Tensile characteristics of carbene-functionalized CNTs subjected to physisorption of polymer chains: a molecular dynamics study Abstract Tensile properties such as Young’s modulus and ultimate tensile force are important properties in understanding the characteristics of nanocomposites. Besides, the importance of functionalization methods in modification of the unique mechanical and elastic properties of carbon nanotubes (CNTs) is being widely recognized. In this paper, the tensile properties of CNTs functionalized with carbene under physisorption of polymer chains, i.e., aramid and polyketone chains, are investigated by using a series of molecular dynamics (MD) simulations. The results illustrated that Young’s modulus of carbene-functionalized CNTs (cfCNTs) decreases by rising the weight percentage of carbene. By contrast, Young’s modulus of cfCNTs under physisorption of polymer chains (cfCNTs/polymers) increases as the carbene weight rises. In a particular carbene weight, Young’s modulus of cfCNTs/polymers decreases by increasing the chains of non-covalent functional groups. Moreover, it is shown that similar to Young’s modulus, ultimate tensile force of cfCNTs reduces by increasing the weight percentage of carbene whereas the ultimate tensile force of cfCNTs/polymers has an increasing trend with raising the carbene weight.

Molecular simulation of PcCel45A protein expressed from Aspergillus nidulans to understand its structure, dynamics, and thermostability Abstract PACS and mathematical subject classification numbers as needed. Molecular dynamic simulation is a very usable tool to understand various factors, including structure temperature dependence, dynamics, and stability for protein structure. The three main components, namely endoglucanase, exoglucanase, and β-glucosidase, effectively convert lignocellulosic biomass into fermentable sugar. Cellulose is the major component of plant cell walls and is the most abundant organic compound on the earth. Somewhat organisms can use cellulose as a food source, possessing cellulases (cellobiohydrolases and endoglucanases) that can catalyze the hydrolysis of the β-(1,4) glycosidic bonds. In this work, we investigated conformational and structural properties of PcCel45A protein by changing at temperatures with 300 K, 333 K, and 352 K. We found that the ASN92 residue was the major contributor to the stability of structure; some other residues correlated significantly with thermal stability. We also compared the theoretical results of the current study with the experimental ones published in previous studies.

Understanding structure-activity relation in V x O y clusters of varied stoichiometry and sizes through conceptual density functional approach Abstract Computations have been performed on VxOy clusters (with x = 1–8, y = 1–21) to explore their structure, stability, and reactivity based on local and global reactivity descriptors defined within the formalism of density functional theory (DFT). The vertical and adiabatic ionization energies and electron affinities are in accordance with Franck–Condon principle and suggest that the VxOy clusters are more likely to be electron acceptors than donors. The structure and reactivity of VxOy clusters delicately depend on their oxygen content and environment. Distinct active sites have been identified for each cluster species on the basis of coordination, symmetry, and charge distribution. The propensity of all the reactive sites towards an approaching electrophile and/or nucleophile has been studied using local reactivity descriptor. In oxygen-poor clusters, the vanadium atoms are more prone to nucleophilic attack. With an increase in oxygen concentration, the coordination number of vanadium increases and reaches four-fold, the site for nucleophilic attack shifts to terminal oxygens. We conclude that of all the stoichiometries, the stable VxOy clusters have the (VO3)a(V2O5)b formula unit. The localization of positive charge density in cubic cage structure of V8O20 successfully traps halide ions (F−, Cl−, and Br−). In view of increasing use of metal oxide clusters in heterogeneous catalysis, the understanding of structure-activity relationship in vanadium oxides’ clusters provided in the current study is highly desirable.

The any particle molecular orbital/molecular mechanics approach Abstract A computational scheme is proposed to broaden the range of applications of multicomponent methodologies for the study of local properties of big molecular systems existing in the gas phase and in solvated environments. This scheme extends the any particle molecular orbital (APMO) approach in the quantum mechanics/molecular mechanics (QM/MM) framework. As a first assessment of the performance of the proposed approach, we estimate the proton affinities (PAs) of seventy amines in the gas phase and the proton binding energies (PBEs) in the gas phase and in an explicitly solvated environment of the sixty-one protons present in the chignolin protein. These calculations are performed with the QM/MM versions of the APMO second-order proton propagator (APMO-PP2) and the APMO extended Koopmans’ theorem (APMO-KT) approaches. Calculated PAs and PBEs show significant reductions in the computational effort with a reduced loss in accuracy. These results suggest that the APMO/MM scheme might be used as a low-cost multi-component alternative for studies of local properties in big molecular systems. Graphical Abstract QMMM regions and CPU times for the APMO/MM approach

Theoretical determination of the effects of various linkages between trinitrobenzenes on energetic properties and sensitivity Abstract Density functional theory (DFT) has been applied to understand the influence of various linkages on the energetic properties and stability of the polynitro-biphenyl compounds. Structures were optimized using the B3PW91/6-31G(d,p) level, and the heats of formation (HOFs) were computed by employing the selected isodesmic reactions. The results reveal that the –N=N– linkage helps to gain high HOF while the –O–, –NH–C(O)NH–, and –NH–C(O)–C(O)–NH– show a negative impact on energy content. Kamlet-Jacobs (K-J) equations were used to determine detonation properties based on the computed densities and HOFs, while stability and sensitivity were investigated by correlating with the bond dissociation energy (BDE), charge on the nitro group, and the balance parameter on surface potentials. Comparing the effect of different linkages on performance and stability of selected polynitro-biphenyl derivatives reveals that –NH–NH– and –N=N– are suitable for a connection between energetic moieties and these results are expected to demonstrate primary information for designing new energetic materials. Graphical abstract

Correlation between molecular charge densities and sensitivity of nitrogen-rich heterocyclic nitroazole derivative explosives Abstract Nitroazole derivatives are nitrogen-rich heterocyclic ring molecules with potential application as energetic materials. Thirty-three of them—nitroimidazoles, nitrotriazoles, and nitropyrazoles—were investigated. Computed density functional theory molecular charge densities were partitioned employing the accurate distributed multipole analysis (DMA) method. Based on the magnitude of the DMA atom-centered electric multipoles (monopole, dipole, and quadrupole values), mathematical models were developed to compute the impact sensitivity of the explosives composed of these molecules. Charge localization and delocalization of the ring nitrogen atoms as well as charges of the atoms of the nitro group affect the sensitivity of explosives composed of nitroazole derivatives. The sensitivity is strongly dependent on the ring position of the nitrogen atoms and the bonding site of the substituent groups. The N/C ratio and the repulsion of the non-bonding electron pairs of the vicinal nitrogen atoms of the ring also play an important role in the stability of nitroazoles. The influence of the withdrawing group (NO2) and the electron injector groups (NH2 and CH3) including their bonding position on the ring could be quantified.

Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy Abstract Detailed study of Jensen’s polarization-consistent vs. Dunning’s correlation-consistent basis set families performance on the extrapolation of raw and counterpoise-corrected interaction energies of water dimer using coupled cluster with single, double, and perturbative correction for connected triple excitations (CCSD(T)) in the complete basis set (CBS) limit are reported. Both 3-parameter exponential and 2-parameter inverse-power fits vs. the cardinal number of basis set, as well as the number of basis functions were analyzed and compared with one of the most extensive CCSD(T) results reported recently. The obtained results for both Jensen- and Dunning-type basis sets underestimate raw interaction energy by less than 0.136 kcal/mol with respect to the reference value of − 4.98065 kcal/mol. The use of counterpoise correction further improves (closer to the reference value) interaction energy. Asymptotic convergence of 3-parameter fitted interaction energy with respect to both cardinal number of basis set and the number of basis functions are closer to the reference value at the CBS limit than other fitting approaches considered here. Separate fits of Hartree-Fock and correlation interaction energy with 3-parameter formula additionally improved the results, and the smallest CBS deviation from the reference value is about 0.001 kcal/mol (underestimated) for CCSD(T)/aug-cc-pVXZ calculations. However, Jensen’s basis set underestimates such value to 0.012 kcal/mol. No improvement was observed for using the number of basis functions instead of cardinal number for fitting. Graphical Abstract

Designing indaceno thiophene–based three new molecules containing non-fullerene acceptors as strong electron withdrawing groups with DFT approaches Abstract Nowadays, scientists are trying to develop low-cost fullerene free acceptors for small organic photovoltaic cells in order to overcome the limitations of fullerene derivatives. Current research work deals with theoretical study on three non-fullerene acceptors based on indaceno, dithiophene core, and thiophene bridge units linked with dissimilar end non-fullerene groups which act as strong acceptor moieties. Different optoelectronic characteristics of the designed molecules were calculated and compared with the reference compound R (indaceno dithiophene–based fused ring acceptor) which is recently reported. Results shows that C2 and C3 exhibit broad absorption spectrum and lower band gap whereas C2 and C1 exhibit highest open-circuit voltages VOC value with B3LYP and MPW1PW91 functionals respectively as compared with the R. All designed molecules have high dipole moment values, lower value of hole reorganization energy λh than electron reorganization energy λe which reflects that our designed acceptor molecules are good candidates for organic photovoltaics. Graphical abstract Absorption spectra of R and three designed non-fullerene acceptors with strong absorption band in the visible region of solar cells spectrum.

Computational characterization of the glutamate receptor antagonist perampanel and its close analogs: density functional exploration of conformational space and molecular docking study Abstract Perampanel approved by FDA in 2012 is a first-in-class antiepileptic drug which inhibits α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor currents. It is markedly more active than many of its close analogs, and the reasons for this activity difference are not quite clear. Recent crystallographic studies allowed the authors to identify the location of its binding site. Unfortunately, the resolution is low, and the detailed description of perampanel binding mode is still in part speculative. Here we provide a detailed DFT-level conformational analysis of perampanel in a vacuum and in the solvents, mimicking the protein environment, followed by quantum theory of atoms in molecules (QTAIM), non-covalent interactions (NCI), and natural bond orbital (NBO) analyses. The findings indicate the electrostatic nature of the intramolecular interactions which contribute to energy differences of the conformations in a vacuum whereas the increase of dielectric constant leads to the energy equalization of conformations. Based on these results, the docking study was performed to investigate possible binding modes of perampanel and its close analogs in AMPA receptors. The influence of the pyridine nitrogen and cyano group position was explained based on the results of conformational analysis and molecular docking. These findings may contribute to the design of novel antiepileptic drugs and the development of novel approaches to treat neurodegenerative diseases and major depressive disorder.

Acrylic acid hydrodeoxygenation reaction mechanism over molybdenum carbide studied by DFT calculations Abstract Platinum- and palladium-based catalysts are commonly used in hydrogenation reactions, but they present a great disadvantage of being quite expensive. In most cases, they can be substituted by cheaper alternative catalysts formed by transition metal carbides, such as molybdenum carbide (Mo2C). Among the reactions that can be catalyzed by Mo2C, hydrodeoxygenation (HDO) presents a great technological interest, especially in biofuel production. Nonetheless, the selectivity of carbides in HDO reactions of fatty acids is not well understood yet. In the present work, the reaction mechanism of the acrylic acid HDO over Mo2C, a fatty acid model molecule, was studied by density functional theory (DFT), with Perdew-Burke-Ernzerhof (PBE) functional and periodic boundary conditions. A global mechanism is proposed, divided in four steps, from acrylic acid to propane. In the first reaction step, decomposition by C–OH bond cleavage, with 24 kcal mol− 1 of activation energy, dominates over C=C and C=O hydrogenation. This result is in line with the absence of propanoic acid among the products and the formation of acrolein, as shown in an experimental work previously published. The proposed global mechanism is in fair agreement with the experimental findings. The main product is propane, which has the same number of carbon atoms of the reactant. This mechanism can be viewed as a model for HDO of any fatty acid catalyzed by Mo2C, since acrylic acid has the minimal structural features of fatty acids, i.e., a carboxyl group and a C=C double bond. Graphical Abstract HDO over Mo2C provides a product with same carbon atoms number of the reactant.