Structure–property relationships of energetic nitrogen-rich salts composed of triaminoguanidinium or ammonium cation and tetrazole-based anions

Density functional theory and volume-based thermodynamics calculations have been performed to study the crystal densities, heats of formation (HOFs), energetic properties, and thermodynamics of formation for a series of ionic salts composed of triaminoguanidinium or ammonium cations and tetrazole-based anions. Substitution with NF₂, CH₂NF₂, CF₂NF₂, or C(NO₂)₂NF₂ groups increased the densities of the salts. The densities of the tetrazole-based salts are affected not only by different substituents but also by different cations. The CN or N₃ groups are effective substituents for increasing the HOFs of the salts. The triaminoguanidinium cation is more effective than the ammonium cation for increasing the HOF of the tetrazole-based salts. Substitution with NO₂, NF₂, or C(NO₂)₂NF₂ groups enhances the explosive properties of the salts. The thermodynamics of formation of the salts reveal that all of the tetrazole-based salts with the triaminoguanidinium or ammonium cation could be synthesized using the proposed reactions. Our calculated methods provide a straightforward and inexpensive route for screening a large number of potentially energetic ionic salts.     

Hydrogen-bond-directed-linking solving transparence-efficiency tradeoff in nonlinear optical molecule

It is well known that settling transparency-efficiency tradeoff is important to design nonlinear optical (NLO) materials. In this work, we constructed one-dimensional polymeric cyanoacetylene (NCCCH)_n by hydrogen-bond-directed-linking to understand this tradeoff from molecular level. Results show that the first hyperpolarizability of (NCCCH)_n (n = 2–8) gradually increased with the increase of n, and what is more important is that the red-shifts, associated with the increase of n, were very little. It is proposed that these polymeric structures possess double-degenerated charge transitions, which contribute to the hyperpolarizability in an additive fashion, and that the coupled oscillators are gradually improved, which lead to the increase of the first hyperpolarizability. Therefore, we propose the hydrogen-bond-directed-linking idea is helpful to develop the potential high-performance NLO materials.     

Identification of the transition state for fast reactions: The trapping of hydroxyl and methyl radicals by DMPO—A DFT approach

Up to date, attempts to locate the transition state (TS) for the trapping reaction between OH and DMPO have been unsuccessful, and the lack of molecular mechanisms by which OH binds to the spin-trap constitutes a question still unsolved. Herein, we have taken a step forward on this task by describing the theoretical TS for the trapping of OH and CH₃ by DMPO and the intrinsic reaction coordinates. This work aims to provide new understandings on the molecular orbital (MO) interactions that rule these reaction paths. Besides we assessed the degree of involvement of weak interactions and the charge transfer (CT) phenomenon involved in such interactions. Regarding the trapping of OH, the beginning of the reaction would be ruled by weak interactions to then give way to stronger MO interactions conducive to the formation of the TS. For CH₃, the reaction is, instead, early ruled by significant MO interactions, and a relatively small contribution in the weak interactions range. At the TS, both reactions share the formation of an antibonding orbital responsible for hosting the unpaired electron, and two bonding orbitals between the radical and the spin-trap. Additionally, the charge is transferred primarily from DMPO to OH through β orbitals, while for CH₃, the CT occurs in both directions, so that while DMPO behaves like an α-acceptor/β-donor, CH₃ acts as a β-acceptor/α-donor. Finally, we provide evidence showing that the resultant theoretical models are in agreement with the hyperfine coupling constants as obtained from biological-ESR spin trapping experiments.     

Designed inhibitors with hetero linkers for gastric proton pump H+,K+-ATPase: Steered molecular dynamics and metadynamics studies

Acid suppressant SCH28080 and its derivatives reversibly reduce acid secretion activity of the H⁺,K⁺-ATPase in a K⁺ competitive manner. The results on homologation of the SCH28080 by varying the linker chain length suggested the improvement in efficacy. However, the pharmacokinetic studies reveal that the hydrophobic nature of the CH₂ linker units may not help it to function as a better acid suppressant. We have exploited the role of linker unit to enhance the efficacy of such reversible acid suppressant drug molecules using hetero linker, i.e., disulfide and peroxy linkers. The logarithm of partition coefficient defined for a drug molecule relates to the partition coefficient, which allows the optimum solubility characteristics to reach the active site. The logarithm of partition coefficient calculated for the designed inhibitors suggests that inhibitors would possibly reach the active site in sufficient concentration like in the case of SCH28080. The steered molecular dynamics studies have revealed that the Inhibitor-1 with disulfide linker unit is more stable at the active site due to greater noncovalent interactions compared to the SCH28080. Centre of mass distance analysis suggests that the Cysteine-813 amino acid residue selectively plays an important role in the inhibition of H⁺,K⁺-ATPase for Inhibitor-1. Furthermore, the quantum chemical calculations with M11L/6-31 + G(d,p) level of theory have been performed to account the noncovalent interactions responsible for the stabilization of inhibitor molecules in the active site gorge of the gastric proton pump at different time scale. The hydrogen bonding and hydrophobic interaction studies corroborate the center of mass distance analysis as well. Well-tempered metadynamics free energy surface and center of mass separation analysis for the Inhibitor-1 is in good agreement with the steered molecular dynamics results. The torsional angle of the linker units seems to be crucial for better efficacy of drug molecules. The torsional angle of linker units of SCH28080 (COCH₂C) and of Inhibitor 1 (CSSC) prefers to lie within ∼60°–90° for a longer time during the simulations, whereas, the peroxy linker (COOC) of Inhibitor 2 prefers to adopt ∼120–160°. Therefore, it appears that the smaller torsion angle of linker units can achieve better interactions with the active site residues of H⁺,K⁺-ATPase to inhibit the acid secretion activity. The reversible drug molecules with disulfide linker unit would be a promising candidate as proton pump antagonist to H⁺,K⁺-ATPase.     

Understanding the potency of fatty acids with the amino acid side chains of bovine β lactoglobulin—A quantum chemical approach

The present study aims to spotlight on the strength of interaction between different fatty acids with the Bovine−lactoglobulin (LGB) protein side chains along with the crystal water molecules at M062X/def2-QZVP level of theory. To analyse the role of carboxylic acid and its interaction with side chains and to reveal the significance of carboxylic acid, it was replaced by Acyl chloride (COCl), Acyl Bromide (COBr) and Acyl-Fluorine (COF) group and COS group. The ligands are linear with a straight and branched chain of carbon atoms, but extended methyl group make the ligand bend resulting in non-planar geometry. The least and highest band gap energy reveals the conductivity properties of ligands. 3UEW, the Palmitic acid is well-built owing to the interaction with the amino acid side chains Lys 69 and Glu 62 resulting in interaction energy of −124.98 kcal/mol. 3D-NCIplot isosurface map and 2D-NCIplot graph plays a key role to confirm and analyse the occurrence of various non covalent interactions. The overall analysis of the fatty acids implies the fact that depending on the aliphatic chain length, the carboxyl group was capable of positioning favourable binding site.     

Mechanism,kinetics and atmospheric fate of CF3CHCH2, CF3CFCH2, and CF3CFCF2 by its reaction with OH-radicals: CVT/SCT/ISPE and hybrid meta-DFT methods

The dual level direct dynamic study is carried out for the reactions of CF₃CHCH₂, CF₃CFCH₂ and CF₃CFCF₂ with hydroxyl radicals. The dynamic calculations are performed using the variational transition state theory (VTST) with interpolated single-point energies (ISPE) method at M06-2X/MG3S//M06-2X/6-31+G(d,p) level of theory. All the possible reactions such as abstraction and addition–elimination pathways are explored for the title reactions. The temperature dependent rate coefficients using canonical variational transition state theory with small curvature tunneling for the reaction of OH radicals with test molecules over the temperature range of 200–3000 K are computed. The predicted rate coefficients (in 10⁻¹² cm³ molecule⁻¹ s⁻¹) using CVT/SCT/ISPE methodology for the reaction of CF₃CHCH₂, CF₃CFCH₂ and CF₃CFCF₂ with OH radicals are 1.48, 1.02 and 1.77, respectively, are in good agreement with reported ones at 298 K. The atmospheric lifetimes for the test molecules CF₃CHCH₂, CF₃CFCH₂ and CF₃CFCF₂ are calculated at 277 K to be 8, 11 and 6 days, respectively. Global warming potentials are also reported for the different time horizon of 20, 100 and 500 years.     

Interactions of small gold clusters,Aun (n = 1–3), with graphyne: Theoretical investigation

The interactions of gold atom and clusters (Au₂ and Au₃) with the active sites of graphyne (GY) have been investigated using density functional theory (PBE, PBE-D3, and B3LYP-D3). In order to compare performance of DFT functional (BP86, PBE, TPSSh, B3LYP, PBE-D3, TPSSh-D3, and B3LYP-D3), the interactions of Au₂ with various functional groups such as sp, sp² and aromatic sp² carbon atoms, sp, sp² and aromatic sp²-bonds have been investigated and also compared with the ab initio MP2 results. Additionally, the nature of interactions for graphyne–Au₂ complexes are interpreted by means of the natural bond orbital (NBO), the quantum theory of atoms in molecules (QTAIM) and energy decomposition analysis (EDA) and compared with those of related graphene–Au₂. This study suggests that graphyne shows complex behavior in comparison to those of graphene and could also be useful in modeling of the next generation electronic devices.     

Theoretical studies on the common catalytic mechanism of transketolase by using simplified models

Transketolase is a convenient model system to study enzymatic thiamin catalysis. By using density functional theory (DFT) method, the transfer mechanism of a 2-carbon fragment between a donor ketose X5P and an acceptor aldose R5P catalyzed by transketolase has been studied on simplified models. The calculation results indicate that the whole reaction cycle contains several proton transfer processes as well as CC bond formation and cleavage steps. Each CC bond formation or cleavage step is always accompanied by a proton transfer process, which follows a concerted but asynchronous mechanism. The CC bond formation is always prior to the proton transfer, and the CC bond cleavage is always later than proton transfer, suggesting that the CC bond ligation facilitates the proton transfer, and proton transfer promotes the CC bond cleavage. In the first half- and second half-reactions, the energy barriers of CC bond formations are always higher than those of CC bond cleavages. The 4-amino group of cofactor ThDP and histidine residue can act as the proton donor/acceptor during the catalytic reaction.     

Structure,antioxidative potency and potential scavenging of OH and OOH of phenylethyl-3,4-dihydroxyhydrocinnamate in protic and aprotic media: DFT study

DFT methods including B3LYP, B3PW91 and M05–2 x associated to 6–31 + G(d,p) were used for the structural and antioxidant potency studies of phenylethyl-3,4-dihydroxy-hydrocinnamate (PDH). Solvents were employed according to their protric and aprotic character. So, calculated structures agree with the experimental data. O₄H₄ is propitious to scavenge radicals whatever the medium except in water where O₃H₃ and O₄H₄ are competitive. The explicit solvents of dichloromethane (DCM) and water present a disparity of OH bond dissociation enthalpy and free energy (BDE and BDFE). These parameters are low in continuum except in water. The ionization potentials (IP) and potential affinities (PA) are low in solvents. BDE, IP and PA are each, approximatively constant in mixed solvent treatment in water using n-H₂O (n = 3,5,8). Elsewhere, H-atom transfer (HAT) mechanism is favoured in vacuum and DCM, whereas sequential proton loss electron transfer (SPLET) is likely in protic solvents. A discord between HAT and SPLET in benzene is observed. The PDH compound is more antioxidant and resistant to oxidation than caffeic acid phenethyl ester (CAPE). The potential of scavenging of OH and OOH whatever the reaction channel shows that they decay rapidly in any media through HAT. PDH is easily deprotonated in the protic solvents and the resulting product is the most antioxidant and the least resistant to oxidation.     

Mechanism and regioselectivity of the reversible Diels–Alder cycloaddition of 2-methyl-1,3 butadiene with C48B6N6 heterofullerene: A DFT approach

A theoretical study of the mechanism and regioslectivity of Diels–Alder [4+2] cycloaddition reactions between 2-methyl-1,3 butadiene and hetero bonds of the most stable isomer of C₄₈B₆N₆ heterofullerene have been studied at the B3LYP/6-31G^* level. Three heterobond pathways BC, BN and NC including two regioisomers for each one are considered by different approaches. All studied reactions have normal electron demand nature and corresponding regioisomers are produced via asynchronous processes. Predicted regioselectivities using electronic and energetic results are in complete agreement with each other and show that BC heterobond pathway is more active than others and regioisomer 16 is the major. The local reactivity difference values (R_k) show that all reaction sites at C₄₈B₆N₆ present ambiphilic activation while reaction sites at 2-methyl-1,3 butadiene show nucleophilic activation. Therefore, it is predictable that C₄₈B₆N₆ should present electrophilic nature. Plotting of ΔR_k and Δs values of six studied channels toward corresponding activation Gibbs free energies showed that the regioisomeric channel with lower ΔR_k and Δs values is faster and vice versa.     

Theoretical investigation of the structures,stabilities, and NLO responses of calcium-doped pyridazine: Alkaline-earth-based alkaline salt electrides

Currently, whether alkaline-earth-doped compounds with electride characteristics are novel candidates for high-performance nonlinear optical (NLO) materials is unknown. In this paper, using quantum chemical computations, we show that: when doping calcium atoms into a family of alkaline-substituted pyridazines, alkaline-earth-based alkaline salt electrides M-H₃C₄N₂⋯Ca (MH, Li, and K) with distended excess electron clouds are formed. Interestingly, from the triplet to the singlet state, the chemical valence of calcium atom changes from +1 to 0, and the dipole moment direction (μ₀) of the molecule reverses for each M-H₃C₄N₂⋯Ca. Changing pyridazine from without (H₄C₄N₂⋯Ca) to with one alkaline substituent (M-H₃C₄N₂⋯Ca, MLi and K), the ground state changes from the triplet to the singlet state. The alkaline earth metal doping effect (electride effect) and alkaline salt effect on the static first hyperpolarizabilities (β₀) demonstrates that (1) the β₀ value is increased approximately 1371-fold from 2 (pyridazine, H₄C₄N₂) to 2745 au (Ca-doped pyridazine, H₄C₄N₂⋯Ca), (2) the β₀ value is increased approximately 1146-fold from 2 in pyridazine (H₄C₄N₂) to 2294 au in an Li-substituted pyridazine (Li-H₃C₄N₂), and (3) the β₀ value is increased 324-(MLi) and 106-(MK) fold from 826 (MLi) and 2294 au (MK) to 268,679 (MLi) and 245,878 au (MK), respectively, from the alkalized pyridazine (M-H₃C₄N₂) to the Ca-doped pyridazine (M-H₃C₄N₂⋯Ca). These results may provide a new means for designing high-performance NLO materials.     

Linear σ-hole⋯CO⋯σ-hole intermolecular interactions between carbon monoxide and dihalogen molecules XY (X,Y = Cl,Br)

Carbon monoxide can interact with two dihalogen molecules XY (X, Y = Cl, Br) in the form of X(Y)⋯COX(Y)⋯CO⋯X(Y)X(Y) trimeric complex, and their nature and characteristics were investigated at MP2/aug-cc-pVDZ level without and with counterpoise method, together with single point calculations at CCSD(T)/aug-cc-pVDZ level. The optimized geometries, stretching modes and interaction energies of a series of X(Y)⋯COX(Y)⋯CO⋯X(Y)X(Y) trimeric complexes were obtained and discussed. The cooperativity in these complexes was evaluated. EDA analyses reveal that the electrostatic interaction is the dominant net driving force in each trimer, but the contributions of other interactions like exchange, dispersion and polarization interactions are also important. QTAIM and NCI analyses confirm the existence of attractive halogen-bonding interactions. Additionally, EDDMF analysis was employed for the component dimers of these trimers, which indicates that the formation of halogen-bonding interactions is closely related to the charge shift and the rearrangement of electronic density in the formation of these complexes. The results would provide valuable insight into for these linear halogen bonds.     

Theoretical investigation on gas-phase reaction of CF3CH2OCH3 with OH radicals and fate of alkoxy radicals (CF3CH(O)OCH3/CF3CH2OCH2O)

Detailed theoretical investigation has been performed on the mechanism, kinetics and thermochemistry of the gas phase reactions of CF₃CH₂OCH₃ (HFE-263fb2) with OH radicals using ab-initio and DFT methods. Reaction profiles are modeled including the formation of pre-reactive and post-reactive complexes at entrance and exit channels, respectively. Our calculations reveal that hydrogen abstraction from the CH₂ group is thermodynamically and kinetically more facile than that from the CH₃ group. Using group-balanced isodesmic reactions, the standard enthalpies of formation for CF₃CH₂OCH₃ and radicals (CF₃CHOCH₃ and CF₃CH₂OCH₂) are also reported for the first time. The calculated bond dissociation energies for the CH bonds are in good agreement with experimental results. At 298 K, the calculated total rate coefficient for CF₃CH₂OCH₃ + OH reactions is found to be in good agreement with the experimental results. The atmospheric fate of the alkoxy radicals, CF₃CH(O)OCH₃ and CF₃CH₂OCH₂O are also investigated for the first time using the same level of theory. Out of three plausible decomposition channels, our results clearly point out that reaction with O₂ is not the dominant path leading to the formation of CF₃C(O)OCH₃ for the decomposition of CF₃CH(O)OCH₃ radical in the atmosphere. This is in accord with the recent report of Osterstrom et al. [CPL 524 (2012) 32] but found to be in contradiction with experimental finding of Oyaro et al. [JPCA 109 (2005) 337].     

Toward an ab initio potential energy surface for paclitaxel: A C-13 isoserine side chain conformational study

(S)-3-Methyl-3-butenyl-(2R,3S)-N-benzoyl-3-phenylisoserinate is used as a model of the C-13 side chain, an essential subunit for the cytotoxicity of the diterpenoid paclitaxel, a chemotherapeutic drug used in the treatment of cancer. The potential energy surface (PES), calculated using a density functional theory method (DFT) and refined with MP2 single-point energy calculations, based on B3LYP geometries, was evaluated. Twelve intramolecular hydrogen bond patterns were identified for 103 in vacuo conformers. The most stable subset of these structures was found to have cooperative NH ⋯ OH ⋯ OC(O) motifs and six minima of importance that lie within 1.2 kcal/mol of each other. The oxygen atoms of the ester groups effectively compete with the 2′-oxygen as a proton acceptor of NH to form stable internal hydrogen bonded structures. Additionally, the conventional OH ⋯ OC(N) hydrogen bond, which is represented by almost one third of the located minima, donates a number of stable conformers. However, the PES of the conformationally flexible model is highly dependent on the polarity of the environment. For example, the OH ⋯ OC(N) feature dominates over the cooperative motif in water. The side chain of the experimental T-taxol shaped structure agrees nicely with the respective theoretical lowest energy minimum. The π-π interactions of the phenyl rings and ethylene moiety of this structure are also discussed.     

Third-order nonlinear optical properties of molecules containing aromatic diimides: Effects of the aromatic core size and a redox-switchable modification

The third-order nonlinear optical (NLO) properties of aromatic diimide molecules have been studied for the first time using density functional theory (DFT) with a finite field (FF). This study shows that the size of the aromatic core can affect the static second hyperpolarizability (γ). Increasing the number of benzenes along the longitudinal axis can effectively improve the γ values because the degree of charge transfer along the longitudinal direction increases, whereas an increase in the number of benzenes along the perpendicular axis does not enhance the γ values. Furthermore, the NLO responses of the reduced form radical anions 1⁻, 5⁻ and 6⁻, which were obtained by a reversible redox process, are discussed. The results show that the γ values of the radical anions are changed by the redox process. For the reduced form radical anion 6⁻, the γ value is −1906.71 × 10⁻³⁶ esu, and its absolute value is ∼7.3 times larger than that of its neutral parent. An analysis of the BLA values demonstrates that the γ value is closely related to the conjugation of the aromatic core used in the redox process.     

DFT study on the chemical sensing properties of B24N24 nanocage toward formaldehyde

It has been previously shown that the toxic formaldehyde gas (H₂CO) cannot be detected by pristine BC₂N, carbon, and BN nanotubes, BC₃ nanosheet and graphene. Herein, density functional theory calculations were employed to investigate the electronic and structural behavior of a pristine B₂₄N₂₄ nanocluster toward H₂CO molecules. It was found that [4], [6] BN bonds of the nanocluster are the most favorable sites for the H₂CO adsorption, compared to the [4], [8], and [6], [8] ones. When an H₂CO molecule is adsorbed on a [4], [6] BN bond, an energy of about 16.40 kcal/mol is released and the HOMO-LUMO gap of the cluster is decreased from 6.45 to 2.98 eV. Thus, the electrical conductivity of the cluster is significantly increased, indicating that it can produce an electronic noise at the presence of H₂CO molecules. Increasing the number of adsorbed H₂CO molecules, the electrical conductivity more increases. The recovery time for the H₂CO from the surface of B₂₄N₂₄ is calculated to be very short (∼1.02 s). Also, the UV–vis spectrum shows that the λ_max of the B₂₄N₂₄ shows a large redshift upon the adsorption process and transfers from the UV to the visible region.     

Theoretical studies on kinetics,mechanism and thermochemistry of gas-phase reactions of HFE-449mec-f with OH radicals and Cl atom

A theoretical study on the mechanism and kinetics of the gas phase reactions of CF₃CHFCF₂OCH₂CF₃ (HFE-449mec-f) with the OH radicals and Cl atom have been performed using meta-hybrid modern density functional M06-2X using 6-31+G(d,p) basis set. Two conformers have been identified for CF₃CHFCF₂OCH₂CF₃ and the most stable one is considered for detailed study. Reaction profiles for OH-initiated hydrogen abstraction are modeled including the formation of pre-reactive and post-reactive complexes at entrance and exit channels. Our calculations reveal that hydrogen abstraction from the CH₂ group is thermodynamically and kinetically more facile than that from the CHF group. Using group-balanced isodesmic reactions, the standard enthalpies of formation for HFE-449mecf and radicals generated by hydrogen abstraction, are also reported. The calculated bond dissociation energies for CH bonds are in good agreement with experimental results. The rate constants of the two reactions are determined for the first time in a wide temperature range of 250–450 K. The calculated rate constant values are found to be 9.10 × 10⁻¹⁵ and 4.77 × 10⁻¹⁷ cm³ molecule⁻¹ s⁻¹ for reactions with OH radicals and Cl atom, respectively. At 298 K, the total calculated rate coefficient for reactions with OH radical is in good agreement with the experimental results. The atmospheric life time of HFE-449mec-f is estimated to be 0.287 years.     

The derivation of a chiral substituent code for secondary alcohols and its application to the prediction of enantioselectivity

A chiral substituent code was proposed based on the features of secondary alcohols, in which a chiral center is attached to two substituents in addition to OH and H substituents. The new chirality code, which was generated by predefining positional information of four substituents attached to stereocenter, was applied to two datasets composed of secondary alcohols as the enantioselective products of asymmetric reactions. In the first dataset, the chemical reaction was catalyzed by a biocatalyst, lipase from Candida rugosa. The catalyst for the second dataset was (−)-diisopinocampheylchloroborane. The structure–enantioselectivity relationship models were constructed using random forests with the chiral substituent code as the input. The resulting models were assessed both in terms of single enantiomers and pairs of enantiomers. Satisfactory results were obtained for both datasets. Although the chiral substituent code was specifically developed for secondary alcohols, it can easily be extended to represent chiral compounds possessing a specific chiral center bonded to two variable substituents.