is a promising therapeutic target in widespread diseases, and the search for novel agonists and antagonists appears to be clinically relevant. The mechanism of binding to the receptor (R) for antagonists and agonists varies. In the present study, we conducted an in-depth computational study, teasing out key similarities and differences in binding modes, complex dynamics, and binding energies for D4R agonists and antagonists. The dynamic network method was applied to investigate the communication paths between the ligand (L) and G-protein binding site (GBS) of human D4R. Finally, the fragment molecular orbitals with pair interaction energy decomposition analysis (FMO/PIEDA) scheme was used to estimate the binding energies of L-R complexes. We found that a strong salt bridge with D3.32 initiates the inhibition of the dopamine D4 receptor. This interaction also occurs in the binding of agonists, but the change in the receptor conformation to the active state starts with interaction with cysteine C3.36. Such a mechanism may arise in the case of agonists unable to form a hydrogen bond with the serine S5.46, considered, so far, to be crucial in the activation of GPCRs. The energy calculations using the FMO/PIEDA method indicate that antagonists show higher residue occupancy of the receptor binding site than agonists, suggesting they could form relatively more stable complexes. Additionally, antagonists were characterized by repulsive interactions with S5.46 distinguishing them from agonists.

Sensing potential of C6N8 for ammonia (NH3) and nitrogen triflouride (NF3): A DFT study.

The detection of toxic gases (NH3 and NF3) in regulating and monitoring air quality in the atmosphere has drawn a lot of attention. Herein, we explored a novel material (C6N8) for the detection of the important but toxic gases (NH3 and NF3). We investigated the interactions of the NH3 and NF3 with C6N8 through DFT at B3LYP, ωB97XD, and non-DFT M06-2X. Counterpoise interaction energy values (Eint. cp.) of NH3@C6N8 and NF3@C6N8 are -0.45 eV and -3.51 eV (for B3LYP), -0.42 eV and 2.11 eV (for ωB97XD) and -0.44 eV and -3.41eV (for M06-2X), respectively. Complexes having the most stable configurations were then subjected to further analyses including frontier molecular orbitals, H-L gap, and conductivity of complexes. An increase in the H-L gap in complexes (NH3@C6N8 and NF3@C6N8) is observed. The conductivity of NH3@C6N8 and NF3@C6N8 decreases as compared to C6N8. A considerable change in dipole moment was seen in C6N8 before and after complex formation. This is because of the shifting of charge between C6N8 and gases (NH3 and NF3). CHELPG and NBO charge analysis were used to evaluate the amount of charge transfer between C6N8 and gases. These analyses demonstrate that NH3 and NF3 withdraw electron density from C6N8. It was found that NH3 tends to be physically adsorbed on C6N8 while NF3 adsorbs chemically on C6N8. NCI and QTAIM analyses were performed to investigate the kind of interactions between the surface (C6N8) and gases (NH3 and NF3). Furthermore, the recovery time of NH3@C6N8 and NF3@C6N8 shows that C6N8 can be a better choice for sensing NH3 and NF3 gases.

Reliable Dimerization Energies for Modeling of Supramolecular Junctions.

Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed "silver standard" approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed "ωB97X-3c/vDZP" by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes.

Revealing the contradiction between DLVO/XDLVO theory and membrane fouling propensity for oil-in-water emulsion separation.

Oil fouling is the crucial issue for the separation of oil-in-water emulsion by membrane technology. The latest research found that the membrane fouling rate was opposite to the widely used theoretical prediction by Derjaguin-Landau-Verwey-Overbeek (DLVO) or extended DLVO (XDLVO) theory. To interpret the contradiction, the molecular dynamics was adopted to explore the molecular behavior of oil and emulsifier (Tween 80) at membrane interface with the assistance of DLVO/XDLVO theory and membrane fouling models. The decreased flux attenuation and fitting of fouling models proved that the existence of Tween 80 effectively alleviated membrane fouling. Conversely, DLVO/XDLVO theory predicted that the membrane fouling should be exacerbated with the increase of Tween 80 concentration in O/W emulsion. This contradiction originated from the different interaction energy between oil/Tween 80 molecules and polyether sulfone (PES) membrane. The favorable free energy of Tween 80 was resulted from the sulfuryl groups in PES and hydrogen bonds (O-H…O) formation further strengthened the interaction. Therefore, Tween 80 could preferentially adsorb on membrane surface and form an isolation layer by demulsification and steric hindrance and resist the aggregation of oil, which effectively alleviated membrane fouling. This study provided a new insight in the interpretation of interaction in O/W emulsion.

Interfacial residues in protein-protein complexes are in the eyes of the beholder.

Interactions between proteins are vital in almost all biological processes. The characterization of protein-protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein-protein complex are assumed to have the following two properties: (a) they always interact with a residue of a partner protein, which forms the basis for distance-based interface residue identification methods, and (b) they are solvent-exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)-based methods. The study interrogates this popular assumption by recognizing interface residues in protein-protein complexes through these two methods. The results show that a few residues are identified uniquely by each method, and the extent of conservation, propensities, and their contribution to the stability of protein-protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics, and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics, and function of protein-protein complexes are identified in a complementary manner.

Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome.

Cyanobacteriochromes (CBCRs) are linear tetrapyrrole bilin-binding photoreceptors of cyanobacteria that exhibit high spectral diversity, gaining attention in optogenetics and bioimaging applications. Several engineering studies on CBCRs were attempted, especially for designing near-infrared (NIR) fluorescent proteins with longer fluorescence wavelengths. However, despite continuous efforts, a key component regulating fluorescence emission property in CBCRs is still poorly understood. As a model system, we focused on red/green CBCR Slr1393g3, from the unicellular cyanobacterium Synechocystis sp. PCC 6803 to engineer Pr to get far-red light-emitting property. Energy profiling and pairwise structural comparison of Slr1393g3 variants effectively reveal the mutations that are critical to the fluorescence changes. H497 seems to play a key role in stabilizing the chromophore environment, especially the α3 helix, while H495, T499, and Q502 are potential key residues determining fluorescence emission peak wavelength. We also found that mutations of α2 and α4 helical regions are closely related to the chromophore binding stability and likely affect fluorescence properties. Taken together, our computational analysis suggests that the fluorescence of Slr1393g3 is mainly controlled by the stabilization of the chromophore binding pocket. The predicted key residues potentially regulating the fluorescence emission property of a red/green CBCR will be advantageous for designing improved NIR fluorescent protein when combined with in vitro molecular evolution approaches.

Molecular dynamics simulation of the interaction between monofluoronitrobenzene and Ti electrode.

In the process of degradation of aqueous fluoro-nitrobenzene (FNB) solution by titanium (Ti) electrode, the interaction between aqueous FNB solution and Ti electrode has an important impact on the performance and catalytic performance of electrode materials. The interaction involves complex physical, chemical and physical chemical processes, however, the mechanism of action is still unclear. In this study, Materials Studio software was used to design and construct molecular models of the interactions between aqueous FNB (p-, m-, o-FNB) solutions and Ti electrode, and molecular dynamics (MD) simulation was carried out in the absence of applied electric field and external electric field of 0.02 V/Å, respectively. Density functional theory (DFT) method was used to calculate the frontier molecular orbitals of three FNB molecules. Based on the calculation and analysis of the interaction energy (ΔE), diffusion coefficient (D) and radial distribution function (RDF), the interaction mechanism was discussed. It provides a theoretical basis for further research and development of Ti electrode degradation of fluorine compounds. The results showed that the order of ΔE between the three different aqueous FNB solutions and Ti surface is m-FNB > p-FNB > o-FNB when there is no external electric field. Under electric field of 0.02 V/Å, the order is p-FNB > m-FNB > o-FNB. The substitution position of F has an important effect on the HOMO of the nitro group and the LUMO of C-H in the three FNB molecules, and also affects the chemical reaction activity. In the model system, the diffusivity of different FNB solutions with electric field is less than that without electric field. The presence of an external electric field makes the diffusion of water and FNB molecules more orderly. The analysis results of RDF show that the bonding interactions between different FNB molecules and Ti surface is not much different before 3.5 Å, and all of them are weak. At about 8 Å, FNB molecule forms a non-bond with Ti electrode. ΔE, D and RDF of the model system can be changed by applying a certain external electric field, and the results are in better agreement with the experimental results.