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.
Protonation in the two-electron/two-proton reduction processes of 2,6-dichlorophenolindophenolate (DCIP) is investigated combining density functional theory (DFT) and molecular dynamics (MD) methods. DCIP (anion), DCIP?– (radical anion), and DCIP2? (dianion) are considered, including the electronic structure analysis from the prospective of quantum theory of atoms and molecules (QTAIM). It is shown that oxygen on the indophenolate moiety and nitrogen are the first and/or the second proton acceptor sites and their energetic order depends on the total charge of the system. MD simulations of differently charged species interacting with the solvent molecules have been performed for methanol, water, and oxonium cation (H3O+). Methanol and water molecules are found to form only hydrogen bonds with the solute irrespective of its charge. The calculated pKa values show that the imino group of DCIPH? is a weaker acid than water. While in the case of DCIP (and DCIP?–) plus oxonium cation, proton transfer from the solvent to the solute was evidenced for both aforementioned acceptor sites. In addition, MD simulations of bulks containing 15 and 43 molecules of water around the DCIP molecule have been performed, revealing the formation of 2–4 hydrogen bonds.
Graphical Abstract 2,6-Dichlorophenolindophenolate interacts with solvent molecules (water, oxonium cation and methanol). Hydrogen transfer and electronic structure are studied by DFT and molecular dynamics methods
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.
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.
Efficient design of ionic compounds requires a systematic understanding of cation–anion interactions. Weakening of electrostatic attraction is essential to increase the liquid range of the ionic compound and decrease its melting point. Here, we report simulations of the closest-approach cation–anion distances in a variety of ion pairs containing the tetrakis(pentafluorophenyl)borate (TFPB–) anion. Small alkali cations (Li+, Na+) penetrate the TFPB– core, whereas K+ and larger organic cations do not. In the latter case, the shortest possible distance from the cations to the boron atom of TFPB– ranges from 0.50 nm to 0.63 nm. TFPB– was shown to be substantially rigid, providing a steric hindrance to thermodynamically efficient cation–anion coordination. Our results prove that TFPB– is more efficient for electrostatic charge confinement than the tetraoctylammonium cation, whereas the perfluorophenyl group is more efficient than linear alkyl chains. These simulations will motivate development of TFPB–-based ionic liquids with low phase transition points.
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.
Density functional theory calculations were carried out to investigate the formation mechanism of the thymine-thymine (6–4) dimer ((6–4)TT), which is one of the main DNA lesions induced by ultraviolet radiation and is closely related to skin cancers. The DNA backbone was found to have nonnegligible effects on the triplet reaction pathway, particularly the reaction steps involving substantial base rotations. The mechanism for the isomerization from (6–4)TT to its Dewar valence isomer (DewarTT) was also explored, confirming the necessity of absorbing a second photon. In addition, the solvation effects were examined and showed considerable influence on the potential energy surface.
The present paper reports the analysis of surface decoration on the structural, electronic, and optical properties of (n,0) ZnO nanotubes, performed by means of a density function theory based ab-initio approach. Fe functionalization induced buckling in ZnO nanotubes affects its electronic and optical properties. Increase in Fe functionalization leads to better stability of ZnO nanotube and shows enhanced metallic character. The possibility of its use in optoelectronics has been analyzed in terms of dielectric constant, absorption coefficient, and refractive index. In another observation, the high sensitivity of the HCN molecule for the Fe-incorporated ZnO nanotube suggests it as a potential gas sensor.
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.
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.
The factors that explain the competition between intramolecular NO linkage photoisomerization and NO photorelease in five ruthenium nitrosyl complexes were investigated. By applying DFT-based methods, it was possible to characterize the ground states and lowest triplet potential energy surfaces of these species, and to establish that both photoisomerization and photorelease processes can occur in the lowest triplet state of each species. This work highlights the crucial role of the sideways-bonded isomer, a metastable state also known as the MS2 isomer, in the photochemical loss of NO, while the results obtained also indicate that the population of the triplet state of this isomer is compulsory for both processes and show how photoisomerization and photorelease interfere.
A theoretical 1H NMR spectroscopy and thermodynamic analysis of the host–guest inclusion process involving the norfloxacin (NFX) into β-cyclodextrin (β-CD) was carried out. DFT structure and stabilization energies were obtained in both gas and aqueous phases. We could establish that the complex formation is enthalpy driven, and the hydrogen bonds established between NFX and β-CD play a major role in the complex stabilization. Besides, a theoretical 1H NMR analysis has shown to be a supplementary proceeding to predict appropriately the inclusion mode of norfloxacin molecule into the β-CD. In this work, a theoretical study of the NFX@β-CD complex is reported for the first time, seeking a deep understanding of topology and thermodynamics of the inclusion complex formation.
In this work, we address the effects of molecular doping on the electronic properties of fluorinated and chlorinated silicon nanowires (SiNWs), in comparison with those corresponding to hydrogen-passivated SiNWs. Adsorption of n-type dopant molecules on hydrogenated and halogenated SiNWs and their chemisorption energies, formation energies, and electronic band gap are studied by using density functional theory calculations. The results show that there are considerable charge transfers and strong covalent interactions between the dopant molecules and the SiNWs. Moreover, the results show that the energy band gap of SiNWs changes due to chemical surface doping and it can be further tuned by surface passivation. We conclude that a molecular based ex-situ doping, where molecules are adsorbed on the surface of the SiNW, can be an alternative path to conventional doping.
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.
In this work, we demonstrate that the inclusion of long-range interactions has a significant impact on the estimation of ligand–protein binding energies. Within the scope of the electrostatically embedded adaptation of the molecular fragmentation with conjugated caps (EE-AMFCC) scheme, we unveil the role played by long-range contributions in distinct levels of quantum mechanical calculations. As a prototypical system, we consider ibuprofen coupled to the human serum albumin. In particular, we show that some relevant ligand–residue interaction energies can only be accurately captured in density functional theory (DFT) approaches when the electrostatic background is properly represented by an explicit point charge distribution.
Graphical Abstract (left) The binding site FA3/FA4 of HSA containing the attached IBU. (right) Absolute value of difference between the biding energies calculated including the electrostatic embedding and the energies calculated without the electrostatic embedding using the HF, B3LYP, CAM-B3LYP, and MP2 methodologies
The aldol reaction in the presence of L-proline acting as an organocatalyst is a well-known example of asymmetric synthesis. Many theoretical and experimental studies have been carried out to probe the mechanism of this reaction. In this work, two levels of density functional theory in the gas phase and DMSO were used to elucidate the best pathways for this reaction, with the enamine and enol considered intermediates and L-proline considered either a reactant or a facilitator. The calculations indicated that both intermediates are formed simultaneously in the reaction medium. Interestingly, the formation of the enamine intermediate predominates in DMSO at room temperature, whereas the enol becomes the predominant intermediate upon the addition of water.
Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecular systems; however, the parameters for DMSO published by Fox and Kollman in 1998 have only been tested for pure liquid DMSO. We have conducted an MD simulation study of DMSO in a water mixture and computed several structural and dynamical properties such as of the mean density, self-diffusion coefficient, hydrogen bonding and DMSO and water ordering. The AMBER force field of DMSO is seen to reproduce well most of the experimental properties of DMSO in water, with the mixture displaying strong and specific water ordering, as observed in experiments and multiple other MD simulations with other non-polarizable force fields.
As one of the most important antiviral drugs against 2009 influenza A (H1N1), will zanamivir be effective for the possible drug resistant mutants? To answer this question, we combined multiple molecular dynamics simulations and molecular mechanics generalized Born surface area (MM-GBSA) calculations to study the efficiency of zanamivir over the most frequent drug-resistant strains of neuraminidase including R293K, R152K, E119A/D and H275Y mutants. The calculated results indicate that the modeled mutants of the 2009-H1N1 strains except H275Y will be significantly resistant to zanamivir. The resistance to zanamivir is mainly caused by the loss of polar interactions. The identified potential resistance sites in this study will be useful for the development of new effective anti-influenza drugs and to avoid the occurrence of the state without effective drugs to new mutant influenza strains.
A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree–Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r?=?0.9216) was obtained with the AM1 Ford–Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r?=?0.9220). Nevertheless, in spite of a marginally lower performance (r?=?0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values.
