High-energy Molecules Research Articles

Vicinal Combination of N—NH2 and C—NO2 Benefitting for Low Sensitivity and High Energy Azole Molecules: A Strategy Developed from Isomerization

It is nowadays challenging to create low sensitivity and high energy molecules (LSHEMs), largely restricted by the high complexity and difficult interpretation of composition-structure-property relationships of energetic materials. In the present theoretical modeling work on energetic materials, we propose a strategy for constructing LSHEMs based on energetic azole isomerism to reduce the molecular complexity while maintain composition. That is, we firstly find that the vicinal combination of N—NH2 and C—NO2 is an effective unit to enhance both energy and molecular stability of azoles. The advantage of the combination largely stems from the oxygen balance improvement to be close to zero to elevate reaction heat and packing density, and the intramolecular hydrogen bond formation to enhance molecular stability. Thus, this unit can be widely considered in constructing N-rich low sensitivity and high energy azole molecules. In addition, we confirm that the N—NO2 generally seriously do harm to the molecular stability of azoles, especially in the case of the existence of steric effect around it.

Modeling High Energy Molecules and Screening to Find Novel High Energy Candidates.

High energy materials (HEMs) play pivotal roles in diverse military and civil-commercial sectors, leveraging their substantial energy generation. Integrating machine learning (ML) into HEM research can expedite the discovery of high-energy compounds, complementing or replacing traditional experimental approaches. This manuscript presents an application of our in-house Iterative Stochastic Elimination (ISE) algorithm to identify HEMs. ISE is a generic algorithm that produces reasonable solutions for highly complex combinatorial problems. In molecular discovery, ISE focuses on physicochemical properties to distinguish between different classes of molecules. Due to its long track record in discovering novel, highly active biomolecules, we decided to apply ISE to another type of molecular discovery: High-energy materials. Two distinct ISE models, Model A (92 HEMs) and Model B (169 HEMs), integrated non-HEMs for comprehensive analysis. The results showcase significant achievements for both Models A and B. Model A identified 69% of active molecules in Model B, of which 62% had the highest score. Model B identified 80% of active molecules in Model A, with 61% having the highest score among those 80%. Subsequently, Model C was developed, merging all active molecules (261) from Models A and B. Statistical data indicate that Model C is a high-quality model. It was used to screen and score nearly 2 million molecules from the Enamine database. We find 66 molecules with the highest score of 0.89, plus 8 with that score which are active molecules included in the learning set of Model C. From the 66 molecules, 21 (32%) contain at least one nitro group. In conclusion, this study positions the ISE algorithm as a potential tool for discovering novel HEM candidates, offering a promising pathway for efficient and sustainable advancements in high-energy materials research.

Integrating strategy to investigate the formation and stabilization mechanisms of Curcumin-Cyclodextrin inclusion complexes: Experimental characterizations and multi-scale computational simulations

The Cyclodextrin (CD) encapsulation technology can significantly enhance the water solubility of Curcumin (CUR) and effectively protect it against chemical degradations. In the current study, a combination of experimental and multi-scale computational approaches was used to investigate the binding mechanism between CUR and β-CDs (β-CD, 2-HP-β-CD, Me-β-CD, and DM-β-CD). Phase solubility studies showed that β-CDs exhibited a strong binding affinity with CUR and significantly enhanced its solubility. SEM, PXRD, DSC, and TG analysis confirmed the formation of inclusion complexes, resulting in the transition of CUR from crystalline to an amorphous state. FTIR, 1H, and 13C NMR spectra deduced that CUR may have multiple binding conformations with β-CDs. The rationality of molecular dynamics simulation systems was confirmed by comparing the simulated IR spectrum from quantum mechanics with the experimental IR spectrum. MM-PBSA and umbrella sampling simulation calculated the binding free energy of the CUR/CD inclusion complexes, ranking Me-β-CD > DM-β-CD > 2-HP-β-CD > β-CD, and clarified that van der Waals interaction played a major role in stabilizing the inclusion complexes. RDF analysis confirmed that the release of high-energy water molecules drove the formation of the CUR/CD inclusion complex, and the β-CD substituents affected their exterior hydration layer. Additionally, principal component analysis (PCA) and non-covalent interaction analysis revealed three CUR/CD binding modes: bead-on-string, terminal insertion, and V-shaped-folding. The research strategy adopted here can serve as a paradigm for investigating the encapsulation mechanism of poorly soluble drugs with CDs.

Manifold Fluorescence Enhancement of a Styryl(pyridinium)-chromene Hybrid Dye upon Binding with an Elongated β-Cyclodextrin Cavity.

The interaction of a styryl(pyridinium)-chromene hybrid dye (DSP-C) with the 2-hydroxypropyl-β-cyclodextrin (HPβCD) macrocycle leads to a remarkably large increase (∼310-fold) in its fluorescence intensity, in contrast to the relatively smaller (∼45-fold) enhancement observed with native β-cyclodextrin (βCD). Both macrocycles (βCD and HPβCD) bind with the styryl(pyridinium) as well as the chromene fragments of the hybrid dye, with the simultaneous formation of 1:1 and 2:1 host:guest complexes. However, the binding constant (Keq1) is more than an order of magnitude higher for HPβCD than for βCD. The improved binding affinity of HPβCD is attributed to its elongated and deeper hydrophobic cavity. This is supported well by the optimized geometries of the host-guest complexes. Theoretical calculations also reveal that the energy change due to the release of high-energy water molecules from the host nanocavity is more favorable for HPβCD than βCD, resulting in greater stability of the HPβCD:DSP-C complex. Interestingly, though the fluorescence of DSP-C arises from its styryl(pyridinium) fragment, the complexation of the chromene unit with the host plays a major role in augmenting the fluorescence enhancement of the hybrid dye. The large fluorescence change in the HPβCD:DSP-C system has been utilized for the detection of bile salts by the indicator displacement strategy.

The chemistry of heterocycles in the 21st century

The chemistry of heterocyclic compounds has traditionally been and remains a bright area of chemical science in Russia. This is due to the fact that many heterocycles find the widest application. These compounds are the key structural fragments of most drugs, plant protection agents. Many natural compounds are also derivatives of heterocycles. At present, more than half of the hundreds of millions of known chemical compounds are heterocycles. This collective review is devoted to the achievements of Russian chemists in this field over the last 15–20 years. The review presents the achievements of leading heterocyclists representing both RAS institutes and university science. It is worth noting the wide scope of the review, both in terms of the geography of author teams, covering the whole of our large country, and in terms of the diversity of research areas. Practically all major types of heterocycles are represented in the review. The special attention is focused on the practical applications of heterocycles in the design of new drugs and biologically active compounds, high-energy molecules, materials for organic electronics and photovoltaics, new ligands for coordination chemistry, and many other rapidly developing areas. These practical advances would not be possible without the development of new fundamental transformations in heterocyclic chemistry.<br> Bibliography — 2237 references.

Unveiling the dynamic and thermodynamic interactions of hydrocortisone with β-cyclodextrin and its methylated derivatives through insights from molecular dynamics simulations

Cyclodextrins (CDs) can enhance the stability and bioavailability of pharmaceutical compounds by encapsulating them within their cavities. This study utilized molecular dynamics simulations to investigate the interaction mechanisms between hydrocortisone (HC) and various methylated CD derivatives. The results reveal that the loading of HC into CD cavities follows different mechanisms depending on the degree and position of methylation. Loading into βCD and 6-MeβCD was more complete, with the hydroxyl groups of HC facing the primary hydroxyl rim (PHR) and the ketone side facing the secondary hydroxyl rim (SHR). In contrast, 2,3-D-MeβCD and 2,6-D-MeβCD showed a different loading mechanism, with the ketone side facing the PHR and the hydroxyl groups facing the SHR. The root mean square fluctuation (RMSF) analysis demonstrated that methylation increases the flexibility of CD heavy atoms, with 3-MeβCD and 2,3-D-MeβCD exhibiting the highest flexibility. However, upon inclusion of HC, 3-MeβCD, 2,3-D-MeβCD, 2-MeβCD, and 6-MeβCD showed a significant reduction in flexibility, suggesting a more rigid structure that effectively retains HC within their cavities. The radial distribution function revealed a significant reduction in the number of water molecules within the innermost layer of the methylated CD cavities, particularly in TMeβCD, indicating a decrease in polarity. The presence of HC led to the release of high-energy water molecules, creating more favorable conditions for HC loading. Conformational analysis showed that methylation caused a partial decrease in the area of the PHR, a significant decrease in the area of the middle rim, and a notable decrease in the area of the SHR. The loading of HC increased the area of the PHR in most derivatives, with the most pronounced increase observed in 2,6-D-MeβCD and 6-MeβCD. The analysis of interaction energies and binding free energies demonstrated that the binding of HC to methylated CD derivatives is thermodynamically more favorable than to βCD, with the strongest association observed for 6-MeβCD, 2-MeβCD, and 2,3-D-MeβCD.

Efficiency of high energy fluorocarbon molecule bombardment for fast etch rate and its limitation: A molecular dynamics study

The RF power of the High Aspect Ratio (HAR) patterning equipment used for 3D NAND memory etching processes rapidly increased recently. However, despite implementing higher ion energy, its effect on increasing the etch rate is not satisfactory. This letter studies the energy transfer efficiency between bombarding fluorocarbon (FC) molecules and the SiO2 substrate, and discusses the limitation of securing the etch rate by high-energy FC molecules.

A Prebiotic Precursor to Life's Phosphate Transfer System with an ATP Analog and Histidyl Peptide Organocatalysts.

Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. While this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chemical fuels. Biochemistry solves this problem by combining kinetically stable and thermodynamically activated molecules (e.g., ATP) with enzyme catalysts. Here, we demonstrate a prebiotic phosphate transfer system involving an ATP analog (imidazole phosphate) and histidyl peptides, which function as organocatalytic enzyme analogs. We demonstrate that histidyl peptides catalyze phosphorylations via a phosphorylated histidyl intermediate. We integrate these histidyl-catalyzed phosphorylations into a complete prebiotic scenario whereby inorganic phosphate is incorporated into organic compounds though physicochemical wet-dry cycles. Our work demonstrates a plausible system for the catalyzed production of phosphorylated compounds on the early Earth and how organocatalytic peptides, as enzyme precursors, could have played an important role in this.

KinPred-RNA—kinase activity inference and cancer type classification using machine learning on RNA-seq data

Kinases as important enzymes can transfer phosphate groups from high-energy and phosphate-donating molecules to specific substrates and play essential roles in various cellular processes. Existing algorithms for kinase activity from phosphorylated proteomics data are often costly, requiring valuable samples. Moreover, methods to extract kinase activities from bulk RNA sequencing data remain undeveloped. In this study, we propose a computational framework KinPred-RNA to derive kinase activities from bulk RNA-sequencing data in cancer samples. KinPred-RNA framework, using the extreme gradient boosting (XGBoost) regression model, outperforms random forest regression, multiple linear regression, and support vector machine regression models in predicting kinase activities from cancer-related RNA sequencing data. Efficient gene signatures from the LINCS-L1000 dataset were used as inputs for KinPred-RNA. The results highlight its potential to be related to biological function. In conclusion, KinPred RNA constitutes a significant advance in cancer research by potentially facilitating the identification of cancer.

Structure and properties of new composites composed of the all compound molecule cyclo[18]carbon and the polynitrogen molecule pentazole: A density functional theory study

In order to develop new composites composed of all carbon molecules and polynitrogen molecules, composites formed by a new all-carboatomic ring cyclo[18]carbon (C18) and a famous high energy molecule pentazole (N5H) with different proportions and sizes including N5H@C18, N5H@ 2 C18, 2 N5H@C18 and 2 N5H@ 2 C18 were designed. The intermolecular interactions, molecular and electronic structures, properties like conjugation effect and impact sensitivity, electrical conductivity and electrostatic sensitivity, recovery time, UV-Vis spectrum and IR spectrum were investigated theoretically. The results showed that N5H can be adsorbed inside the center of big C18 ring through the chemisorption. Intermolecular interactions in composites were mainly contributed by the dispersion interaction, but the electrostatic interaction also could not be neglected for 2 N5H@C18 and 2 N5H@ 2 C18 composites. The conjugation effect and ESP value in high positive region of N5H may be enhanced and decreased by C18, respectively, leading to better structural stability and lower impact sensitivity of composites than sole N5H. Due to the obviously decrease in energy GAP caused by C18, the electron transition ability and electrical conductivity of composites were greatly better than sole N5H, leading to lower electrostatic sensitivity and better safety performance markedly. Besides, the recovery time was very short, the difference in the UV-Vis and IR spectrum between sole N5H and composites was very obviously, showing the second function of C18 used as a new sensor for polynitrogen molecules like N5H.

Energetic derivatives substituted with trinitrophenyl: improving the sensitivity of explosives.

The incorporation of trinitrophenyl-modified 1,3,4-oxadiazole fragments is commonly observed in high-energy molecules with heat-resistant properties. This study explores the strategy of developing heat-resistant energetic materials by incorporating trinitrophenyl and an azo group into 1,3,4-oxadiazole, which involved the synthesis and characterization of (E)-1,2-bis(5-(2,4,6-trinitrophenyl)-1,3,4-oxadiazol-2-yl)diazene (2), N-(5-(2,4,6-trinitrophenyl)-1,3,4-oxadiazol-2-yl)nitramide (3), and the energetic salts of 3. Characterization techniques employed included 1H and 13C NMR, IR and elemental analysis. Additionally, the structures of 2 and 3 were validated using single crystal X-ray analysis. To further understand the physical and chemical characteristics of these novel energetic compounds, various calculations and measurements were performed. Compound 2 exhibits excellent thermostability (Td = 294 °C), which is comparable to that of traditional heat-resistant explosive HNS (Td = 318 °C). But 2 is insensitive towards impact (>40 J) and friction (>360 N), surpassing HNS (5 J, 240 N), suggesting that compound 2 deserves further investigation as a potential heat-resistant explosive.

COMPLEXES OF p-METHOXYPHENYLTELLURIUM TRICHLORIDE WITH ALLYL THIOETHERS OF 5-ARYL-1,3,4-OXADIAZOLE

1,3,4-Oxadiazole and its functional derivatives have a wide spectrum of biological activity. There are well-known examples of the use of oxadiazoles in materials science as high-energy molecules. Therefore, the synthesis of new functional derivatives based on them is an urgent problem. This paper describes the synthesis of allylic thioethers of 5-nitrophenyl-1,3,4-oxadiazole by the alkylation reaction of the corresponding thiones with allyl bromide in an alcohol-alkaline medium. Such thioethers were studied in reactions with phenylselentrihalides, as a result of which oxadiazolo[2,3-d][1,3,4]thiaselenazinium halides were synthesized. We investigated the interaction of the tellurium-containing analogue p-methoxyphenyltellurium trichloride with allylic thioethers of 5-nitrophenyl-1,3,4-oxadiazole. It was established that the reaction between p-methoxyphenyl tellurium trichloride and the investigated alkenyl thioethers within 8 hours occurs with the formation of adducts of the substrate-electrophile composition 1:1, regardless of the ratio of reagents. Attempts to change the polarity of the solvent, increase the reaction time, and change the temperature regime did not change the direction of the reaction. Based on the obtained experimental spectral data and elemental analysis data, the structure of the obtained complexes is proposed.
 Keywords: p-methoxyphenyltellurium trichloride; 1,3,4-oxadiazole; allyl thioethers; organotellurium compounds; molecular complexes.

Synthesis and characterization of energetic molecules based on pyrimidine rings: Selection and verification of computational-assisted synthesis pathways

The current rise in performance prediction techniques for energetic compounds provides the possibility of prejudging the effectiveness of derived patterns. In this work, 2,4-diamino-6-chloropyrimidine was used as the precursor, and the three possible derived pathways were systematically explored (guest oxidant, nitration, and N-oxidation). Theoretical calculations were adopted to predict the energy and stability parameters of possible products. The calculations indicated that constructing bridged-ring energetic molecules with N-oxide and nitro group is an effective way to balance energy and safety. Based on this protocol, we synthesized a series of pyrimidine-based energetic molecules within three steps and tested and analyzed their physicochemical properties, verifying the consistency between experimental results and theoretical predictions. This work provides a research model for determining the feasibility and effectiveness of the derivative pathway based on a specific energetic compound precursor and can offer guidance for the directed and large-scale synthesis of high-energy and low-sensitivity explosive molecules.

Tris(3-nitropentane-2,4-dionato-κ2 O,O′) Complexes as a New Type of Highly Energetic Materials: Theoretical and Experimental Considerations

Decreasing the sensitivity towards detonation of high-energy materials (HEMs) is the ultimate goal of numerous theoretical and experimental studies. It is known that positive electrostatic potential above the central areas of the molecular surface is related to high sensitivity towards the detonation of high-energy molecules. Coordination compounds offer additional structural features that can be used for the adjustment of the electrostatic potential values and sensitivity towards detonation of this class of HEM compounds. By a careful combination of the transition metal atoms and ligands, it is possible to achieve a fine-tuning of the values of the electrostatic potential on the surface of the chelate complexes. Here we combined Density Functional Theory calculations with experimental data to evaluate the high-energy properties of tris(3-nitropentane-2,4-dionato-κ2 O,O′) (nitro-tris(acetylacetonato)) complexes of Cr(III), Mn(III), Fe(III), and Co(III). Analysis of the Bond Dissociation Energies (BDE) of the C-NO2 bonds and Molecular Electrostatic Potentials (MEP) showed that these compounds may act as HEM molecules. Analysis of IR spectra and initiation of the Co(AcAc-NO2)3 complex in the open flame confirmed that these compounds act as high-energy molecules. The measured heat of combustion for the Co(AcAc-NO2)3 complex was 14,133 J/g, which confirms the high-energy properties of this compound. The results also indicated that the addition of chelate rings may be used as a new tool for controlling the sensitivity towards the detonation of high-energy coordination compounds.

Resonant vibrations produce quantum bridge over high-energy states in heterogeneous antenna.

Photosynthetic light-harvesting complexes usually contain several pools of molecules with a big difference in transition energies, for example, chlorophylls a and b in plant antennas. Some pathways of the excitation energy transfer may include pigments from the low-energy pool separated by a site occupied by a high-energy molecule. We demonstrate that such pathways may be functional if high-frequency intramolecular vibrations fall in resonance with the energy gap between the neighboring molecules belonging to different pools. In this case, a vibration-assisted mixing of the excited states can produce delocalized vibronic states playing a role of 'quantum bridge' that facilitates a passage over high-energy barrier. We perform calculations of the excitation dynamics in the model three-state system with the parameters emerging from our previous studies of real antennas. Simulation of the dynamics in an explicit electron-vibrational basis demonstrates that the rate of transfer between the two chlorophylls a through the chlorophyll b intermediate is increased by a factor of 1.7-2 in the presence of resonant vibration. A possible influence of energetic disorder and other (non-resonant) vibrations on this effect is discussed.

Identifying the determining factors of detonation properties for linear nitroaliphatics with high-throughput computation and machine learning

In this work, a high-throughput computation (HTC) and machine learning (ML) combined method was applied to identify the determining factors of the detonation velocity (vd) and detonation pressure (pd) of energetic molecules and screen potential high-energy molecules with acceptable stability in a high-throughput way. The HTC was performed based on 1725 sample molecules abstracted from a dataset of over 106 linear nitroaliphatics with 1- to 6-membered C backbones and three types of substituents, namely single nitro group (-NO2), nitroamine (-NNO2), and nitrate ester (-ONO2). ML models were established based on the HTC results to screen high-energy molecules and to identify the determining factors of vd and pd. Compared with quantum chemistry calculation results, the absolute relative errors of vd and pd obtained using the ML models were less than 3.63% and 5%, respectively. Furthermore, eight molecules with high energy and acceptable stability were selected as potential candidates. This study shows the high efficiency of the combination of HTC and ML in high-throughput screening.

Sparkling Organic Phosphorescence from Fluorinated Tetrathia[7]helicenes: Synthesis and Photophysical, Electrochemical and Computational Studies.

Structure-property correlations in the thiahelicene family are often not trivial beacuse most of the functional groups present on the helical scaffold modify the conjugation size of the π-system. Selecting fluorine-containing groups to provide strong inductive effects without interacting with low-lying orbitals of the system could be the way to overcome the issue. Here we report a study on three fluorine-functionalized tetrathia[7]helicenes, highlighting interesting correlations between the position of the functional groups and the conjugated skeleton properties. Helicenes Heli-F2 and Heli-CF-F2 were prepared by photoinduced isomerization-electrocyclization (the Mallory photocyclization) of the corresponding fluorinated benzodithienyl-ethenes Alk-F2 and Alk-CF-F2, which were prepared in high yields through stereo-conservative Stille reaction. Notably these helicenes were found to display green phosphorescence around 530-550 nm, and the studies suggest an efficient spin-orbit coupling mechanism in these high-energy triplet nonplanar conjugated molecules. Both helicenes and their precursors were thoroughly characterized by means of optical and electrochemical measurements, while DFT calculations enable a rationale on their structure-property correlations to be defined.

Searching for the analogues of 1,1-dinitro-2,2-diamino ethylene (FOX-7) by high-throughput computation and machine learning

1,1-dinitro-2,2-diamino ethylene (FOX-7) is typically representative of low sensitivity and high energy compound. In this work, analogues of FOX-7 are screened using a combined method of high-throughput computation (HTC) and machine learning (ML). The molecules are generated with typical unsaturated hydrocarbons backbones and random combination of substituents -H, -NH2 and -NO2, then HTC is performed based on 200 sample molecules. ML models are established based on the HTC results, with detonation parameters predicted using the most accurate model of extreme gradient boosting (XGB). Finally, stability of the filtered high energy molecules are confirmed by quantum chemistry calculations, and besides FOX-7, 8 more energetic molecules with high energy as well as high stability (detonation velocity ≥ 8841.1 m/s, detonation pressure ≥ 34.6 GPa and stability parameter bond dissociation energy ≥ 201.7 kJ/mol) are achieved. This work has shown the efficiency of HTC and ML methods in searching new target molecules.

Transient and Dissipative Host-Guest Hydrogels Regulated by Consumption of a Reactive Chemical Fuel.

The transient self-assembly of molecules under the direction of a consumable fuel source is fundamental to biological processes such as cellular organization and motility. Such biomolecular assemblies exist in an out-of-equilibrium state, requiring continuous consumption of high energy molecules. At the same time, the creation of bioinspired supramolecular hydrogels has traditionally focused on associations occurring at the thermodynamic equilibrium state. Here, hydrogels are prepared from cucurbit[7]uril host-guest supramolecular interactions through transient physical crosslinking driven by the consumption of a reactive chemical fuel. Upon action from this fuel, the affinity and dynamics of CB[7]-guest recognition are altered. In this way, the lifetime of transient hydrogel formation and the dynamic modulus obtained are governed by fuel consumption, rather than being directed by equilibrium complex formation.

Transient and Dissipative Host–Guest Hydrogels Regulated by Consumption of a Reactive Chemical Fuel

AbstractThe transient self‐assembly of molecules under the direction of a consumable fuel source is fundamental to biological processes such as cellular organization and motility. Such biomolecular assemblies exist in an out‐of‐equilibrium state, requiring continuous consumption of high energy molecules. At the same time, the creation of bioinspired supramolecular hydrogels has traditionally focused on associations occurring at the thermodynamic equilibrium state. Here, hydrogels are prepared from cucurbit[7]uril host–guest supramolecular interactions through transient physical crosslinking driven by the consumption of a reactive chemical fuel. Upon action from this fuel, the affinity and dynamics of CB[7]–guest recognition are altered. In this way, the lifetime of transient hydrogel formation and the dynamic modulus obtained are governed by fuel consumption, rather than being directed by equilibrium complex formation.