Second group metal dimers can replace the carbon atom in benzene to form metallabenzene (C5H6M2) compounds. These complexes possess some aromatic character and promising hydrogen adsorption properties. In this study, we investigated the aromatic character of these compounds using aromaticity indices and molecular orbital analysis. To determine the nature of interactions between hydrogen and the metallic center, variation-perturbational decomposition of interaction energy was applied together with ETS-NOCV analysis. The results obtained suggest that the aromatic character comes from three π orbitals located mainly on the C5H5? fragment. The high hydrogen adsorption energy (up to 6.5 kcal mol?1) results from two types of interaction. In C5H6Be2, adsorption is controlled by interactions between the empty metal orbital and the σ orbital of the hydrogen molecule (Kubas interaction) together with corresponding back-donation interactions. Other C5H6M2 compounds adsorb H2 due to Kubas interactions enhanced by H2–π interactions.
Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode between AgamOBP7 and novel (E)-β-farnesene (EBF) analogues with an aromatic ring. The ligand-binding cavity in OBP7 was found to be mostly hydrophobic due to the presence of several nonpolar residues. The interactions between the EBF analogues and the hydrophobic residues in the binding cavity increased in strength as the distance between them decreased. The EBF analogues with an N-methyl formamide or ester linkage had higher docking scores than those with an amide linkage. Moreover, delocalized π–π and electrostatic interactions were found to contribute significantly to the binding between the ligand benzene ring and nearby protein residues. To design new compounds with higher activity, four EBF analogues D1–D4 with a benzene ring were synthesized and evaluated based on their docking scores and binding affinities. D2, which had an N-methyl formamide group linkage, exhibited stronger binding than D1, which had an amide linkage. D4 exhibited particularly strong binding due to multiple hydrophobic interactions with the protein. This study provides crucial foundations for designing novel EBF analogues based on the OBP structure.
In this study, the doped defects in nitromethane crystals were investigated using first-principles calculations for the first time. We introduce dopant atoms in the interstitial sites of the nitromethane lattice, aiming to study the effects of element-doping on the structural properties, electronic properties, and sensitivity characteristics. The obtained results show that doped defects obviously affect the neighboring nitromethane molecules. The modification of electronic properties shows that the band gaps are significantly influenced by doped defects. Partial density of states and population analysis further reveal the mechanism for sensitivity control of nitromethane. It is shown that the new electronic states were introduced in the forbidden bands and the doped defects resulted in charge redistributions in the systems.
Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has been successfully applied to predict catalytic effects resulting from intermolecular interactions with individual water molecules constituting the first hydration shell, aminoacid mutations in enzymes or Si→Al substitutions in zeolites. In this contribution, hydrogen to fluorine (H→F) substitution effects for two model reactions have been examined indicating qualitative applicability of the catalytic field concept in the case of systems involving intramolecular interactions.
When electronic correlation energy is partitioned topologically, a detailed picture of its distribution emerges, both within atoms and between any two atoms. This methodology allows one to study dispersion beyond its more narrow definition in long-range Rayleigh-Schrödinger perturbation theory. The interacting quantum atoms (IQA) method was applied to MP2/6-31G(d,p) (uncontracted) wave functions of a wide variety of systems: glycine…water (hydration), the ethene dimer (π-π interactions), benzene (aromaticity), cyclobutadiene (antiaromaticity), and NH3BH3 (dative bond). Through the study of molecular complexes it turns out that dispersion energy is either important to a system’s stabilization (for the C2H4 dimer) or not important (for Gly…H2O). We have also discovered that the delocalization in benzene lowers the strength of Coulomb repulsion in the bonds, which has been quantified for the first time through IQA. Finally, we showed that the nature of the dative bond is much different from that of a regular covalent bond as it is not destabilized by electronic correlation. Finally, the conclusions obtained for these archetypical systems have implications for the future of the quantum topological force field FFLUX in the simulation of larger systems.
Graphical abstract Atomic and bond dynamic correlation energies are now available thanks to IQA. Larger molecules can now be accessed to include resonance and solvation of FFLUX force field
Development of new energetic salts is the key factor in replacing low performance compounds in conventional formulations of high explosives as well as propellants. Ten salts based on the nitroformate anion and various nitrogen-rich cations were designed and their geometric optimizations carried out using the density functional method. With reasonable oxygen balance (from ?36 % to 0 %), heats of formation (47–624 kJ mol?1) and high densities (1.81–1.89 g cm?3), the detonation velocity (D) and pressure (P) values of salts were calculated as 8.62–9.36 km s?1 and 33.10–40.01 GPa, respectively. Lastly, the nitroformate salts studied in this work are of prospective interest as high performance explosives.
The anti-hypertensive drugs amlodipine, atenolol and lisinopril, in ordinary and PEGylated forms, with different combined-ratios, were studied by molecular dynamics simulations using GROMACS software. Twenty simulation systems were designed to evaluate the interactions of drug mixtures with a dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane, in the presence of water molecules. In the course of simulations, various properties of the systems were investigated, including drug location, diffusion and mass distribution in the membrane; drug orientation; the lipid chain disorder as a result of drug penetration into the DMPC membrane; the number of hydrogen bonds; and drug surface area. According to the results obtained, combined drugs penetrate deeper into the DMPC lipid bilayer membrane, and the lipid chains remain ordered. Also, the combined PEGylated drugs, at a combination ratio of 1:1:1, enhance drug penetration into the DMPC membrane, reduce drug agglomeration, orient the drug in a proper angle for easy penetration into the membrane, and decrease undesirable lipotoxicity due to distorted membrane self-assembly and thickness.
Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391–5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100–200 pN range, consistent with published experimental estimates.
In this article, we explore the capacity of formed Schiff base complexes to trap metal atoms or ions, using their aromatic ends. The intrinsic geometry of each complex defines the process of substitution. Two cases were studied; one involving a trans Schiff base complex and the other considering how a salen ligand, with nickel systems traps chromium. We also assessed the nature of the new bonds and the frontier molecular orbitals.
Magnetic shielding constants for an isolated fullerene C60, cucurbituril CB[9], and the host-guest complex C60@CB[9] were calculated as a function of separation of the monomers. Our results in the gas phase and water indicate a significant variation of the magnetic properties for all atoms of the monomers in the complex and after liberation of fullerene C60 from the interior of the CB[9] cavity. The interaction between the two monomers results in a charge transfer that collaborates with a redistribution of electron density to deshield the monomers.
Density functional theory (DFT) was utilized to elucidate the reaction mechanisms of and the key factors that influence the Ni(0)-catalyzed cross-dimerization and -trimerization of trimethylsilylacetylene (R1) and diphenylacetylene (R2). Calculated results revealed that the electron-donating ability of the ligand plays a crucial role in determining the regionselectivity of this tandem reaction. The use of strongly electron-donating ligands favors the formation of cross-dimer intermediates, whereas cross-trimer products can easily be synthesized using weakly electron-donating ligands. A simple method of estimating the electron-donating abilities of different ligands based on the Mulliken charge distribution of the ligand–ligand pair was employed. The present theoretical results allow us to elucidate the reaction mechanisms for and to identify the factors that exert the greatest influence on the ligand-controlled cross-dimerization and -trimerization of trimethylsilylacetylene and diphenylacetylene. Guidelines for the design of novel ligand systems with Ni(0) catalysts are also proposed.
The electric dipole transitions between pure spin and mixed spin electronic states are calculated at the XMC-QDPT2 and MCSCF levels of theory, respectively, for different intermolecular distances of the C6H6 and O2 collisional complex. The magnetic dipole transition moment between the mixed-spin ground (“triplet”) and the first excited (“singlet”) states is calculated by quadratic response at MCSCF level of theory. The obtained results confirm the theory of intensity borrowing and increasing the intensity of electronic transitions in the C6H6?+?O2 collision. The calculation of magnetically induced current density is performed for benzene molecule being in contact with O2 at the distances from 3.5 to 4.5 Å. The calculation shows that the aromaticity of benzene is rising due to the conjugation of π-MOs of both molecules. The C6H6?+?O2 complex becomes nonaromatic at the short distances (r?<?3.5 Å). The computation of static polarizability in the excited electronic states of the C6H6?+?O2 collisional complex at various distances supports the theory of red solvatochromic shift of the a?→?X band.
The structure and stability of various ternary complexes in which an extended aromatic system such as coronene interacts with ions/atoms/molecules on opposite faces of the π-electron cloud were investigated using ab initio calculations. By characterizing the nature of the intermolecular interactions using an energy decomposition analysis, it was shown that there is an interplay between various types of interactions and that there are co-operativity effects, particularly when different types of interactions coexist in the same system.
Graphical abstract Weak OH-π, π-π and van der Waals-π ternary systems are stabilized through dispersion interactions. Cation-π ternary systems are stabilized by through-space electrostatic interactions.
A perfectly planar Al13+ cluster (CI) and a quasi-planar Al13+ cluster (CII) have been found for the first time. Both clusters have a triangular core surrounded by a set of ten Al atoms in the form of a ring. These cationic clusters have substantial aromatic character. The planar CI cluster has local antiaromatic patches within global aromatic sea. It is doubly aromatic having both σ and π aromatic character. The quasi-planar CII cluster is also aromatic but it has more σ-delocalization.
Differing from the weakly antiaromatic B80 buckyball, the medium-sized C1–B28 and D2h–B38, as well as their mono- to tetra-anions, are highly aromatic, as indicated by the negative nucleus-independent chemical shifts (NICSs) at their cage centers. The interior cavities and high aromaticity of the B28 and B38 cages render them very promising hosts to accommodate diverse metal atoms. Accordingly, we carried out systematic density functional theory (DFT) computations on the structures, stabilities and electronic properties of metalloborofullerenes MBn (M?=?Li, Na, K, Rb, Cs, Be, Mg, Ca, Sr, Ba, Sc, Y, La and Ti; n?=?28 and 38). Among them, besides the recently reported M@B38(M?=?Sc, Y and Ti) [Lu et al. (2015) Phys Chem Chem Phys 17:20897–20902], Ti@B28 and M@B38 (M?=?Ca and La) also favor endohedral structures with large binding energies, and are suggested promising targets for experimental applications. Note that Ti@B28 is the first endohedral derivative based on the new B28 fullerene, and La@B38 features the largest metal size inside a B38 cage thus far. These endohedral derivatives, as exemplified by Ca@B38, may exhibit σ and π double aromaticity over the whole cage surface, indicating their considerable stability. In contrast, the other metals prefer to reside at the exterior cage surface, due mainly to the mismatch of their sizes with the boron cages, though the size match is not the only factor to determine their doping form. Furthermore, the infrared absorption spectra and 11B nuclear magnetic resonance spectra of the three new M@Bn complexes were computed to assist future experimental characterization.
Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and \( {HO}_2/{O}_2^{-} \) radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of \( {HO}_2/{O}_2^{-} \) radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton.
The activation mechanism of dopamine receptors is unknown. The amino acids S5.42, S5.43, and S5.46 located in helix 5 appear to be crucial, but their specific roles in receptor activation have not been studied. We modeled the D1 dopamine receptor using the crystal structures of the D3 dopamine and β2 adrenergic receptors. Molecular dynamics simulations show that the interaction of dopamine with the D1 receptor leads to the formation of a hydrogen-bond network with its catechol group and helices 3, 5, and 6, including water molecules. The para hydroxyl group of dopamine binds directly to S5.42 and N6.55, the latter also interacting with S5.43. Unexpectedly, S5.46 does not interact directly with the catechol; instead, it interacts through a water molecule with S5.42 and directly with T3.37. The formation of this hydrogen-bond network, part of which was previously observed in docking studies with dopamine agonists, triggers the opening of the E6.30–R3.60 ionic lock associated with the activation of GPCRs. These changes do not occur in the unbonded (apo) receptor or when it is in a complex with the antagonist 3-methoxy-5,6,7,8,9,14-hexahydrodibenz[d,g]azecine. Our results provide valuable insight into the T3.37–S5.46–water–S5.43–ligand interaction, which may be crucial to the activation of the D1 dopamine receptor and should be considered during the design of novel agonists.
4-[N-(2-cyanoethyl)-N-ethylamino]-4′-nitroazo-benzene (disperse orange 25, DO25) is one of the main components in dyeing wastewater. In this work, supercritical water oxidation (SCWO) process of DO25 has been investigated using the molecular dynamic simulations based on the reactive force field (ReaxFF). For the SCWO system, the effects of temperature, the molecular ratio of DO25, O2 and H2O as well as the reaction time have been analyzed. The simulated results showed that the aromatic rings in DO25 could be attacked by hydroxyl radical, oxygen molecule, and hydroxyl radical together with oxygen molecule, respectively, which caused the aromatic ring-opening reaction to happen mainly through three different pathways. The hydroxyl radicals were mainly from water clusters and H2O2 (which was produced from oxygen molecules reacting with water clusters). However, for the SCW system as comparison, the aromatic rings in DO25 could be attacked by hydroxyl radical only, and the OH radicals just come from water clusters. During the DO25 SCWO degradation process, we also found that N elements in one DO25 molecule were difficult to be converted into environmentally friendly N2 molecules because of steric hindrance, but increasing the number of DO25 molecules could improve the possibility for the connection of N elements, thus promoting N element converting into N2. Extending reaction time could also improve N elements in DO25 to transform into N2 rather than carbonitride.
