Theoretical study of formate, tartrate, tartronate, and glycolate production from 6-carbon trioxylate intermediate in the citric acid cycle Abstract Reaction pathways of side products (formate, glycolate, and tartronate) from dihydroxyfumarate (DHF) were theoretically investigated as DHF is an intermediate in the process of producing tartrates and oxalate from glyoxylate of the citric acid cycle. The proposed pathways for each reaction were mapped by density functional theory (DFT) calculations. The transitions states were confirmed by analyzing the vibrational frequency and the intrinsic reaction coordinate (IRC) theory. The corresponding reaction activation energy, enthalpy change, Gibb’s free energy change, and rate of reactions were calculated to get a clear picture of the whole reaction pathway. In the whole process, the decarboxylation reaction showed the highest energy barrier of 20–23 kcal/mol. Proton transfer and hydroxylation reactions were almost barrierless. As most of these reactions have very low energy barrier, our findings elucidate the high probability of those reactions under experimental conditions.

Exploring properties of potassium 6-X-2-isonicotinoyltrifluoroborate (X=H, F, Cl, Br) salts and their anions by using ab initio calculations Abstract The structural, electronic, and topological properties of a series of four members of potassium 6-X-2-isonicotinoyltrifluoroborate (X=H, F, Cl, Br) salts have been explored by using ab initio calculations with the hybrid B3LYP/6-311++G** method. According to the potential energy surface only the properties for the most stable conformer of each member of the series and their anions were analyzed in function of electronegativity and atomic radius of X. The results show that when X=H, the salt and its anion have symmetry CS while the symmetry change to C1 for the halogenated F, Cl, and Br derivatives and their anions. Both, electronegativity and atomic radius properties show higher effects on V than on μ. Similar behaviors are observed when the Mulliken charges on N and X atoms are analyzed vs electronegativites, and atomic radius of X while an important decreasing on NPA charges of X is observed when increase its electronegativity. The strong influence of electronegativity and atomic radius of X are evidenced in the low bond order value observed in the C1 atom of F salt. The strong energetic π*C2-C3 → π*C4-C5 transition observed only for the F salt confer to it a high stability. The frontier orbitals have revealed that the 6-H-IFTB salt is the less reactive species while the higher reactivity is predicted for the Br salt. Evidently, the smaller electronegativity and higher atomic radius of Br justify the high reactivity predicted for its salt. Graphical abstract Exploring properties of potasium 6-X-2-isonicotinoyltrifluoroborate (X= H, F, Cl, Br)

Theoretical study on the mechanisms of the decomposition of nitrate esters and the stabilization of aromatic amines Abstract The nitrate esters are important components of double-base propellants. Aromatic amines are recommended as the stabilizers to delay the decomposition of nitrate esters and increase their storage time. The decomposition mechanisms of alkyl, alkoxy dinitrate, and poly-fluoride nitrate esters and the stabilizing effect of aromatic amines including new designed phenols are studied at the level of B3LYP/6-31G**. Alkyl and alkoxyl dinitrate esters are likely to be transformed by hydrogen abstraction, which is consistent with that of mononitrate and trinitrate esters. However, for poly-fluoride nitrate esters, NO2 catalyzed self-decomposition is preferred. In addition, comparing with mononitrate and trinitrate esters, the order of their stability is mononitrates > dinitrates > trinitrates. Poly-fluoride nitrate esters have a poorer stability than non-fluorinated nitrate esters. Comparing with parent nitrate esters, the stability of new designed poly-fluoride oxygen-containing nitrate esters is slightly improved. Aromatic amines including new designed phenols are effective stabilizers of nitrate esters, especially when introduced hydroxyl in the para position, can enhance the effects of stabilizers. The rate constants for the decomposition of nitrate esters and the bimolecular reaction between stabilizers and NO2 are calculated by using traditional transition state theory. Graphical abstract Comparison between the reaction energy barrier of nitrate esters and stabilizers with NO2

Strategy for chemically riveting catenated nitrogen chains Abstract Catenated nitrogen chains (CNCs) attract considerable attention because of their structural novelty, their high energy, and their potential as precursors for all-nitrogen materials. However, pure CNCs are unstable under ambient conditions, limiting their on-site or practical applications. Chemical riveting of a CNC involves the maintenance of the structure of a CNC and placing the CNC in a special chemical structure as a moiety of an entire molecule to stabilize it. Other structures, except from the CNC, are named rivets. In this study, the molecular geometry, bond order, natural bond orbital charge, and frontier orbital among the pure CNCs (Nx), Nx−, Nx+, and NxHy (x = 2–11) and CNCs riveted and implemented experimentally in several former studies are systematically analyzed and compared. The lone-pair repulsion between two neighboring N atoms is one of the primary factors for the low molecular stability of the pure CNCs and their derivatives. The riveted CNCs with rings are usually more stable than those with open chains. Moreover, the standard deviation of the bond orders or the bond lengths can be employed as an indicator for molecular stability, i.e., a lower standard deviation suggests higher molecular stability. Hence, electron-donating groups, groups with electronegativity within those of H and N atoms, as well as atoms or groups with empty orbitals are proposed to trap the lone pairs of CNCs as rivets to stabilize the CNCs. This strategy is expected to facilitate the creation of stable CNC-contained compounds with high structural novelty or high energy contents. Graphical abstract A strategy is proposed for chemically riveting instable CNCs to transform them into more stable ones.

Conformational switching of CO on graphene: the role of electric fields Abstract Molecular switches on solid surfaces raise an important issue in digital electronic devices. It has been frequently tried to design devices to perform basic functions at the molecular scale. In this paper, the Perdew-Burke-Ernzerhof (PBE) and PBE+van der Waals (vdW) were utilized in the framework of density functional theory (DFT) to model CO optimization on a graphene surface. Among the different external stimuli, electric fields serving as a useful probe were used to activate CO switching properties. The molecular conformation of CO, total dipole orientation, and charge transfer orientation were manipulated by turning an external electric field ON and OFF. The molecular conformation switched from a parallel orientation in a negative electric field towards a perpendicular orientation in a positive electric field. The total dipole moment switched from − 8.56 Debye (D) in an electric field of − 1.0 V/Å to 3.64 D in an electric field of + 1.0 V/Å. Charge transfer was seen to switch with the electric field switching. In the negative electric field, the charges were transferred from graphene to CO, while a reverse transfer occurred in the positive electric field. In addition, it was shown that CO desorption occurred in an electric field of greater than ± 1.0 V/Å. Eventually, the ON-to-OFF state transition was accompanied by switching between the positive and negative dipole moments, adsorption and desorption states, and positive and negative charge transfers when the external field direction and intensity were switched.

Study of molecular interactions by hydrogen bond of charged forms of makaluvamines and complex stability with H 2 O and glutamic acid (Glu Ac) by the theory of the functional of density (B3LYP) Abstract This work was undertaken to understand the mode of interaction of makaluvamines, a class of marine pyrroloiminoquinone alkaloids isolated from sponges of the genus Zyzzya, used in the treatment of several human cancer cell lines. This analysis was done by the quantum chemistry method. First, we used electrostatic potential (ESP) to reveal the different sites that accept and donate hydrogen bonds (HB) of charged forms (protonated and methylated) of makaluvamines (at level B3LYP/6-311++G(d,p)). In a second step, we studied the interactions by hydrogen bond between these molecules and water molecule on the one hand (at level B3LYP/6-311++G(d,p)) and on the other hand glutamic acid a protein residue of topoisomerase II (at level B3LYP/6-31+G(d,p)). Finally, we calculated the corrected BSSE interaction energies and estimated the relative stability of the formed complexes.

Theoretical design of novel high energy metal complexes based on two complementary oxygen-rich mixed ligands of 4-amino-4 H -1,2,4-triazole-3,5-diol and 1,1′-dinitramino-5,5 ′ -bistetrazole Abstract In this study, 16 new energetic metal complexes [M(DNABT)(ATDO), M=Cu, Ni] were designed using the mixed complex construct strategy, which was based on two complementary oxygen-rich high-energy ligands of 1,1′-dinitramino-5,5′-bistetrazole (DNABT) and 4-amino-4H-1,2,4-triazole-3,5-diol (ATDO), then combined with metals Cu and Ni, and further adjusted by the introduction of NO2 and NH2. The molecular and electronic structures, heat of formation (HOF), density, detonation velocity, detonation pressure, and sensitivity were investigated by the density functional theory method. The results showed that in metals, the position and amount of NO2/NH2 have great effects on the structure and property of metal complexes, and these effects coupled with each other. N-NO2 bond is the relatively weak bond, and its max length is related with the sensitivity closely. The designed metal complexes all have high HOF (673~868 kJ mol−1), high density (2.06~2.14 g cm−3), and ideal oxygen balance (− 19.2~− 6.7%), which further make them have higher detonation velocity (8.76~9.84 km s−1) and detonation pressure (37.4~46.6 GPa) than three famous high-energy compounds 1,3,5-trinitro-1,3,5-triazine (RDX); 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX); or even 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20). At the same time, they are less sensitive than RDX, HMX, and CL-20, making them potential candidates for high-energy density compounds.

Investigation of the reactivity indices for the formation of substituted dinitroanilines and correlations to their dockings on α-tubulin of Plasmodium falciparum Abstract The local and global reactivity descriptors of substituted dinitroaniline analogues were investigated using M06-2X/6-31 + G(d,p) method. It was observed that NH2 (m = 3.53 eV; p = 3.70 eV) substituent conveyed the highest nucleophilic character on the benzene ring system than the other groups under study. For the substrates 4-substituted-1-chloro-2,6-dinitrobenzenes, the condensed to atom electrophilicity (\( {\omega}_k^{+} \)) increases in the order COOCH3 > NO2 > F > SO3H > CN > Cl > Br. The para substituted groups with the halogens follow the order of increasing electronegativity, F > Cl > Br. However, the nucleophilicity of the halo substituents of the products increases in the order, F > Br > Cl. Molecular docking simulations using the homology model with the crystallographic structure of zinc-induced bovine tubulin heterodimer (1JFF) as one of the templates reveal that the interactions between the tubulins of Plasmodium falciparum and dinitroaniline analogues are due to H-bonding. In general, the binding interaction is with the following residues: Met137, ARG64, Lys60, Glu183, Val4, His28, Cys171, Tyr224, Asn206, 228, Ile235, and Leu238. The pKas of the residue decrease as the ring activating power of the substituents increases from strongly activating to weakly activating groups. There is no evidence of intra or intermolecular H-bonding between Arg64 and Cys171. Electronegativity (χ) gives a better generic description of the dinitroanilines than any other parameters considered. Short-range hydrophobic interaction contributes to reduced binding affinities of the ligands. Graphical abstract Reaction of substituted 2,6-dinitro chlorobenzene with diisopropylamine. Orbital interaction between the substrates and diisopropylamine in the formation of the dinitroanilines

Compressibility of 2 M 1 muscovite-phlogopite series minerals Abstract Muscovite (Ms) and phlogopite (Phl) belong to the 2:1 dioctahedral and trioctahedral layer silicates, respectively, and are the end members of Ms-Phl series minerals. This series was studied in the 2M1 polytype and modeled by the substitution of three Mg2+ cations in the Phl octahedral sites by two Al3+ and one vacancy, increasing the substitution up to reach the Ms. The series was computationally examined at DFT level as a function of pressure to 9 GPa. Cell parameters as a function of pressure and composition, and bulk moduli as a function of the composition agrees with the existing experimental results. The mixing Gibbs free energy was calculated as a function of composition. From these data, approximated solvi were calculated at increasing pressure. A gap of solubility is found, decreasing the gap of solubility at high pressure.

Insights into the activation process of CO 2 through Dihydrogenation reaction Abstract Based on first principle calculation, activation of CO2 has been analyzed thoroughly by using different conceptual density functional theory based descriptors like reaction force, reaction force constant, reaction electronic flux, dual descriptor, etc. via dihydrogenation reaction of B3N3, H2 and CO2. The total reaction is a two-step reaction where initially B3N3H2 is formed from the reaction between B3N3 and H2 and in the second step HCOOH is form due to the reaction of CO2 by B3N3H2. It has been found that the di-hydrogen reaction for the CO2 activation is endothermic in nature, which can be changed to exothermic reaction by applying proper external electric field. Movement of H2 plays an important role in the CO2 activation process. The reaction force constant, Wiberg bond index and its derivative reveal that the reaction is slightly asynchronous and concerted in nature.