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.
The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in methanol, water, and chloroform in the molecularly imprinted recognition were investigated systematically. The M06-2X results revealed that: 1) the hydroxyl groups in polar solvents such as methanol and water may markedly influence the weak interactions, and then alter the adsorption and emission spectra; 2) the electronic excitation in absorption spectra of dichlorvos is dominated by the configuration HOMO?→?LUMO, but in the most stable dichlorvos-MAA it becomes the ππ* excitation of HOMO?→?LUMO?+?1; 3) Mulliken charges reveal that dichlorvos almost dissociates to Cl- and a cation in its S1 excitation state; 4) the phosphorescence spectra of dichlorvos-MAA are relatively weak.
Graphical Abstract The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in the molecularly imprinted recognition of dichlorvos were investigated systematically in methanol, water, and chloroform as solvents.
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.
Mechanisms for the activation of water, ammonia, and other small molecules by the PCcarbeneP nickel pincer complex were studied computationally with the aid of density functional theory. The calculation results indicate that the strongly donating, nucleophilic carbene center can engage in a variety of heterolytic splitting of E?H (E=H, C, N, O) bonds, some of which are reversible. The cleavage of E?H bonds across the Ni=C bond represents a new mode of bond activation by ligand cooperativity in nickel pincer complex. On the basis of the calculations, we also demonstrate that reversible H2 activation across the Ir=C bond via the PCcarbeneP iridium pincer complex was observed in the experiments, while other E?H (E=C, N, O) bonds were not activated. Our calculations are in good agreement with experimental observations and could provide new insights into ligand cooperativity in nickel pincer complexes.
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.
Present molecular dynamics simulations indicate that the methanol component in a methanol/water mixture is more likely to be trapped in a cyclic peptide nanotube (CPNT), while water molecules tend to be present at the channel mouths as transient guests. Channel water resides mainly between methanol and the CPNT wall, resulting in a distinct decrease in the H-bond number per channel methanol. Six designed CPNTs with different channel diameters and outer surface characteristics all possess distinct selectivity to methanol over water. Of these, the amphipathic 8?×?(AQ)4-CPNT exhibits the best performance. Results in this study provide basic information for the application of a CPNT to enrich methanol from a methanol/water mixture.
The interaction of external water molecules with hydrated pyrrole-2-carboxaldehyde PCL/(H2O)n complexes was investigated. The work was supported by both theoretical [DFT/TD-DFT methods using 6-311G++(d,p) basis set in the ground (S0) and excited (S1, S2, S3)states] and experimental [UV-Vis, FTIR and Raman] verification. The focus of the present work was on the weak intermolecular O–H?O, N–H?O–H hydrogen bonded interaction (IerHB) between PCL and external water molecules, and the influence of increasing the number of water molecules to form hydrated PCL/(H2O)n complexes. Effects were observed on different vibrational normal modes and on electronic transition levels. A hydrogen-bonded network of water induces a shift to higher energy in certain normal modes of PCL to form stable PCL/(H2O)n complexes by lowering the barrier energy. Potential energy distribution (PED) analysis indicates a significant charge transfer from PCL to water by creating a water bridge. Hydrogen bonding effects account for the substantial red shift and broadness in νNH, νCO vibrational modes. Water rearrangement turns out to be the main driving force for hydrated complex formation.
Utilizing first-principles calculations, we studied the electronic and optical properties of C24, C12X6Y6, and X12Y12 fullerenes (X?=?B, Al; Y?=?N, P). These fullerenes are energetically stable, as demonstrated by their negative cohesive energies. The energy gap of C24 may be tuned by doping, and the B12N12 fullerene was found to have the largest energy gap. All of the fullerenes had finite optical gaps, suggesting that they are optical semiconductors, and they strongly absorb UV radiation, so they could be used in UV light protection devices. They could also be used in solar cells and LEDs due to their low reflectivities.
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.
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.
In this work, through a docking analysis of compounds from the ZINC chemical library on human β-tubulin using high performance computer cluster, we report new polycyclic aromatic compounds that bind with high energy on the colchicine binding site of β-tubulin, suggesting three new key amino acids. However, molecular dynamic analysis showed low stability in the interaction between ligand and receptor. Results were confirmed experimentally in in vitro and in vivo models that suggest that molecular dynamics simulation is the best option to find new potential β-tubulin inhibitors.
In advanced oxidation processes (AOPs), the detailed degradation mechanisms of a typical explosive of 2,4-dinitrotoluene (DNT) can be investigated by the density function theory (DFT) method at the SMD/M062X/6-311+G(d) level. Several possible degradation routes for DNT were explored in the current study. The results show that, for oxidation of the methyl group, the dominant degradation mechanism of DNT by hydroxyl radicals (?OH) is a series of sequential H-abstraction reactions, and the intermediates obtained are in good agreement with experimental findings. The highest activation energy barrier is less than 20 kcal mol?1. Other routes are dominated by an addition-elimination mechanism, which is also found in 2,4,6-trinitrotoluene, although the experiment did not find the corresponding products. In addition, we also eliminate several impossible mechanisms, such as dehydration, HNO3 elimination, the simultaneous addition of two ?OH radials, and so on. The information gained about these degradation pathways is helpful in elucidating the detailed reaction mechanism between nitroaromatic explosives and hydroxyl radicals for AOPs.
Graphical Abstract The degradation mechanism of an important explosive, 2,6-dinitrotoluene (DNT), by the hydroxyl radical for advanced oxidation progresses
The ternary complexes ML???PyZX2???NH3 (ML?=?CuCl, CuCN, AgCN, and AuCN; Z?=?P, As, and Sb; X?=?H and F) have been investigated with quantum chemical calculations. The results showed that the existence of coordination interaction has a prominent enhancing effect on the strength of pnicogen bonding. Even in ML???PySbH2???NH3, ML???PyAsF2???NH3, and ML???PySbF2???NH3, the pnicogen bond varies from a purely closed-shell interaction to a partially covalent interaction. The coordination interaction results in the enlargement of the σ-hole on the pnicogen atom and thus the enhancement of pnicogen bonding. In addition, the contribution of orbital interaction is also important.
We designed three novel cage energetic anions by introducing ionic bridges containing NΘ, N(OΘ) and N(NΘNO2) into cis-2,4,6,8-tetranitro-1H,5H-2,4,6,8- tetraazabicyclo[3.3.0] octane (bicyclo-HMX or BCMHX). The properties of 21 energetic salts, based on cage anions and ammonium-based cations, were studied by density functional theory (DFT) and volume-based thermodynamics (VBT) calculations. Compared to the parent nonionic BCHMX, most title salts have lower predicted impact sensitivities, higher predicted densities, larger predicted heats of formation (HOFs) and better predicted detonation properties. In particular, 11 energetic salts not only exhibit excellent predicted energetic properties, superior to 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20), but also have lower predicted sensitivity than CL-20. The best salt had a predicted detonation velocity of 10.06 km s?1, a predicted detonation pressure of 48.54 GPa and a predicted sensitivity (h50) of 23.99 cm. By introducing ionic bridges into highly nitrated rings, or modifying the original bridge with ionic bridges, some highly nitrated cage compounds with both excellent performance and low sensitivity can be developed strategically.
The adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO2) has been investigated under the scheme of density functional theory. Through the analysis of adsorption geometries, amino group and side chains of AAs have been identified as the major side to adsorb on TiO2, while the carboxyl group prefers to stay outside to avoid the repulsion between negatively charged oxygen from TiO2 and AAs. On the surface, two-coordinated oxygen is the major site to stabilize AAs through O–H interactions. The above conclusion does not change when it is in the aqueous solution based on the calculations with AAs surrounded by explicit water molecules. The above knowledge is helpful in predicting how AAs and even peptides adsorb on inorganic materials.
Graphical abstract The adsorption of 20 amino acids (AAs) on the (101) surface of anatase titanium dioxide (TiO2) has been investigated under the scheme of density functional theory.
The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol?1) reactive toward hydroxylation.
Figure The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21 G level, and in some cases at the B3LYP/6-31 G* level, and the energy associated with the attachment of the OH substituent was determined.
In order to study the effects of N-oxide on structure and performance, six categories of energetic compounds were systemically investigated. The results indicated that the C–C bonds in the rings were shortened, and the C–N bonds close to the N?→?O bond were elongated when N atoms was oxidized to form N?→?O bonds. N?→?O bonds can increase the densities of most categories of compounds, and the increment will increase with the number of N?→?O bonds. As to their detonation performances, almost all categories of compounds had an increased trend, except for some NO2-, NHNO2- and ONO2-substituted compounds. The contribution of 1,2,3,4-tetrazine and 1,2,4,5-tetrazine to performances was better than that of pyrazine and [1,2,5] oxadiazolo [3,4-b] pyrazine on the whole, and the groups, especially energetic groups, made a huge contribution to performance. When R was a NH2 or ONO2 group, all compounds had lower impact sensitivities, and thus represent candidates for novel energetic compounds. However, other than the sixth category of compounds, all compounds had higher impact sensitivities when R was a NO2 or NHNO2 group, and have little significance in application.
Graphical abstract To study the effects of N-oxide on the structure and performance of energetic compounds, and to propose theoretical guidance for the design of novel compounds, the six categories (94 species) listed in the figure were investigated systemically by density functional theory methods and some empirical formulae
High-level ab initio calculations on the complexes between noble gas atoms (He, Ne, Ar, Kr, and Xe) and dihalogen molecules (F2, Cl2, Br2, and I2) reveal trends, both in interaction energies and the energy difference between the linear and T-shaped structures, that can be explained well in terms of dispersion interactions enhanced by polar flattening of the halogens. The partial discrepancies with experimental findings are discussed.
There are four types of aromaticity criteria: energetic, electronic, magnetic and geometric. The delocalization, density and degeneracy-based index of aromaticity, D3BIA, is an electronic aromaticity index from QTAIM that is not reference dependent and can be used for aromatic, homoaromatic, sigma aromatic and other aromatic systems with varying ring size containing hetereoatoms or not. We used B3LYP, MP2 and MP3 methods to search for linear relations between well-known aromaticity indices and D3BIA for a series of acenes. We found that the D3BIA versus FLU correlation exceeded 91 % and reasonably good correlations exist between D3BIA and HOMA and between D3BIA and PDI. Previous works have shown that D3BIA can be used for homoaromatic systems and tetrahedrane derivatives (sigma aromaticity), but no previous work has validated D3BIA for benzenoid systems. This is the first time we have shown that D3BIA can be used successfully for benzenoid systems, for example, acenes. This work supports and validates the use of D3BIA in classical aromatic systems.
