Showing papers in "Structural Chemistry in 2018"

Index of Ideality of Correlation: new possibilities to validate QSAR: a case study

Abstract: New criterion of the predictive potential of quantitative structure – property/activity relations (QSPRs/QSARs) named Index of Ideality of Correlation (IIC) is suggested. This criterion is calculated using the correlation coefficient between experimental and calculated values of an endpoint for the calibration set, taking into account positive and negative differences between experimental and calculated values of the endpoint. Using this criterion improves the predictive potential of QSAR models of toxicity towards fathead minnow (Pimephales promelas). Comparison of IIC with other metrics of predictive potential shows that (i) the IIC is not identic to other metrics; and (ii) the IIC seems more reliable criterion at least for examined data on toxicity towards fathead minnow.

Computational studies on the doped graphene quantum dots as potential carriers in drug delivery systems for isoniazid drug

Abstract: In this study, the application of graphene quantum dots (GQDs) and doped GQDs as potential carriers for the delivery of isoniazid (Iso) drug has been investigated, using density functional theory (DFT) calculations. For this purpose, the hexa-peri-hexabenzocoronene (as a GQD model) and its BN-, BP-, AlN-, and AlP-doped (C36X3Y3H18 where X = B, Al and Y = N, P) forms were selected. Our results indicated that the adsorption energies of isoniazid on doped GQDs were more negative than that of pure GQD. Moreover, the calculations showed that adsorption of isoniazid on AlN- and AlP-doped GQDs was thermodynamically favorable. The dipole moments of BP-, AlN-, and AlP-doped GQDs were much greater (5.799, 1.860, and 3.312 D, respectively) than that of pristine GQD (0 D). The AlN-Iso and AlP-Iso complexes had small energy gaps, low chemical potentials, and low global hardnesses, which were appropriate for their attachments to the target site. The nature of interactions was analyzed by the quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) analyses. Overall, the results confirmed that the AlN- and AlP-doped GQDs could be used as potential carriers for drug delivery application.

QSAR study of 2,4-dihydro-3 H -1,2,4-triazol-3-ones derivatives as angiotensin II AT 1 receptor antagonists based on the Monte Carlo method

Abstract: The Monte Carlo method was used for QSAR modelling 2,4-dihydro-3H-1,2,4-triazol-3-ones derivatives as angiotensin II AT1 receptor antagonists. QSAR models were calculated with the representation of the molecular structure by the simplified molecular input-line entry system (SMILES) and with optimal molecular descriptors based on the SMILES notation and local graph invariants. One random split into the training and the test set was used. The statistical quality of the developed model was good. The best calculated QSAR model had the following statistical parameters: r 2 = 0.8701 for the training set and r 2 = 0.8430 for the test set. Novel statistical metric entitled as the index of ideality of correlation was used for final model assessment, and the obtained results were good. Structural indicators defined as molecular fragments responsible for increases and decreases of the studied activity were calculated. The computer-aided design of new compounds as potential angiotensin II AT1 receptor antagonists with the application of defined structural alerts was presented.

A DFT study of H 2 CO and HCN adsorptions on 3 d , 4 d , and 5 d transition metal-doped graphene nanosheets

Abstract: The binding of 3d (Sc, Ti, V), 4d (Y, Zr, Nb), and 5d (La, Hf, Ta) transition metals on graphene nanosheet (TM–GNS) with hydrogen-terminated edges and the adsorption of H2CO and HCN molecules on the pristine and TM-doped GNSs were theoretically studied using a density functional theory method. The calculation showed that all TM atoms had strong binding with GNS, in which the Ta atom displayed the strongest interaction with GNS. The H2CO and HCN molecules showed much stronger adsorption on the TM–GNSs than that on the pristine GNS. The H2CO showed stronger interactions with TM–GNSs than that of HCN, in which the Ta-doping displayed the strongest interactions between the GNS and H2CO or HCN. The adsorption interactions induced dramatic changes of TM–GNS electronic properties. The results revealed that the adsorption strength and sensor ability of GNS can be greatly improved by introducing appropriate TM dopants. Therefore, TM-doped GNSs are suitable for application in H2CO and HCN storage and sensor.

QSAR modeling of dihydrofolate reductase inhibitors as a therapeutic target for multiresistant bacteria

Abstract: Antibacterial resistance is a growing public health threat of major concern around the world so development of new therapeutic approaches to prevent bacterial multidrug resistance has become a primary consideration for medicinal chemistry research. QSAR models for the dihydrofolate reductase inhibition with 2,4-diamino-5-(substituted-benzyle)-pyramidine derivatives were developed with further computer-aided design of new derivatives with desired activity. The Monte Carlo method has been used as a computational tool for QSAR modeling. For the representation of molecular structure and optimal descriptor calculation, the simplified molecular input line entry system (SMILES) together with the molecular graph (hydrogen-suppressed graph—HSG, hydrogen-filled graph—HFG, and the graph of atomic orbitals-GAO) was used. One-variable models have been calculated for one data split into training, test, and validation set. The impact of Morgan’s extended connectivity index on built QSAR models and outliers was determined. Statistical parameters for the best QSAR model are satisfying. Structural indicators (molecular fragments) responsible for the increase and the decrease of the stated activity are defined, and with the application of defined structural alerts, the computer-aided design of new derivatives with desired activity is presented. Computational experiments presented and applied in this research can satisfactorily predict desired endpoint and can be used further for computer-aided antibacterial drug design.

Fluorine-functionalized nanoporous graphene as an effective membrane for water desalination

Abstract: Most water in the world is as saline water in seas and oceans. Desalination technology is a promising method to solve the global water crisis. Recently, many attentions have been paid to the graphene-based membranes in water desalination due to their low production cost and high efficiency. In this paper, molecular dynamics simulations are employed to investigate the effect of functionalized graphene nanosheet (GNS) membranes on the performance of salt separation from seawater in terms of water permeability and salt rejection. For this purpose, the hydrogenated (–H) and fluorinated (–F) pores were created on the GNS membrane. Then, the functionalized graphene membrane was placed in the middle of the simulation box in an aqueous ionic solution containing Na+ and Cl− ions. The applied pressure (in the range of 10–100 MPa) was used as the driving force for transport of water molecules across the reverse osmosis (RO) graphene-based membrane in order to obtain the water permeability and salt rejection. Also, radial distribution functions (RDFs) of ion–water and water–water as well as the water density map around the membrane were obtained. The results indicated that the hydrophilic chemical functions such as fluorine (–F) can improve the water permeability at low pressures.

Gas-sensing properties of armchair silicene nanoribbons towards carbon-based gases with single-molecule resolution

Abstract: Using non-equilibrium Green’s function (NEGF) formalism combined with first-principle density functional theory (DFT), we explore the nature of adsorption of carbon-based gases and the resulting structural, electronic (band structure, density of states, Mulliken population, and electron density), and transport properties (current-voltage characteristics and transmission eigenstates) on pure and defected armchair silicene nanoribbons (ASiNRs) for sensing applications. It is observed that CH4 and CO2 are weakly adsorbed on pristine (P-ASiNR) as well as defective (D-ASiNR) nanoribbons owing to their low adsorption energy and charge transfer, thereby exhibiting low sensitivity and high recoverability. On the other hand, CO is chemisorbed on both nanoribbons exhibiting greater adsorption energy and current, thereby having more sensitivity and more recovery time. Mulliken population analysis reports that a significant amount of charge transfer prevails between ASiNR and gas molecules, validating our results for adsorption energies of the systems. CO2 and CO donates charge to the ASiNR, showcasing their electron-donating nature; contrariwise, CH4 behaves as electron-withdrawing gas by accepting electronic charge from ASiNRs. Our calculations reveal that introduction of vacancy defect increases the sensitivity significantly which is promising for future gas-sensing applications as well.

Electronic and transport properties of silicene-based ammonia nanosensors: an ab initio study

Abstract: Using density functional theory (DFT) and non-equilibrium Green’s function (NEGF) formalism, the electronic and transport properties of ammonia (NH3) molecule adsorbed on armchair silicene nanoribbons (ASiNRs) are calculated. Different variants of ASiNR have been considered viz. pristine, defective, Al-doped, and P-doped. It has been observed that though the pristine ASiNR is not much sensitive to this gas molecule, but its sensitivity can be drastically enhanced by introducing defects and dopants. NH3 gas molecule exhibits stronger adsorption on ASiNRs with addition of defect and dopants. The findings are suggestive of defective and Al-doped ASiNRs being more suitable as sensors for NH3 owing to the strong adsorption and large charge transfer of the gas molecule with these ASiNR variants whereas NH3 exhibits physisorption on pristine and P-doped ASiNRs possessing minimal adsorption energy and charge transfer as well. Defective ASiNRs are found to exhibit the strongest adsorption of all resulting in higher current as well. The study indicates that modified ASiNRs are potential candidates for nanoelectronic NH3 gas sensors.

Highly efficient organic indolocarbazole dye in different acceptor units for optoelectronic applications—a first principle study

Abstract: A series of novel organic dyes (ICZA1, ICZA2, ICZA3, ICZA4) with D-π-A structural configuration incorporating indolo[3,2,1-jk]carbazole moiety as donor (D) unit, thiophene as π-linker and 2-cyanoacrylic acid as acceptor unit were investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT) methods. Indolo[3,2,1-jk]carbazole-based D-π-A dyes composed of different acceptor groups were designed. By modulating acceptor unit, the efficiency of D-π-A dye-based dye-sensitized solar cells (DSSCs) can be further improved. In the present work, four novel push-pull organic dyes only differing in electron acceptor, have been designed based on the experimental literature value of IC-2. In order to further improve the light harvesting capability of indolo[3,2,1-jk]carbazole dyes, the acceptor influence on the dye performance were examined. The NLO property of the designed dye molecules can be derived as polarizability and hyperpolarizability. The calculated value of ICZA2 dye is the best candidate for NLO properties. Furthermore, the designed organic dyes exhibit good photovoltaic performance of charge transfer characteristics, driving force of electron injection, dye regeneration, global reactivity, and light harvesting efficiency (LHE). From the calculated value of ICZA4 dye, it has been identified as a good candidate for DSSCs applications. Finally, it is concluded that the both ICZA2 and ICZA4 dyes theoretically agrees well with the experimental value of IC-2 dye. Hence, the dyes ICZA2 and ICZA4 can serve as an excellent electron withdrawing groups for NLO and DSSCs applications.

Interaction of volatile organic compounds (VOCs) emitted from banana on stanene nanosheet—a first-principles studies

Abstract: Using ab initio calculation, structural stability, including electronic properties of bare/hydrogenated stanene (BSn/HSn) nanosheet, was explored. The geometrical stability of HSn material is verified with the influence of phonon band structure and formation energy. The concentration of the present work is to check the quality of Musa acuminata (banana) fruits when it is in ripe and overripe stage using HSn nanosheet material. Further, the interaction of different volatile organic compounds, namely, isoamyl acetate, isobutyl acetate, acetoin, and 2,3-butanediol aromas on HSn base material is studied with the significant parameter such as Bader charge transfer, band gap, adsorption energy, and average energy band gap changes. The sensitivity of the aromas emitting from ripe and overripe stages of banana on HSn nanosheet was studied using density of states spectrum. The adsorption energy of HSn nanosheet is found in the range of − 0.055 to − 0.989 eV upon the interaction VOCs of Musa acuminata. The novel aspect of the present work is to check the quality of Musa acuminata with the influence of HSn nanosheet using density functional theory.

Aluminum doping makes boron nitride nanotubes (BNNTs) an attractive adsorbent of hydrazine (N 2 H 4 )

Abstract: Adsorption of toxic hydrazine (N2H4) at the surface of pristine and Al-doped single-wall boron nitride nanotubes (BNNTs and Al-BNNTs) has been investigated using density functional theory (DFT). Single hydrazine molecule was allowed to interact with Lewis acid center (i.e., B atom) of BNNTs, where most stable gauche conformer of the guest is used. Both zigzag (8,0) and armchair (4,4) variants of BNNTs were considered and to estimate the effect of tube diameter on adsorption energies wider zigzag (9,0) and (10,0), and armchair (5,5) and (6,6), tubes were included in the host list. Estimated adsorption energies of 2–8 kcal/mol do not support strong binding between pristine BNNTs with hydrazine. However, Al doping makes BNNTs an attractive adsorbent of N2H4 with adsorption energy in the range of 32–35 kcal/mol. Stability of such complexes is found less sensitive to the chirality, but nominally decreases with tube diameter. Thus, a large quantity of hydrazine may be adsorbed by Al-BNNT samples. The dative N: → B/Al bond between hydrazine and host tubes is the source of stability of complexes. Molecular electrostatic potentials (MEPs) and frontier molecular orbitals of host and guest were calculated to explain interaction character and strength.

The influence of the negative hyperconjugation is relevant for the analysis of the π-π * conjugation with the mono-substitution and di-substitution of H 2 C= by O= and/or HN= in trans -buta-1,3-diene?

Abstract: We have studied prop-2-en-1-imine (1), prop-2-enal (2), ethane-1,2-diimine (3), ethanedial (4), and 2-iminoacetaldehyde (5) to investigate the influence of the negative hyperconjugation in π-π* interaction with the substitution of =CH2 by =NH and/or =O in trans-buta-1,3-diene (6). The analyzes of the π-π* interaction performed from evaluation of the π molecular orbital diagrams and electron localization function method demonstrated, that compared to 6, the substituted compounds 1-5 presented lower electron conjugation, especially in the structures bearing =O. The geometric parameters, natural bond orders, and topological analysis realized by quantum theory of atoms in molecules method indicated a predominant C-C and C=C character for the simple and double C-C bonds in the substituted compounds, 1-5, as compared to 6. Compound 4 had the highest enthalpy of formation, which reflected the lowest π-π* interaction, maintained by the two =O conjugated groups. The natural bond orbital (NBO) and natural resonance theory (NRT) methods revealed that the π-π* electron delocalization in substituted compounds, 1-5, is lower than in 6 from, firstly, of the less favorable interactions: π(X=C) ➔ π*(C=C) and π(X=C) ➔ π*(C=X), despite of the larger π(C=C) ➔ π*(C=X) conjugation, with X = N and/or O, of 1-5 than π(C=C) ➔ π*(C=C) of 6. But, most importantly, the weight of the interaction: nπ(O) ➔ σ*(C-C), was determined from NBO and NRT methods as proportional to the π-π* conjugation and thus demonstrating be decisive to establish the level of π electronic delocalization.

Novel X- and Y-substituted heterofullerenes X 4 Y 4 C 12 developed from the nanocage C 20 , where X = B, Al, Ga, Si and Y = N, P, As, Ge: a comparative investigation on their structural, stability, and electronic properties at DFT

Abstract: DFT calculations are performed to compare and contrast C 20 -analogous heterofullerenes of the form X 4 Y 4 C 12 , where X = B, Al, Ga, Si and Y = N, P, As, Ge, at B3LYP/AUG-cc-pVTZ. Substitution of C=C double bonds with the X–Y hetero bonds is an applicable strategy for obtaining highly doped stable heterofullerenes since it avoids weak X–X and Y–Y homo bonds. To be fabricated in the laboratory, heterofullerenes must be not only thermodynamically but also kinetically stable against electronic excitations. As a criterion of thermodynamical stability, the binding energy increases down a group of the periodic table. The calculated band gaps of 2.85 and 1.06 eV for B 4 N 4 C 12 and Al 4 N 4 C 12 , respectively, reveal them as the most and the least chemically stable heterofullerenes against electronic excitations. Al 4 N 4 C 12 is predicted to have the lowest binding energy and the highest conductivity and charge transfer, making it the excellent candidate for hydrogen storage. The full optimizations show that the hybrid cages undergo some distortions due to the substitution of the heteroatoms and the heterofullerenes with a bigger heteroatom (Al 4 N 4 C 12 and Ga 4 N 4 C 12 ) are more chemically reactive. We predict that B 4 N 4 C 12 as the most thermodynamically and kinetically stable species has not only the largest heat of atomization but also the highest energy gap.

Structural diversity of homobinuclear transition metal complexes of the phenazine ligand: theoretical investigation

Abstract: DFT/BP86 calculations have been carried out on a series of hypothetical binuclear compounds of general formula (L3M)2(C12N2H8) (M = Sc–Ni, L3 = (CO)3, (PH3)3 and Cp−, and C12N2H8 = phenazine ligand-denoted Phn). The various structures with syn and anti configurations have been investigated, in order to determine the phenazine’s coordination to first-row transition metals of various spin states with syn and anti conformations. The lowest energy structures depend on the nature of the metal, the spin state, and the molecular symmetry. This study has shown that the electronic communication between the metal centers depends on their oxidation state and the attached ligands. The tricarbonyl and the triphosphine ligands gave rise to comparable results in terms of stability order of isomers, metal-metal bond distances, and the coordination modes. Metal-metal multiple bonding has been evidenced for Sc, Ti, and V complexes to compensate the electronic deficiency. The Cr, Mn, Fe, Co, and Ni-rich metals prefer the anti conformation due to the enhancement of the metal valence electron count. The spin density values calculated for the triplet and quintet spin structures point out that the unpaired electrons are localized generally on the metal centers. The Wiberg bond indices are used to evaluate the metal-metal bonding. Furthermore, calculations using the BP86-D functional which take into account the attractive part of the van der Waals type interaction potential between atoms and molecules that are not directly connected to each other gave comparable results to those obtained by BP86 functional in terms of coordination modes, HOMO-LUMO gaps, metal-metal bond orders, and the stability order between isomers, but with slight deviation of M–C, M–N, and M–M bond distances not exceeding 3%.

Exploring in house glutamate inhibitors of matrix metalloproteinase-2 through validated robust chemico-biological quantitative approaches

Abstract: Matrix metalloproteinase-2 (MMP-2) is established as one of the most important metalloenzymes for targeting cancer. However, homologous MMP-9 of the gelatinase family is implicated as an antitarget of cancer. Therefore, it is an important and challenging task to achieve MMP-2 selectivity over MMP-9. In this article, robust validated chemico-biological quantitative approaches were conducted on a series of in house glutamate-based selective MMP-2 inhibitors over MMP-9 for further refinement of our MMP-2 inhibitor designing approach. The two-dimensional quantitative structure-activity relationship (2D-QSAR) study suggested that arylsulfonamide moiety was better than arylcarboxamide function, which in turn, supported by the hologram QSAR (HQSAR), 3D-QSAR comparative molecular field analysis (CoMFA), and comparative molecular similarity analysis (CoMSIA) studies. Regarding the MMP-2 selectivity, glutamines were better than isoglutamines as evidenced by the quantitative activity-activity relationship (QAAR) and molecular docking studies. Favorable hydrophobic and steric features of aryl function directed towards the S1′ pocket were also well attributed. Naphthyl and p-bromophenoxyphenyl moieties in place of biphenyl function were found to be unfavorable for MMP-2 inhibition and selectivity over MMP-9. Linear or cyclic aliphatic group directed towards the S2′ pocket was favorable, whereas branching was unfavorable for MMP-2 inhibition and selectivity. The importance of biphenyl and 3,5-bistrifluoromethylbenzyl functions directed towards the S1′ and S2′ pockets, respectively, was well attributed for potent MMP-2 inhibition and selectivity over MMP-9.

Quantum chemical properties investigation and molecular docking analysis with DNA topoisomerase II of β-carboline indole alkaloids from Simaba guianensis: a combined experimental and theoretical DFT study

Abstract: A theoretical and experimental DFT study of the vibrational, structural, and quantum properties of 9-methoxy-canthin-6-one (I) and 7-methoxy-(9H-β-carbolin-1-il)-(Z)-prop-2-enoic acid (II) alkaloids is presented using B3LYP exchange-correlation functional with 6-311G(2d,p) basis set. The theoretical geometry optimization data of both structures were compared with the X-ray data for a similar structure in the associated literature and a conformational study is presented for (II), providing a good comprehension of its conformers’ stability. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap, mapped molecular electrostatic potential surface (MEPS) calculations, and first- and second-order hyperpolarizabilities were also performed at the same calculation level. The calculated UV spectra agreed well with the measured experimental data, with transitions assigned. Calculated HOMO/LUMO energy gaps revealed the excitation energy of the structures, justifying their stability and kinetics reaction. IR studies showed that for structure II the intramolecular hydrogen bond of the conformations and the intermolecular hydrogen bonds of the dimeric form influence the results and also revealed several characteristic vibrations for both structures. Molecular docking studies with DNA topoisomerase II-DNA complex showed binding free energies of − 8.4 and − 9.6 kcal/mol for II and I, respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of − 9.9 kcal/mol, showing a good binding affinity of alkaloid I.

A theoretical study on the antioxidant activity of Uralenol and Neouralenol scavenging two radicals

Abstract: Uralenol and neouralenol are two typical licorice root extracts that presents multiple reactive hydroxyl groups, which are considered as good free radical scavengers. A theoretical study on the primary antioxidant activity of uralenol and neouralenol toward hydroxyl and hydroperoxyl radicals has been carried out using the density functional theory (DFT). A total of 10 reaction pathways of uralenol and neouralenol scavenging two radicals in gas phase and in water phase have been tracked. Neouralenol was found to be a better hydroxyl and hydroperoxyl scavenger than uralenol. In vivo, the more reactive sites in uralenol are U5 and U’1, respectively, for scavenging ·OH and ·OOH; and the more reactive sites in neouralenol are N4 and N’5 for scavenging ·OH and ·OOH, respectively.

Mutual interplay between pnicogen–π and tetrel bond in PF3⊥X–Pyr…SiH3CN complexes: NMR, SAPT, AIM, NBO, and MEP analysis

Abstract: The mutual interplay between pnicogen–π and tetrel bond in the formation of PF3⊥X–Pyr…SiH3CN ternary complexes has been investigated via a computational chemistry at MP2/aug-cc-pVDZ level of theory. We proved by computational NMR data the effect of electron-withdrawing and electron-donating substituents on 1tJ(N-Si) across 15N...35Si tetrel bonds was investigated at M06-2X/aug-cc-pVDZ levels of theory in PF3⊥CN–Pyr…SiH3CN complex. The nature of the interactions has been studied by means of symmetry-adapted perturbation theory (SAPT) and molecular electrostatic potentials (MEP). The electrostatic interaction played a major role in the change of tetrel bond interaction strength in the X–Pyr…SiH3CN binary systems, whereas the change of pnicogen–π strength in the PF3⊥X–Pyr complexes was caused jointly by the dispersion interactions. Energy decomposition indicates that the percentage of the electrostatic term in the tetrel bond system constitutes in the total attractive binding energies, while the percentage of the dispersion term in the pnicogen bonding constitutes in the attractive binding energies. In addition, atoms in molecules (AIM) and natural bond orbital (NBO) analyses were also performed to unveil the mechanism of these interactions in the title complexes.

Furanone derivatives as new inhibitors of CDC7 kinase: development of structure activity relationship model using 3D QSAR, molecular docking, and in silico ADMET

Abstract: Cell division cycle 7 (CDC7) is a serine/threonine kinase, which plays a vital role in the replication initiation of DNA synthesis. Overexpression of the CDC7 in various tumor growths and in cell proliferation makes it a promising target for treatment of cancers. To investigate the binding between the CDC7 and furanone inhibitors, and in order to design highly potent inhibitors, a three-dimensional quantitative structure activity relationship (3D-QSAR) with molecular docking was performed. The optimum CoMSIA model showed significant statistical quality on all validation methods with a determination coefficient (R2 = 0.945), bootstrapping R2 mean (BS-R2 = 0.960), and leave-one-out cross-validation (Q2) coefficient of 0.545. The predictability of this model was evaluated by external validation using a test set of nine compounds with a predicted determination coefficient R2test of 0.96, besides the mean absolute error (MAE) of the test set was 0.258 log units. The extracted contour maps were used to identify the important regions, where the modification was necessary to design a new molecule with improved activity. Furthermore, a good consistency between the molecular docking and contour maps strongly demonstrates that the molecular modeling is reliable. Based on those obtained results, we designed several new potent CDC7 inhibitors, and their inhibitory activities were validated by the molecular models. Additionally, those newly designed inhibitors showed promising results in the preliminary in silico ADMET evaluations.

Characterisation of the reaction mechanism between ammonia and formaldehyde from the topological analysis of ELF and catastrophe theory perspective

Abstract: A prototypical reaction between ammonia and formaldehyde has been investigated at the DFT(M06)/6-311++G(d,p) computational level using the Bonding Evolution Theory (BET). BET is a very useful tool for studying reaction mechanisms as it combines topological analysis of electron localisation function with the catastrophe theory. Each of two studied reactions: H2C=O + NH3 ↔ HO–C(H2)–NH2 (hemiaminal) and HO–C(H2)–NH2 ↔ HN = CH2 (Schiff base) + H2O consists of six steps. Formation of hemiaminal starts from a nucleophillic attack of nitrogen lone pair in NH3 on the carbon atom in H2C=O and is subsequently followed by hydrogen transfer within the N–H..O bridge. A Schiff base is formed via the dehydration reaction of the hemiaminal, where the C–O bond is broken first, followed by hydrogen transfer towards the [HO]δ− moiety, resulting in water and methanimine. The present paper focuses on differences in reaction mechanisms for the processes described above. The results have been compared to the reaction mechanism for stable hemiaminal synthesis from benzaldehyde and 4-amine-4H-1,2,4-triazole studied previously using the BET theory.

Prediction of density of energetic cocrystals based on QSPR modeling using artificial neural network

Abstract: Among the most important factors affecting the destructive power of explosive materials is density. In order to correlate the molecular structure of energetic cocrystals (ECs) with their density (ρ), a quantitative structure-property relationship (QSPR) study was undertaken. An artificial neural network (ANN) model was developed to predict the density of cocrystals by using three out of more than 1600 molecular descriptors, computed by Dragon software, as input variables. The complete set of 26 ECs was randomly divided into a training set of 16, a test set of 5, and a validation set of 5 compounds. Also, multiple linear regression (MLR) analysis was utilized to build a linear model by using the same descriptors. Correlation coefficient (R2) of the ANN and MLR models (for the whole dataset) was 0.9716 and 0.9309, respectively. The ANN model was further investigated, and average absolute relative deviation for the complete dataset was 2.48%, indicating good accuracy and reliability of the model.

DFT study of small aluminum and boron hydrides: isomeric composition and physical properties

Abstract: The structure, energetics, and physical properties, including rotational constants, characteristic vibrational temperatures, dipole moment, static polarizability, HOMO-LUMO gap, formation enthalpy and collision diameter of different isomeric forms of atomic Al n H m and B n H m clusters with n = 1..4 and all feasible m numbers are studied within the density functional theory framework. The search of isomer structures has been accomplished using multistep hierarchical algorithm. Temperature dependences of thermodynamic functions (enthalpy, entropy and specific heat capacity) have been calculated both for the individual isomers and for the ensemble of isomers with equilibrium composition for each class of clusters, taking into account the anharmonicity of cluster vibrations and the contribution of excited electronic states. The prospects of the application of small atomic Al n H m and B n H m clusters as the components of energetic and hydrogen storage materials are also discussed.

Solvent impact on the planarity and aromaticity of free and monohydrated zinc phthalocyanine: a theoretical study

Abstract: A theoretical investigation on the planarity of molecular structure of zinc phthalocyanine (ZnPc) and its aromaticity has been performed using B3LYP and M06-2X density functionals combined with selected Pople-type basis sets. The effect of the applied calculation method on the optimized structure of ZnPc and ZnPc∙∙∙H2O, both in the gas phase and in the polar solvent, was analyzed. To quantify the aromaticity of the ZnPc and ZnPc∙∙∙H2O complexes, both the geometric and magnetic criteria, i.e., Harmonic Oscillator Model of Aromaticity (HOMA) index and the nucleus-independent chemical shift (NICS) values at the centers or 1 A above the centers of structural subunits, were calculated. The energies of highest energy occupied molecular orbital (HOMO) and lowest energy unoccupied molecular orbital (LUMO) and energy gaps were also estimated. The results show that the free ZnPC molecule is flat in the gas phase and nonplanar in the polar environments (DMSO and water). ZnPC∙∙∙H2O is nonpolar in the gas phase and polar solvent which is in agreement with recent X-ray reports. Both HOMA and NICS indexes indicate the presence of highly aromatic macrocycle and benzene rings while these parameters for pyrrolic ring are significantly smaller than in free pyrrole. The presence of polar solvents practically does not change aromaticity of the ring subunits of the studied compounds.

Combining ligand-based and structure-based drug design approaches to study the structure-activity relationships of a β-carboline derivative series

Abstract: In this study, we investigated the structure-activity relationships of a series of β-carboline alkaloid derivatives using the 2D-QSAR and molecular docking, in order to identify the mode of interaction between β-carboline derivatives and the PLK1 kinase, and determine their key substituents responsible for the cytotoxic activity. The obtained QSAR models using multiple linear regression (MLR) and partial least squares (PLS) methods showed a high correlation between the experimental activity and the predicted one by PLS (R2PLS = 0.82, q2 = 0.72) and MLR (R2MLR = 0.82, q2 = 0.72). An external dataset was used to test the extrapolation power of the models which resulted in an R2PLS (EV) = 0.76; RMSE = 0.39. The 2D-QSAR analysis reveals that lipophilicity plays an important role in the cytotoxic activity of this group of β-carboline derivatives. Indeed, the molecular docking study into the active site of the polo-like kinase (PLK1) revealed that the most active ligand 57 shows higher binding energy and interacts, especially by H-bonds and hydrophobic interactions, with the active site of the PLK1 kinase. Consequently, the results obtained from the 2D-QSAR and docking studies provided a useful tool to design new and potent β-carboline derivatives as cytotoxic agents.

A mechanistic MEDT study of the competitive catalysed [4+2] and [2+2] cycloaddition reactions between 1-methyl-1-phenylallene and methyl acrylate: the role of Lewis acid on the mechanism and selectivity

Abstract: The selectivity and the nature of the mechanism of the competitive Lewis acid catalysed [4+2]/[2+2] cycloaddition reactions of 1-methyl-1-phenylallene (MPA) with methylacrylate (MA) have been theoretically studied within the Molecular Electron Density Theory using DFT methods at the B3LYP/6-31G(d) theoretical level. DFT reactivity indices indicate that MPA is a strong nucleophile and the LA-MA complex is a strong electrophile. The coordination of LA to MA enhances the reaction rate and increases the asynchronicity of the [4+2] CA reaction, changes the nature of the mechanism from one step to stepwise for the [2+2] CA reaction and increases the polar character of these cycloaddition reactions, which become demands a relatively low activation energy. Analysis of different energy profiles indicates that these competitive LA-catalysed CA reactions favour the formation of a mixture of meta regioisomers in both types of cycloaddition, in which the [4+2] cycloadducts were obtained in majority amount, in agreement with the experiment. Analysis based on Electron Localisation Function topological shows that the favoured [4+2] CA reaction takes place through a non-concerted two-stage one-step mechanism.

Carbon-doped boron-nitride fullerenes as efficient metal-free catalysts for oxidation of SO 2 : a DFT study

Abstract: The aim of this study is to explore the potential of utilizing carbon-doped fullerene-like boron-nitride nanocages (B11N12C and B12N11C) as an efficient metal-free catalyst for the oxidation of SO2 to SO3 molecule in the presence of N2O. The oxidation of SO2 over B11N12C includes two steps. First, the N2O molecule is decomposed into an activated oxygen atom (O*) and N2 molecule, and then the SO2 molecule is oxidized by the O* species. In the case of B12N11C and B12N12, however, the reaction starts with the coadsorption of SO2 and N2O molecules, followed by the decomposition of N2O and the formation of SO3 and N2 species. According to our results, B11N12C exhibits larger catalytic activity for the SO2 oxidation compared with B12N11C and B12N12 clusters. The estimated activation energy for the SO2 + O* → SO3 reaction catalyzed over the B11N12C surface is 5.8 kcal/mol, which is comparable with those reported about noble-metal catalysts. The results of this study can be useful for developing metal-free catalysts based on C-doped BN nanostructures.

Influence of swelling in supercritical carbon dioxide of Ultem and polyhexafluoropropylene thin films on their gas separation properties: comparative analysis

Abstract: Thin films of polyetherimide Ultem and polyhexafluoropropylene serially underwent different treatments: drying to a constant weight, annealing at temperature slightly higher than glass transition temperature, and swelling in supercritical carbon dioxide and their gas transport properties were investigated.

Four supramolecular transition metal(II) complexes based on triazole-benzoic acid derivatives: crystal structure, Hirshfeld surface analysis, and spectroscopic and thermal properties

Abstract: Four new complexes [M(3-tba)2(H2O)4] (1–3) and [Co(4-tba)2(H2O)4] (4) {M = Zn (1), Ni (2), Co (3), 3-Htba = 3-(1H-1,2,4-triazol-1-yl)benzoic acid, 4-Htba = 4-(1H-1,2,4-triazol-1-yl)benzoic acid} have been synthesized under solvothermal conditions and structurally characterized by single crystal X-ray diffraction. Complexes 1–4 are also determined by elemental analysis, X-ray powder diffraction, IR and electronic spectroscopy. Single crystal X-ray diffraction reveals that complexes 1–3 are isostructural and they crystallize in the orthorhombic space group of Pbca, while complex 4 belongs to triclinic system with Pī space group. Based on different intermolecular hydrogen bonding and π···π stacking interactions, complexes 1–4 further assembled into 3D supramolecular frameworks. Hirshfeld surface analysis was used to further study the intermolecular interactions of the complexes. The thermogravimetric analyses (TGA) reveal that these complexes possess good thermal stability, and the differential scanning calorimetry (DSC) analyses show intense exothermic phenomena in the decomposition processes of triazole groups. Besides, the photoluminescence property of complex 1 in the solid state is also determined.

3-Cyclopropyl-1,2-dimethyldiaziridine: synthesis and study of molecular structure by gas electron diffraction method

Abstract: The molecular structure and conformational behavior of 3-cyclopropyl-1,2-dimethyldiaziridine have been for the first time experimentally studied by gas-phase electron diffraction and quantum chemical calculations. The two most stable conformers at 298 K possess anti and gauche mutual ring orientation (with prevalence of the anti conformer) whereas only one anti conformer is observed in solution. The determined structural parameters of gaseous 3-cyclopropyl-1,2-dimethyldiaziridine have been compared with those for 3,3-bidiaziridine structural analogues in the crystal phase. The simple and convenient procedure for the synthesis of 3-cyclopropyl-1,2-dimethyldiaziridine comprising cyclopropane and diaziridine rings in one molecule was developed. The standard enthalpy of formation of 3-cyclopropyl-1,2-dimethyldiaziridine in the gas phase was calculated using Gaussian-4 theory, yielding value of 281.9 ± 5.0 kJ/mol.

Influence of intrinsic and extrinsic factors on the antiradical activity of Gallic acid: a theoretical study

Abstract: The factors responsible for the potent antioxidant activity of gallic acid (GA) are explored by employing density functional theory (DFT). It is found that the intrinsic characteristic features of the molecule play a significant role in its overall effectiveness as an antioxidant. The arrangement of the three hydroxyl groups with respect to each other imparts efficient antioxidant and antiradical property to GA. The external factors, such as polarity and pH of the reaction medium, also have a significant role to play. The polarity of the medium substantially affects the electron donating ability of GA, whereas the hydrogen atom donating ability is only marginally influenced. GA is a poor electron donor, but it can efficiently donate the hydrogen atom from its para hydroxyl group and effectively quench free radicals. It proves to be a better antiradical agent at the physiological pH, wherein it exists in the monoanionic form. Further, a comparison with other phenolic acids substantiates the importance of the carboxyl and hydroxyl groups in the antiradical activity of GA.