Diradical-singlet character of 1,3-dipoles affects reactivity of 1,3-dipolar cycloaddition reactions and intramolecular cyclization Abstract 1,3-Dipolar cycloaddition (1,3-DC) reactions are powerful synthetic tool to obtain highly functionalized 5-membered heterocycles, starting from a 1,3-dipole and a dipolarophile in a single step. The reactivity of these systems is usually rationalized in terms of Frontier Molecular Orbital Theory (FMOT), which neglects a possible contribution of an open-shell weakly coupled singlet-diradical specie. In this work, the broken-symmetry approach is used to estimate the singlet-diradical character of 18 dipoles of the second period of the periodic table, classified as allyl-type N-centered, allyl-type O-centered, and propargyl-type 1,3-dipoles, providing a rationalization for 1,3-DC reactivity. The intramolecular cyclization of bent allyl-type N- and O-centered dipoles into 3-membered rings was also analyzed, and revealed that the energetic change is associated with the spin densities of peripheral atoms. Finally, a close relationship between the energy for the ring-opening process of the cyclic configuration and the reactivity of 1,3-dipoles toward 1,3-dipolar cycloaddition reaction was also found. Graphical abstract

Further understanding of the Ru-centered [2+2] cycloreversion/cycloaddition involved into the interconversion of ruthenacyclobutane using the Grubbs catalysts from a reaction force analysis Abstract The chemical reactivity of the first- and second-generation Grubbs catalysts has always been a significant issue in olefin metathesis. In the present work, we study the [2+2] cycloreversion/cycloaddition and the alkylidene rotation involved into the interconversion of the ruthenacyclobutane intermediate, through the reaction force and reaction force constant analysis. It has been found that the structural contribution controls the barrier energy in the interconversion of ruthenacyclobutane via [2+2] cycloreversion/cycloaddition, which is slightly lower in the second generation of Grubbs catalysts while its electronic contribution is slightly higher, which unveils a major rigidity and donor/acceptor properties of the NHC. This finding explains a greater structural contribution in the rate constant. Moreover, on the basis of the reaction force constant, the process can be classified as “two-stage”-concerted reactions, noting a more asynchronous process when the first generation is used as a catalyst. Finally, a similar analysis into the alkylidene rotation was performed. It was determined that [2+2] cycloreversion and alkylidene rotations take place in a sequential manner, the energy barrier is again controlled by structural reorganization, and the pathway is less asynchronous.

Assessment of dynamical properties of mercaptopurine on the peptide-based metal–organic framework in response to experience of external electrical fields: a molecular dynamics simulation Abstract In this work, the effect of the external electric field (EF) on the drug delivery performance of peptide-based metal–organic framework (MPF) for 6-mercaptopurine (6-MP) drug is investigated by means of the molecular dynamics (MD) simulations. It is found that the strength interaction of drug molecule with MPF is decreased under the influence of the electric field. In other words, the adsorbed drug molecules have more tendencies for the interaction with the porous nanostructure in the absence of EF. According to the radial distribution function (RDF) patterns, the probability of finding drug molecules in terms of the intermolecular distance with respect to the MPF surface is lowest during the high field strength. As the EF strength increases, the spread of drug molecules around MPF results in high dynamics movement and further more diffusion coefficient of drug molecule in the simulation system. This result emphasizes the weak intermolecular interaction of drug molecules with MPF with the application of EF. Assessment of dynamical properties of 6-mercaptopurine in the presence of EF with various strengths reveals that the applied electric field can act as a trigger on liberation behavior of drug from the porous nanostructure.

A model of atomic compressibility and its application in QSAR domain for toxicological property prediction Abstract A model for computing the atomic compressibility (β) based on two periodic descriptors, namely, absolute radius (r) and atomic electrophilicity index (ω), is proposed as $$ \beta \propto \left({r}^2/\omega \right) $$ The ansatz is invoked to compute compressibilities of atoms of 57 elements of the periodic table. The computed atomic data exhibits all sine qua non of periodic properties. Further, the concept group compressibility (Gβ) is also established invoking additivity property using some molecules with different functional groups and consequently utilized in correlating with molecular polarizability. Since toxicity prediction is an imperative need of the hour, chemical reactivity descriptors are of paramount importance in the study of toxicological behaviour along with a lot of other molecular reactivity studies within a Quantitative Structure–Activity Relationship (QSAR) context. Hence, this quantity is applied in the modelling of toxicological property through QSAR and a comprehensive study is performed in an effort to investigate and validate the application of compressibility in determining its toxicological power. Consequently, varied 209 organic molecules are selected for studying the toxic effect on Tetrahymena pyriformis. A QSAR model is constructed in terms of compressibility which offers a superior prediction of toxicity independently without adopting additional descriptors or properties as in some other QSAR studies. Graphical abstract

Density functional theory study of π -aromatic interaction of benzene, phenol, catechol, dopamine isolated dimers and adsorbed on graphene surface Abstract We analyze the influence of different groups on the intermolecular energy of aromatic homodimers and on the interaction between a single aromatic molecule and a graphene surface. The analysis is performed for benzene, phenol, catechol, and dopamine. For calculating the energies, we employ density functional theory within the local density approximation (LDA-DFT). Our results show that the lowest intermolecular energies between the aromatic molecules are related to the T-shaped configurations. This lower energy results from the quadrupole interaction. In the case of the interaction between the graphene sheet and the aromatic molecules, the lowest energy configuration is the face to face. The adsorption energy of a molecule on a graphene surface involves π − π interactions that explain the face to face arrangement. These results provide insight into the manner by which substituents can be utilized in crystal engineering, supramolecular chemistry, bioinspired materials, formation of various molecular clusters, parameterization of force fields suitable for classical simulations, and design of novel sensing, drug delivery, and filters based on graphene.

Structural approaches for the DNA binding motifs prediction in Bacillus thuringiensis sigma-E transcription factor (σ E TF) Abstract The sigma-E transcription factor (σETF) can be found in most of the bacteria cells including Bacillus thuringiensis. However, the cellular regulatory mechanisms of these transcription factors in the mass production of δ-endotoxins during sporulation stage are yet to be revealed. In addition, the recognition of DNA towards σETF DNA binding motifs that led to the transcription activities is also being poorly studied. Therefore, this work studied the possible DNA binding motifs of σETF by utilising in silico approaches. The structure of σETF was first built via three different computational methods. A cognate DNA sequence was then docked to the predicted σETF DNA-binding motifs. The binding free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) for triplicate 50 ns simulation of σETF-DNA complex revealed favourable binding energy of DNA to σETF (average ∆Gbind = −34.57 kcal/mol) mainly driven by non-polar interactions. This study revealed that σETF LYS131, ARG133, PHE138, TRP146, ARG222, LYS225 and ARG226 are most likely the key residues upon the binding and recognition of DNA prior to transcription actives. Since determination of genome-regulating protein which recognises specific DNA sequence is important to discriminate between the proteins preferences for different genes, this study might provide some understanding on the possible σETF-DNA recognition prior to transcription initiated for the δ-endotoxins production.

Theoretical study of nitrogen cation modified aromatics containing thiophene as π-linker for p -type photosensitizers Abstract On the basis of triphenylamine as an electron donor with attachment of two –COOH anchoring groups and dicyanovinyl as acceptor, ten dyes with D-π-A structures were designed to investigate the effects of different π-linker groups on the properties of the sensitizers, especially the influence of the π-linkers containing nitrogen cation (N+). The optimized structures and electronic and optical properties were investigated by the density functional theory (DFT) and time-dependent DFT (TD-DFT). The results show that all the investigated dyes can be used as dye sensitizers for the p-type dye-sensitized solar cells (DSSCs) except one dye which contains two N+. The N+ modified dye (named S3-PZL1C) has narrow energy gap (2.02 eV), the best light-harvesting efficiency (LHE, 0.9974), and the smallest internal reorganization energy (λint = 7.00 kcal/mol). Importantly, S3-PZL1C displays the largest red shift of the UV-vis absorption, the maximum integral values of the adsorption-wavelength curves over the visible light (400~800 nm), and the strongest adsorption energy (− 66.84 kcal/mol) on NiO surface. In addition, S3-PZL1C not only enhances the electronic excitation but also improves the reorganization energy and charge separation. The intramolecular charge transfer towards the acceptor is sensitive to the N+ position in π-linkers. Therefore, the suitable introduction of N+ in dyes can improve the performance of the dyes, and the PZL1C moiety may be a promising π-linker for p-type DSSCs. Graphical abstract

Thermal stability and detonation character of nitro-substituted derivatives of imidazole Abstract A series of nitro-imidazole derivatives were designed by replacing hydrogen atoms on imidazole ring with nitro group one by one. In order to investigate the thermodynamic stability, heat of formation (HOF), and bond dissociation energy (BDE) are calculated at the B3PW91/6-311+G(d,p) level. In order to investigate the impact sensitivity and detonation property, the drop height (H50), free space per molecule in crystal lattice (ΔV), detonation velocity (D), and detonation pressure (P) are calculated by using the empirical Kamlet–Jacobs (K-J) equation. The results show that the thermal stabilities of title molecules are determined by whether nitro group is associated to 1-position or not and accompanied with the steric hindrance between nitro groups and the charge population on the carbon atoms of imidazole ring. The excellent impact sensitivity and detonation performance of title molecules are also evaluated. On the consideration both of stability and detonation characters, 2,4,5-trinitro-1H-imidazole (D = 8.98 km/s, P = 36.70 GPa) is screened out as the potential high-energy-density molecule for further research.

Theoretical calculation into the effect of molar ratio on the structures, stability, mechanical properties and detonation performance of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane/ 1,3,5-trinitro-1,3,5-triazacyco-hexane cocrystal Abstract Molecular dynamics (MD) simulation was conducted to research the effect of molar ratio on the thermal stability, mechanical properties, and detonation performance of HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane)/RDX (1,3,5-trinitro-1,3,5-triazacyco-hexane) cocrystal explosive at ambient condition. The binding energy, mechanical properties, and the detonation parameters of the pure β-HMX, RDX crystal, and the cocrystal models were got and contrasted. The results demonstrate that molar ratio has a great influence on the properties of the cocrystal system. The binding energy of the cocrystals has the maximum values at the 1:1 molar ratio, indicating that the stability of HMX/RDX(1:1) cocrystal is the best and HMX and RDX may prefer to cocrystallizing at 1:1 molar ratio. What’s more, the tensile modulus (E) and shear modulus (G) of the HMX/RDX(1:1) cocrystals have the minimum value, while the C12–C44 and K/G have the maximum value, implying that the cocrystal at 1:1 molar ratio has the best mechanical properties. Simultaneously, the E, K, and G of the cocrystals are all smaller than those of β-HMX’s and generally larger than those RDX’s, while the Cauchy pressure (C12–C44) and K/G ratio were greater, demonstrating that cocrystallizing can improve the brittleness and enhance the ductility. The detonation velocity (D) and detonation pressure (P) decrease with the rising RDX content, while the properties are still superior to the pure RDX crystal; thus, the energy properties of the cocrystal are still excellent. In a word, HMX/RDX cocrystal at 1:1 molar ratio has the best thermal stability, mechanical properties, and the excellent energetic performance.

Structural, electronic, optical, and thermodynamic properties of hydrochlorinated Janus graphene: a first-principle study Abstract The structural, electronic, optical, and thermodynamic properties of hydrochlorinated Janus graphene (J-GN) have been studied using first-principle DFT calculations. The band structure and density of states have been discussed. The values of 16 parameters have been calculated for the most stable chair (C) structure of hydrochlorinated J-GN. Out of sixteen, 12 parameters such as static dielectric constant ε(0), refractive index n(0), birefringence Δn(0), threshold conductivity σ(ω), plasmon energy (ћωp), binding energy (Eb), cohesive energy (Ec), enthalpy (E), entropy (S), free energy (F), heat capacity (Cp), and Debye temperature (ΘD) have been calculated for the first time. The structural and electronic properties have also been studied at 0-GPa, 25-GPa, 35-GPa, 50-GPa, 90-GPa, 100-GPa, 150-GPa, 200-GPa, and 220-GPa external pressures. The hydrochlorinated J-GN shows the direct band gap behavior up to 35 GPa and becomes indirect band gap after 35 GPa. Further, it shows a stable structure up to 90 GPa and becomes unstable at 100-GPa external pressure. The calculated values of all parameters agree well with the available reported values of some parameters at 0 GPa.