Finite temperature string by K-means clustering sampling with order parameters as collective variables for molecular crystals: application to polymorphic transformation between ß-CL-20 and ε-CL-20.

Polymorphic transformation of molecular crystals is a fundamental phase transition process, and it is important practically in the chemical, material, biopharmaceutical, and energy storage industries. However, understanding of the transformation mechanism at the molecular level is poor due to the extreme simulating challenges in enhanced sampling and formulating order parameters (OPs) as the collective variables that can distinguish polymorphs with quite similar and complicated structures so as to describe the reaction coordinate. In this work, two kinds of OPs for CL-20 were constructed by the bond distances, bond orientations and relative orientations. A K-means clustering algorithm based on the Euclidean distance and sample weight was used to smooth the initial finite temperature string (FTS), and the minimum free energy path connecting ß-CL-20 and ε-CL-20 was sketched by the string method in collective variables, and the free energy profile along the path and the nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations. In comparison with the average-based sampling, the K-means clustering algorithm provided an improved convergence rate of FTS. The simulation of transformation was independent of OP types but was affected greatly by finite-size effects. A surface-mediated local nucleation mechanism was confirmed and the configuration located at the shoulder of potential of mean force, rather than overall maximum, was confirmed to be the critical nucleus formed by the cooperative effect of the intermolecular interactions. This work provides an effective way to explore the polymorphic transformation of caged molecular crystals at the molecular level.

Multi-aspect and comprehensive atomic insight: the whole process of thermolysis of HMX/Poly-NIMMO-based plastic bonded explosive.

Based on the reactive molecular dynamics, the whole process of thermolysis of HMX/Poly-NIMMO-based PBX was studied in detail at the micro scale, which provided a novel atomic insight into the thermolysis mechanism of HMX/Poly-NIMMO. Further, it was compared with the HMX single substance system to explore the influence of binder on thermolysis of HMX. According to the findings, the activation energy required by pyrolysis of HMX in the mixed system is much less than that required by the pure HMX system at both phases. From the point of view of reaction energy, poly-NIMMO promoted the thermolysis of HMX. Especially, the mechanism analysis confirmed this point. The nitro and hydroxyl groups detached from Poly-NIMMO will react with HMX, and the generated HNO2 will further accelerate the decomposition process of nitrogen heterocycles. In addition, the number of the final products H2O and H2 in the two-component system increased greatly, but the number of CO2 and N2 molecules had not changed much, and C clusters were formed in the system. The evolution trend of bond number further verified the above analysis. While the maximum cluster number does drop with increasing temperature at first, after a particular temperature threshold is reached, it remains unchanged. In a nutshell, poly-NIMMO will hasten HMX's thermolysis and reduce the system's stability when subjected to heat.

Experimental and theoretical investigation into the response to shock wave for booster explosives JO9C, JH14, JH6, and insensitive RDX.

In order to reduce the vulnerability, the responses to shock waves for booster explosives JO9C, JH14, JH6, and insensitive RDX were evaluated using shock wave partition loading test. To explain the experimental results, molecular dynamics simulation, intermolecular interaction and bond dissociation energy (BDE), and shock initiation pressures were evaluated using the B3LYP, MP2 (full), and M06-2X methods with the 6-311 + + G(2df,2p) basis set. The order of the responsivity is JO9C > JH14 > JH6 > insensitive RDX. The binding energies follow the order of JH14* ≈ JO9C* < insensitive RDX* < JH6*. The interaction energies and BDEs are in RDX∙∙∙(CH3COOCa)+ > RDX∙∙∙CH3COOH > RDX∙∙∙CH2FCH2F. Thus, it can be inferred that for the RDX-based explosives, the stronger the binding energy, intermolecular interaction, and BDE are, the more insensitive the booster is, and thus, the larger energy has to be consumed to overcome the above three kinds of energies during the initiation process, leading to the smaller energy output and weaker response. However, it should be noted that it is mainly the density and the type of explosive that influence the depth of the dent produced on the steel witness block. The essence of the responses to shock waves is revealed by the reduced density gradient, atoms in molecules, and surface electrostatic potentials. HIGHLIGHTS: • Response of booster to shock wave was evaluated by shock wave partition loading test. • Responsivity to shock wave is explained by binding energy, intermolecular interaction, and BDE. • Shock initiation pressures were evaluated. • Essence of responses to shock wave is revealed by RDG, AIM and ESP.

Ru doped molybdenum-based nanowire arrays for efficient hydrogen evolution over a broad pH range.

Searching and developing earth-abundant electrocatalysts with predominant activity and favorable stability are significant to resolve increasing environmental pollution and serious energy crisis. In this paper, Mo-based nanowire arrays (NWAs) were synthesized on carbon fiber paper (CFP), and then Ru-MoP NWAs/CFP was successfully assembled through impregnation of Ru and phosphorization. The as-obtained Ru-MoP NWAs/CFP exhibited excellent performance over a broad pH range. As a result, overpotentials of 39.0, 49.9, and 67.1 mV were required to reach the current density of 10 mA cm-2 in 0.5 M H2SO4, 1 M KOH, and 1 M PBS, respectively. The outstanding performance of Ru-MoP NWAs/CFP is mainly related to the introduction of Ru and P atoms, which may enhance the conductivity of the catalyst and develop additional HER active sites. Our work may afford a novel designing approach to develop high performance HER electrocatalysts.

Morphology prediction of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) crystal in dimethyl sulfoxide (DMSO) solvent with different models using molecular dynamics simulation.

The interface interaction between DMSO solution and HMX crystal was simulated by molecular dynamics (MD) method, and the morphology of HMX in DMSO solvent was predicted through the occupancy model and attachment energy (AE) model. The intramolecular and intermolecular interactions in HMX crystals were dominated by O···H/H···O contacts, accounting for 63.0%. The S value and the adsorption position of DMSO on different crystal planes of HMX have been compared, which showed that (1 0 - 1) has a deep cavity for the adsorption of solvent molecules. The density of DMSO in the z direction of the different planes showed that (0 1 1) has the largest density peak and (0 2 0) has the smallest density peak. The DMSO solvent had an attraction effect with each crystal plane of HMX. The absolute value of Eint was sorted as follows: (1 1 0) > (1 0 1) > (0 2 0) > (1 0 - 1) > (0 1 1). The DMSO solvent affected the attachment energy of each crystal plane of HMX. In our simulation system, the prediction results of the occupancy model were the most consistent with the experimental values.

Ru doping induces the construction of a unique core-shell microflower self-supporting electrocatalyst for highly efficient overall water splitting.

Since the large reaction energy barrier caused by multi-step electron transfer processes of the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) gravely restricts the practical application of electrocatalytic water splitting, it is urgent to develop a dual-functional electrocatalyst which can effectively reduce the reaction energy barrier and actually speed up the reaction. Herein, the Ru species are doped into the complex of magnetite and FeNi-layered double hydroxide by a one-step oil bath method, and a self-supporting binder-free bifunctional electrocatalyst was synthesized on the surface of iron foam (named Ru-Fe3O4@FeNi-LDH/IF). The unique 3D core-shell microflower structure of Ru-Fe3O4@FeNi-LDH/IF, the combination of active ingredient and conductive substrate, together with the doping of Ru may immensely provide a large number of active sites, adjust the electronic structure, accelerate electron transfer, and thus greatly improve the electrocatalytic activity and durability. It is worth mentioning that when Ru-Fe3O4@FeNi-LDH/IF is used as the anode and cathode for overall water splitting, only 1.52 V battery voltage can generate a current density of 10 mA cm-2, and also maintain a prominent stability for at least 36 hours. This work provides a feasible strategy for heteroatom-doping LDH as a bifunctional electrocatalyst.

A theoretical investigation into the cooperativity effect on the TNT melting point under external electric field.

External electric field has been regarded as an effective tool to induce the variation of melting points of molecular crystals. The melting point of 2,4,6-trinitrotoluene (TNT) was calculated by molecular dynamics simulations under external electric field, and the electric field effects on the cooperativity effects of the ternary (TNT)3 were investigated at the M06-2X/6-311+G(d) and ωB97X-D/6-311++G(2d,p) levels. The results show that the melting points are decreased while the intermolecular interactions are strengthened under the external electric fields, suggesting that the intermolecular interactions cannot be used to explain the decreased melting points. A deduction based on the cooperativity effect is put forward: the enhanced cooperativity effects create the more serious defects in the melting process of the molecular crystal under the external electric fields, and simultaneously the local order parameters are decreased, leading to the decreased melting point. Thus, the cooperativity effect stemmed from the intermolecular C-H∙∙∙O H-bonding interactions controls the change of TNT melting point under the external electric field. Employing the information-theoretic approach (ITA), the origin of the cooperativity effects on the melting points of molecular crystal is revealed. This study opens a new way to challenge the problems involving the melting points for the molecular crystal under the external electric fields. However, note that above deduction needs to be improved; after all, the simple (TNT)3 model cannot replace the crystal structure.

Synthesis of potential Ca-Mg-Al layered double hydroxides coated graphene oxide composites for simultaneous uptake of europium and fulvic acid from wastewater systems.

High background electrolyte and natural organic matter are favorable to migration of hazardous radionuclides in geochemical repository. Herein, Ca-Mg-Al layered double hydroxide coated onto graphene oxide (Ca-Mg-Al LDH/GO) composites were successfully synthesized, characterized and adopted to decontaminate Eu(III) and fulvic acid (FA) under diverse experimental conditions. Diverse concentration gradients and different addition sequences on Eu(III) and FA were also obtained, which revealed different interaction mechanisms. The experimental results displayed that the coexistence of FA and Eu(III) respectively promoted adsorption performance of Eu(III) and FA under the ternary systems. The acquired Ca-Mg-Al LDH/GO composites were adopted to remove Eu(III) and FA, which further illustrated excellent chemo-physical stability and adsorption capacity of 1.12 × 10-3 mol/g and 3.54 × 10-4 mol/g, respectively. The remarkable adsorption performances of Ca-Mg-Al LDH/GO were confirmed through kinetic procedures and depending-temperature isotherms, illustrating that the kinetics processes were simulated using pseudo-second-order pattern, and the adsorption isotherms were splendidly simulated using Langmuir pattern. XPS spectrum analysis revealed that these containing oxygen groups took significant part in the restricting of Eu(III) and FA onto the surfaces of Ca-Mg-Al LDH/GO composites. In view of experimental results, the Ca-Mg-Al LDH/GO composites can be as potential adsorbents with availably recycled reusability for the decontamination of Eu(III) and FA from nuclear fuel partition or nuclear wastewater systems.

External electric field reduces the explosive sensitivity: a theoretical investigation into the hydrogen transference kinetics of the NH2NO2∙∙∙H2O complex.

Controlling the selectivity of detonation initiation reaction to reduce the explosive sensitivity has been a Holy Grail in the field of energetic materials. The effects of the external electric fields on the homolysis of the N-NO2 bond and initiation reaction dynamics of NH2NO2∙∙∙H2O (i.e., intermolecular and 1,3-intramolecular hydrogen transfers) were investigated at the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p)//MP2/6-311++G(2d,p) levels. The results show that the N-NO2 bond is not the "trigger linkage." The notable transiliences of the activation energy of the intermolecular hydrogen transfer are found with the field strength of - 0.012 a.u. along the -x-direction, leading to the conversion of the main reaction between the intermolecular and 1,3-intramolecular hydrogen transference. The activation energies of two kinds of the hydrogen transferences are increased under the external electric fields along the -y-direction. In particular, due to the conversion of the main reaction, the activation energies of the overall reaction are increased significantly along the -x-direction, leading to the significant reduced explosive sensitivities. Therefore, by controlling the field strengths and orientations between the "reaction axis" and external electric field along the y- and x-directions, the selectivity of the initiation reaction could be controlled and the explosive sensitivity could be reduced. Employing AIM (atoms in molecules) and surface electrostatic potentials, the origin of the control of reaction selectivity and the reduction of sensitivity is revealed. This work is of great significance to the improvement of the technology that the external electric fields are added safely into the energetic material system to enhance the explosive performance. Graphical abstract.

Hydration and swelling: a theoretical investigation on the cooperativity effect of H-bonding interactions between p-hydroxy hydroxymethyl calix[4]/[5]arene and H2O by many-body interaction and density functional reactivity theory.

In order to explore the nature of the hydration and swelling of superabsorbent resin, a theoretical investigation into the cooperativity effect of the H-bonding interactions in the hydrates of four model compounds that can be regarded as the units of hydroquinone formaldehyde resin (HFR) (i.e., O-hydroxymethyl-1,4-dihydroxybenzene, methylene di-O-hydroxymethyl-1,4-dihydroxybenzene, p-hydroxy hydroxymethyl calix[4]arene and p-hydroxy hydroxymethyl calix[5]arene) was carried out by many-body interaction and density functional reactivity theory. The HFR···H2O···H2O complexes, in which the H2O···H2O moieties are bound with both the hydroxyl groups of HFR, are the most stable. For the HFR(H2O)n clusters, the interaction energy per building block is increased as the number of the size n increases, indicating the cooperativity effect. Therefore, a deduction is given that the cooperativity effects of the H-bonding interactions play an important role in the process of the hydration and swelling of HFR, and the swelling behavior is mainly attributed to the cooperativity effects which arised from the interactions between the H2O molecules. The origin of the cooperativity effect was examined employing several information-theoretic quantities in the density functional reactivity theory. The degree of swelling of HFR was quantitated using a measure of volume. Graphical abstract.

A novel fluorescent sensor for specific recognition of GSH based on the copper complex and its bioimaging in living cells.

Given the important role of biothiols in various physiological processes, there is a need to develop novel fluorescent sensors for detecting them. Herein, a novel "on-off-on" fluorescent sensor (E)-N'-((7-(diethylamino)-2-oxo-2H-chromen-3-yl)methylene)-6-((quinolin-8-yloxy)methyl)picolinohydrazide (PQC) was synthesized and its absorbance and fluorescence properties were characterized. The sensor PQC could form a stable complex and showed a significant fluorescence quenching response to Cu2+ with a quenching efficiency of approximately 100%, and the PQC-Cu2+ complex showed a fluorescence enhancement response to GSH with a higher recovery rate of above 80% in a CH3OH/HEPES (9:1 v/v, pH = 7.23) buffer system. Its detection limits were determined to be 0.17 µM for Cu2+ and 0.20 µM for GSH, and the binding stoichiometry of PQC-Cu2+ was determined to be 1: 1 by Job's plot method. Importantly, the sensor PQC can be used for filter paper strip tests and bioimaging in living cells.

A novel fluorescent chemosensor based on coumarin and quinolinyl-benzothiazole for sequential recognition of Cu2+ and PPi and its applicability in live cell imaging.

In this study, a highly selective fluorescent sensor (E)-2-((2-(benzo[d]thiazol-2-yl)quinolin-8-yl)oxy)-N'-((7-(diethylamino)-2-oxo-2H-chromen-3-yl)methylene)acetohydrazide (TQC) was synthesized from 2-methylquinolin-8-ol and 4-(diethylamino)-2-hydroxybenzaldehyde and its structure was characterized by 1H NMR, 13C NMR, ESI-HR-MS and density functional theory (DFT) calculation. Sensor TQC showed an obvious "on-off-on" fluorescence response to Cu2+ and PPi in a DMSO/HEPES (3:2 v/v, pH = 7.4) buffer system. The detection limits of sensor TQC were 0.06 µM to Cu2+ and 0.01 µM to PPi. In addition, sensor TQC showed a 1:1 binding stoichiometry to Cu2+ and TQC-Cu2+ complex showed a 2:1 binding stoichiometry to PPi. The optimum pH range of sensor TQC and TQC-Cu2+ was 3-8. Further studies demonstrated that sensor TQC could be made into test paper strips for the qualitative of Cu2+ and PPi and showed sequentially "on-off-on" fluorescent bio-imaging of Cu2+ and PPi in HeLa cells.

A simple fluorescent probe for detection of Ag+ and Cd2+ and its Cd2+ complex for sequential recognition of S2.

In this study, we designed and synthesized a simple probe 2-(8-((8-methoxyquinolin-2-yl)methoxy)quinolin-2-yl)benzo[d]thiazole (DQT) for detection of Ag+ and Cd2+ in a CH3OH/HEPES (9 : 1 v/v, pH = 7.30) buffer system. Its structure was characterized by NMR, ESI-HR-MS and DFT calculations, and its fluorescence performance was also investigated. Probe DQT showed fluorescence quenching in response to Ag+ and Cd2+ with low detection limits of 0.42 µM and 0.26 µM, respectively. Importantly, the complexation of the probe with Cd2+ resulted in a red shift from blue to green, making it possible to detect Ag+ and Cd2+ by the naked eye under an ultraviolet lamp. The DQT-Cd2+ complex could be used for sequential recognition of S2-. The recovery response could be repeated 3 times by alternate addition of Cd2+ and S2-. A filter paper strip test further demonstrated the potential of probe DQT as a convenient and rapid assay.

A BODIPY-Based Water-Soluble Fluorescent Probe for Naked Eye Detection of pH.

In this study, a BODIPY-based water-soluble fluorescent chemosensor BBP has been synthesized using BODIPY as the fluorescence group and quinoline as the recognition group. BBP can be used for naked eye detection of pH in complete aqueous solution and it shows high specificity in a wide range of cations. The pKa value is determined to be 2.94 and the fluorescence intensity is linearly related to pH in the range of 2.4-3.6.

A dynamic and electrostatic potential prediction of the prototropic tautomerism between imidazole 3-oxide and 1-hydroxyimidazole in external electric field.

In order to obtain an optimum scheme for separating the proton-transfer tautomer, a dynamic investigation into the effect of the external electric field on the proton-transfer tautomeric conversion in imidazole 3-oxide and 1-hydroxyimidazole was carried out at the M06-2X/6-311++G** and CCSD(T)/6-311++G(2d,p) level, accompanied by the analysis of the surface electrostatic potentials. The results show that, for both the forward reaction "imidazole 3-oxide → N-hydroxyimidazole free radical → 1-hydroxyimidazole" and its reverse reaction processes, the fields parallel to the N→O or N-OH bond axis affect the barrier heights and rate constants considerably more than those parallel to the other orientations. As the field strength is increased along the orientation from the O to N atom, the chemical equilibrium moves toward the direction for the formation of 1-hydroxyimidazole, while the amount of imidazole 3-oxide is increased with the increased field strength along the opposite orientation. In the fields along the orientation consistent with the dipole moment, the electrostatic potentials and their variances "abnormally" increase for the transition states with the N→O bond in comparison with those in no field (they decrease generally), which enhances the nucleophilicity of the coordination O atom and the electrophilicity of the activated H atom. The analyses of the AIM (atoms in molecules) and NICS (nucleus-independent chemical shift) were used to explain the above anomaly. Graphical Abstract Electrostatic potentials and their variances "abnormally" increase in the external electric field, which greatly affects tautomeric conversion.

A chemosensor with a paddle structure based on a BODIPY chromophore for sequential recognition of Cu2+ and HSO3.

In this study, a highly selective chemosensor ML based on a BODIPY fluorescent chromophore was synthesized for sequential recognition of Cu2+ and HSO3 - in a CH3OH/H2O (99 : 1 v/v) system, which contained three recognition sites and its structure characterized by 1H NMR, 13C NMR and ESI-HR-MS. The sensor ML showed an obvious "on-off" fluorescence quenching response toward Cu2+ and the ML-Cu2+ complex showed an "off-on" fluorescence enhancement response toward HSO3 -. The detection limit of the sensor ML was 0.36 µM to Cu2+ and 1.4 µM to HSO3 -. In addition, the sensor ML showed a 1 : 3 binding stoichiometry to Cu2+ and the recovery rate of ML-Cu2+ complex identifying HSO3 - could be over 70%. Sensor ML showed remarkable detection ability in a pH range of 4-8.

Theoretical investigation into the cooperativity effect between the intermolecular π∙π and H-bonding interactions in the curcumin∙cytosine∙H2O system.

In order to reveal the mechanism of drug action and design of DNA/RNA-targeted drugs containing aromatic rings, the cooperativity effects between the intermolecular π∙∙∙π and H-bonding interactions in curcumin(drug)∙∙∙cytosine(DNA/RNA base)∙∙∙H2O were investigated by the B3LYP-D3 and MP2(full) methods with the 6-311++G(2d,p) basis set. The π∙∙∙π interaction plays an important role in stabilizing the linear ternary complexes with the cooperativity effects, and the cyclic structures suffer the anticooperativity effects. The cooperativity or anticooperativity effects are notable, which could lead to a possible significant change in drug activity. The hydration is essentially the cooperativity or anticooperativity effect. These results were confirmed by the atoms in molecules (AIM), reduced density gradient (RDG), and surface electrostatic potentials analyses. The cyclic complexes are more stable, from which it can be deduced that the drug always links with the DNA/RNA base and H2O by the π∙∙∙π or H-bonding interactions, and only in this way can the drug activity be shown. Therefore, the designed DNA/RNA-targeted drugs should possess a certain number of hydrophilic groups in contact with the DNA/RNA base and H2O to reconcile drug activity by the cooperativity effect between the π∙∙∙π and H-bonding interactions, as is in agreement with many of the drugs in use. Graphical abstract RDG isosurface of ternary complex.

A highly sensitive and selective chemosensor for Pb2+ based on quinoline-coumarin.

In this study, a highly sensitive and selective fluorescent chemosensor, ethyl(E)-2-((2-((2-(7-(diethylamino)-2-oxo-2H-chromene-3-carbonyl)hydrazono)methyl)quinolin-8-yl)oxy)acetate (1), was synthesized and characterized by 1H NMR, 13C NMR and ESI-MS. Sensor 1 showed an "on-off" fluorescence response to Pb2+ with a 1 : 1 binding stoichiometry in CH3CN/HEPES buffer medium (9 : 1 v/v). The detection limit of sensor 1 to Pb2+ was determined to be 0.5 µM, and the stable pH range for Pb2+ detection was from 4 to 8.

Theoretical Study on the Effects of Hydrogen-Bonding and Molecule-Cation Interactions on the Sensitivity of HMX.

To assess the effects of weak interactions on the sensitivity of HMX, 11 complexes of HMX (where six of them are hydrogen-bonding complexes, and the other five are molecular-cation complexes) have been studied via quantum chemical treatment. The geometric and electronic structures were determined using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df, 2p) and aug-cc-pVTZ basis sets. The changes of the bond dissociation energy (BDE) of the trigger bond (N-NO2 in HMX) and nitro group charge have been computed on the detailed consideration to access the sensitivity changes of HMX. The results indicate that upon complex forming, the BDE increases and the charge of nitro group turns more negative in complexes, suggesting that the strength of the N-NO2 trigger bond is enhanced and then the sensitivity of HMX is reduced. Atom-in-molecules analyses have also been carried out to understand the nature of intermolecular interactions and the strength of trigger bonds.