Atoms In Molecules Research Articles

Structural, energetic and dynamic investigation of poly(ethylene oxide) in imidazolium-based ionic liquids with different cationic structures.

In this work, two imidazolium-based ionic liquids (ILs) with different cations including dications (DIL) and monocations (MIL) were blended with poly(ethylene oxide) (PEO). The influence of ILs' structure on the structural and dynamic properties of a PEO/IL system was investigated by molecular dynamics (MD) simulation and density functional theory (DFT) methods. The simulation results show that DIL exhibits weaker interaction with PEO than MIL due to a stronger IL aggregation effect. The intermolecular interaction also makes the PEO chain tend to organize around the imidazolium ring of ILs, which causes the conformational entropy loss. Compared with PEO/MIL, this phenomenon is more significant in PEO/DIL because of the double positive centers of the dication and a longer hydrogen bond lifetime. MD simulation also demonstrates that DIL could act as a "crosslinker" to promote the formation of a physical crosslinking network which has strong dependence on the concentration of IL. The competition between physical crosslinking and plasticizing effects induces non-monotonic variations of relaxation time in PEO/DIL, which is consistent with its unusual change of the glass transition temperature (Tg). Despite stronger hydrogen bonding interactions between PEO and MIL demonstrated by atom-in-molecules (AIM) and reduced density gradient (RDG) analysis, the segmental mobility is slower in PEO/DIL according to the MSD curve. These differences in multiple structural or energetic factors finally lead to different conductive mechanisms and hence obtain different ionic conductivities.

On the nature of noble gas - metal bond in silver aggregates.

The aim of this paper is to extend the study of the nature of the bond between noble gas to nano- and sub nanoscale silver aggregates. In the framework of DFT-PAW calculations implemented in the abinit package, we carried out a thorough investigation on the nature of the bond between the six noble gases NG (He, Ne, Ar, Kr, Xe and Rn) and numerous neutral silver aggregates Agn from the single atom Ag1 to the nanoparticle Ag147 using atoms-in-molecules (AIM) dual functional analysis,. We evaluated the impact of the silver aggregate size, the adsorption site and of the noble gas on the Ag-NG bond. Our study concluded on the favored adsorption of heavier noble gases (Kr, Xe and Rn) over that of lighter noble gases (He, Ne and Ar) on any aggregate size due to an enhanced chemical contribution in the bond. For these heavier noble gases, in accordance with studies carried out on surfaces, we noted their preferential adsorption on on-top sites rather than on hollow sites, which further evidences the chemical contribution to the bond. Moreover, the slight positive Bader charge on these heavier noble gases implies an electron transfer from the noble gas to the silver atom. Noble gas adsorption is favored on smaller, few-atom, two-dimensional clusters rather than on larger three-dimensional nanoparticles. Finally, we identified a universal power law with a unique exponent linking bond length and electronic density at the bond critical point for all aggregate sizes, noble gases and adsorption sites.

Structural analysis and electronic properties of transition metal ions (Ni2+, Fe2+, Mn+ and Co+) with psoralen biomolecule as an anticancer drug

In the current research, the density functional theory (DFT) method is used to investigate the effects of cation-π interaction on complexes formed by psoralen drug with metal cations (Ni2+, Fe2+, Mn+ and Co+). The calculations are performed in the gas phase and the water and carbon tetrachloride (CCl4) solvents. The interactions generated in the complexes are analyzed using the atoms in molecules (AIM) and the natural bond orbital (NBO) approaches. The results indicate that the absolute amount of the binding energy of complexes in the polar solvent is less than the non-polar solvent while in the gas phase it is more than solution. The obtained data also show that with increasing polarity of the solvent, the stabilization energy of the complexes increases. To gain a better insight into the mentioned interactions, the descriptors of chemical reactivity such as energy gap, hardness, softness and electronic chemical potential are also explored. Our findings display that the studied complexes have high chemical stability and low chemical reactivity in the solution relative to the gas phase.

Design of derivatives of FOX-7-based new four-member heterocyclic insensitive high energy density molecules: a theoretical prospectives

Theoretical analysis of the novel, insensitive and high-energy density compounds based on the 1,1-dinitro-2,2-diamino-ethylene (FOX-7) moiety is presented here. In order to better serve as a prospective insensitive, high-energy molecule, a few novel heterocyclic four-member compounds were developed. The atoms in molecule (AIM) calculations have been used to estimate the stability of the C-NO2 bond as well as the covalent nature of the bonds. Using the Gaussian-16 quantum chemistry software, the electronic structure computations have been retrieved at the B3LYP level of theory with an aug-ccpVDZ basis set. It was discussed the impact sensitivity, thermal stability, detonation characteristics, harmonic vibrational frequency calculations, natural bond orbital calculations, the optimised structure of these molecules and more. The crystal density, activation energy for the nitro (C-NO2) to nitrito (C-ONO) transformation during the first stage of thermal breakdown, and the C-NO2 bond dissociation energy with BSSE correction of these molecules have been comprehensively investigated. These newly modelled compounds have been discovered to exhibit comparable detonation characteristics to those of FOX-7, which implies that they should be synthesised in a lab by experienced experimentalists.

Resolving male infertility that is induced by β-and ca channel antagonist drugs: Propranolol/Verapamil using an optimized nanohybrid formula: Experimental and computational studies

Two major objectives of the current study, the first was to study theoretically the electronic structure of Chitosan-Sodium alginate, Epigallocatechin-gallate (EGCG) and Sodium alginate-EGCG complex using density-functional theory (DFT) calculations. The binding energy (ΔEbind), the atoms in molecules (AIM) theory and the Natural bond orbital (NBO) analysis of Chitosan-Sodium alginate-EGCG complex have been studied in gas and water phases. The second was to investigate the treatment effect of EGCG in normal form and EGCG-loaded chitosan-sodium alginate nanoparticles (EGCG-CS-SA NPs) on the male infertility that was induced in male albino rats by the oral administration of Propranolol Hydrochloride and Verapamil Hydrochloride. Full characterization of the synthesized EGCG-CS-SA NPs were carried out using different techniques. Then eight groups of rats were classified as follows: control negative (A); Propranolol Hydrochloride (B); Verapamil Hydrochloride (C); EGCG normal (D); EGCG nano (EGCG-CS-SA NPs) (E); Propranolol Hydrochloride + EGCG (F); Propranolol Hydrochloride + EGCG-CS-SA NPs (G); and Verapamil Hydrochloride + EGCG-CS-SA NPs (H). The study registered the body weight gain percentage as well the weights of the liver, testes, and seminal vesicles. Malondialdehyde (MDA), glutathione reduced (GSH), and testosterone levels were assessed. The semen analysis was performed, the deoxyribonucleic acid (DNA) damage was detected, and the histopathological sections were examined. The computational study identified that the interaction between chitosan-sodium alginate and EGCG is covalent and electrostatic interactions in nature in the gas and water phases. The results recorded an increase in body weight gain percentage in Propranolol Hydrochloride + EGCG-CS-SA NPs and Verapamil Hydrochloride + EGCG-CS-SA NPs groups but no significant difference (P› 0.05) in organs weight of experimental groups (B, C, D, E, F, G, and H) as compared to control group. In the treated rats (F, G, and H), the MDA decreased significantly, while the GSH increased.The results showed that the formula improved the negative effects of Propranolol Hydrochloride and Verapamil Hydrochloride administration on serum testosterone level, sperm count, motility, percentage of live sperms, and histological structures in the testes and epididymides. Post-administration of EGCG normal and EGCG-CS-SA NPs to Propranolol Hydrochloride and Verapamil Hydrochloride caused no significant difference (P› 0.05) in tail moment value in testes cells as compared to Propranolol Hydrochloride and verapamil Hydrochloride groups. Finally, the herbal nanohybrid formula EGCG-CS-SA NPs was found to be safe and could be used to treat male infertility caused by antihypertensives.

Structural and Spectral Properties of 4-(5-methyl-[1, 2, 4] triazolo [1, 5-a] pyrimidine-7-yloxy) phthalonitrile: Analysis by TD-DFT Method, ADME Analysis, and Molecular Docking Simulations

In this study, 4-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidine-7-yloxy) phthalonitrile (coded as MTPPN) was chosen as the phthalonitrile compound and the quantum chemical and in-silico studies have been done. First, the basis set of the time dependent density functional theory (TD-DFT) method was used and the boundary orbital energies and band gap calculations of the molecule were performed. Analysis of atoms in molecules (AIM) theoretical calculations is presented to learn about electron density and bond critical point. In addition, absorption, distribution, metabolism, and excretion analyzes (ADME) were performed for the drug potential of the compound. On some enzymes effect of MTPPN compound was examined. The docking score was obtained for AChE, BChE, α-GLY proteins -7.864, -6.848, and -5.511 kcal/mol, respectively. MTPPN gave a good inhibitory performance in an in-silico study as a drug candidate.

Theoretical investigations of functionalization of graphene and ZnO monolayers with mercaptopurine at aqueous media: A dispersion-corrected DFT calculations and molecular dynamic simulations

This study presents a theoretical investigation of mercaptopurine adsorption on graphene and ZnO monolayer using first-principles simulations with dispersion-corrected density functional theory (DFT). Two different interaction orientations for interacting mercaptopurine with the surface were evaluated and the energetically most stable configuration was obtained with −1.412 eV. The ZnO surface adsorbs mercaptopurine stronger than graphene. The electronic structure analysis indicates that the adsorption of molecule reduces the band gap of both considered semiconductor substrates while their semiconducting property still remains unchanged. Furthermore, charge analyses based on the Hirshfeld method revealed that around 0.213 e was transferred from the ZnO substrate to the mercaptopurine molecule. Density functional tight binding based molecular dynamics (DFTB-MD) simulations show that mercaptopurine tends to be adsorbed on both monolayers while moving from the water aqueous media toward the surface at room temperature. The DFT-based atoms-in-molecules (AIM) analysis predicted that themercaptopurine-graphene interaction nature is typical for the noncovalent type π-π interactions while mercaptopurine chemisorbed on the ZnO surface by chemical bonding between N/S and Zn atoms. The present results provide atomic insights on the interaction properties of mercaptopurine drug with graphene and ZnO nanosheets and supply new manner and worth data to assist the experiments and potential applications in thebio and nanotechnology area.

Synthesis and Computational and X-ray Structure of 2, 3, 5-Triphenyl Tetrazolium, 5-Ethyl-5-phenylbarbituric Acid Salt

The title compound triphenyl tetrazolium (TPT) of phenobarbital, 5-Ethyl-5-phenylbarbituric acid triphenyl tetrazolium salt (4) was prepared by the reaction of 5-Ethyl-5-phenyl-2,4,6(1H, 3H, 5H)-pyrimidinetrione, monosodium salt (1) with triphenyl tetrazolium chloride (3) in deionized water at an ambient temperature through a cation exchange reaction. Colorless crystals of compound four suitable for an X-ray structural analysis were obtained by slow evaporation from acetonitrile. Compound four had crystallized in the monoclinic space group, P21/c, with a = 15.3678 (9) Å, b = 12.2710 (7) Å, c = 21.8514 (13) Å, β = 109.867 (2)°, V = 3875.5 (4) Å3, and Z = 4. A Through density functional theory (DFT) calculations, the probable molecular association structure in the phenobarbitone -triphenyl tetrazolium solution was studied. With the 6-311G-(d,p) basis set, the gas phase features of the phenobarbital-triphenyl tetrazolium clusters with a phenobarbitone dimer and water molecules, including an optimum structure and intermolecular hydrogen bonding, were investigated in detail. In addition, the positions and strengths of the intermolecular hydrogen bond interactions between the phenobarbitone and triphenyl tetrazolium molecules were analyzed using atoms in molecule (AIM) analysis, reduced density gradient (RDG) methods, the XRD method, and the non-covalent interaction (NCI) index method. In addition, the molecular electrostatic potential (MEP) surfaces were analyzed to determine the electrophilic and nucleophilic centers.

An expedient synthesis spectral characteristic computational studies and target prediction through insilco studies of 24α-ethylcholest-5, 22E-dien-3-yl-2- mercapto-benzoate and 11, 17 di-hydroxy preg-4-ene-3, 20-dione-21-yl-2-mercapto-benzoate

In the current work (24α-ethylcholest-5, 22E-dien-3-yl-2- mercapto-benzoate) (3) and (11, 17 di-hydroxy-preg-4-ene-3, 20-dione-21-yl-2-mercapto-benzoate) (4) were synthesized from Stigmasterol (1) and Hydrocortisone (2), respectively isolated as a major components from chloroform extract of stem part of the plant Allamandaviolacea. The synthesized compound (3) and (4) have been characterized with the aid of 1H, 13C, UV, FT-IR spectroscopy. Density functional theory (DFT) is used to reckonthe molecular geometry of synthesized compounds with B3LYP functional and 631 G (d,p) basis set in ground state.1H and 13C NMR chemical shifts were premeditated in ground state by means of Gauge-Including Atomic Orbital (GIAO) method and these values were correlated with experimental interpretations. Time dependent Density Functional Theory (TD-DFT) is employed in computing electronic properties such as HOMO and LUMO. AIM (Atom in molecule) analysis is used in evaluation of strength of H-bonding and its intra molecular interactions. Global reactivity descriptors were calculated to study the reactive sites within molecules. Dipole moment, polarizability and first hyperpolarizability values have been determined for interpretation of nonlinear optical (NLO) property of the synthesized compounds. Molecular electrostatic potential (MEP) has also been performed.The potential of both the compounds were evaluated against quorum sensing protein of Gram negative bacteria LsrB (1TM2), LsrK (5YA2), LasR (2UV0) and LuxS (5E68). Binding energy ranging from -8.40133 to -12.49721 kcal/mol and virtual score from -9.67971 to -13.81495 suggest that the compounds can play important role in controlling the unwanted growth of Gram negative bacteria by inhibiting their quorum sensing system.

Synthesis, Molecular and Supramolecular Structures of Symmetric Dinuclear Cd(II) Azido Complex with bis-Pyrazolyl s-Triazine Pincer Ligand

A new dinuclear Cd(II)-azido complex of 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine (PMT) pincer ligand is synthesized. Its single crystal X-ray structure reveals the dinuclear [Cd(PMT)(Cl)(N3)]2 formula. The triclinic crystal parameters are a = 9.323(4) Å, b = 10.936(5) Å, c = 11.312(6) Å, α = 112.637(10)°, β = 104.547(11)° and γ = 105.133(10)° while V = 944.1(8) Å3. Due to symmetry considerations, the asymmetric unit comprises a half [Cd(PMT)(Cl)(N3)]2 formula. The Cd(II) is hexa-coordinated with one tridentate PMT ligand in a pincer fashion mode in addition to one terminal chloride and two azide ions bridging the two Cd(II) centers in double μ(1,1) bridging mode. Unusually, the Cd-N(s-triazine) bond is not the shortest among the Cd-N interactions with the PMT pincer ligand. The supramolecular structure of the dinuclear [Cd(PMT)(Cl)(N3)]2 formula is controlled by a significant amount of Cl…H (16.4%), N…H (25.3%), H…C (9.8%) and H…H (37.2%) interactions based on Hirshfeld surface analysis. Careful inspection of the shape index map reveals the presence of some weak π-π stacking interactions between the s-triazine and pyrazolyl moieties. The percentage of C…C contacts is 1.9% where the C2…C8 (3.462 Å) is the shortest while the centroid–centroid distance is 3.686 Å. Natural charge analysis describes the charge transferences from the ligand groups to the Cd(II), while and atoms in molecules (AIM) give an indication on the properties of the Cd-N and Cd-Cl bonds.

Synthesis, Spectroscopic (FTIR, FT-Raman and UV-Vis), Structural Investigation, Hirshfeld, AIM, NBO, Chemical Reactivity, In-Vitro and In-Silico Analysis of N-(2-Hydroxyphenyl)-4-Toluenesulfonamide

The prospective antimicrobial molecule N-(2-Hydroxyphenyl)-4-methylbenzene sulfonamide has been synthesized and characterized by single crystal XRD, FT-IR, FT-Raman, UV-Vis spectra and antimicrobial analysis. The quantum chemical computations of energies, geometrical structure, charge transfer and vibrational wavenumbers were carried out using density functional method (DFT/B3LYP) with 6-311 G (d, p) basis set. The complete vibrational assignment for the vibrational modes were performed with vibrational energy distribution analysis (VEDA4) and these assignments were compared with the experimental FT-IR and FT-Raman spectrum. In FT-IR spectrum, strong intense absorption bands are observed at 3408 and 3273 cm−1 corresponding to OH and NH group, which is involved in N–H…O and C–H…O intermolecular interaction. Hirshfeld surface analysis determines the stability of crystal packing within the crystal packing ensured by C–H…O and O–H…O intermolecular interactions. The 2 D fingerprint plot shows that H…H, C…H and O…H interaction exhibit the most significant contribution. Natural bond orbital (NBO) analysis suggests that the electronic transitions are mainly attributed to π→π* transitions. The strength of N–H…O and C–H…O intermolecular interactions were analyzed using reduced density gradient (RDG) analysis and atom in molecule (AIM) analysis. The frontier molecular orbital analysis reveals the possibility of charge transfer within the molecule. Electrophilic and nucleophilic sites were found by molecular electrostatic potential (MEP) analysis and Fukui analysis. Molecular docking shows that sulfonamide and hydroxyl groups are biologically active through their hydrogen bonding interaction with amino acids, which reveals the antimicrobial activity of the compound. Antimicrobial activity of the compound was confirmed by the Kirby Bauer disk diffusion method. The band gap energy and antimicrobial evaluation of the title molecule were compared with the reported relative compounds, which reveals the significant antimicrobial activity. Besides, drug likeness and ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction analysis suggest that the title compound can be used as an antimicrobial drug.

Mercurophilic interactions in heterometallic Ru-Hg carbonyl clusters

The reaction of [HRu3(CO)11]– (1) with 0.35 mol equivalents of Hg(CH3CO2)2 afforded [HgRu6(CO)22]2– (3), whereas a mixture of 3 and [Hg2Ru7(CO)26]2– (4) was obtained using 0.5 mol equivalents of Hg(CH3CO2)2 per mole of 1. A few crystals of [Ru3(CO)10(CH3COO)]– (7) were obtained as side products of the latter reaction. The reaction of 1 with one mole equivalent of Hg(CH3CO2)2 or HgCl2 afforded [Hg3Ru8(CO)30]2– (5) as the major product. By employing HgCl2, formation of 5 was accompanied by traces of the new homometallic cluster [Ru2Cl4(CO)5]2– (8). [HRu4(CO)12]3– (2) reacted with one mole equivalent of HgCl2 resulting in [Hg4Ru10(CO)32]4– (6). The molecular structures of the new clusters 3–8 were determined by single crystal X-ray diffraction (SC-XRD) as their [NEt4]2[3], [NEt4]2[4]·0.5CH2Cl2, [NEt4]2[5], [NEt4]4[6], [NEt4][7], [NEt4]2[8]·0.5CH3CN salts. Heterometallic Ru-Hg clusters 3–6 contain [Hg]2+, [Hg2]4+, [Hg3]6+, and [Hg4]8+ cores stabilized by [Ru(CO)4]2–, [Ru3CO)11]2– and [Ru4(CO)12]4– fragments. Metal-metal bonds were investigated by DFT calculations and atoms-in-molecules (AIM) analyses.

Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic.

It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum-chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree-Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM-binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.

Topological Analysis of the Electron Density of Molecules with Bridging Hydrogens To Tackle the Chemical Structure Monolith

AbstractThe assumption, common at the undergraduate level, that hydrogen with its single electron can form only one covalent bond is belied by the many structures that have been characterized with hydrogens bonded to two atoms. The 3‐center bond responsible for such bridging hydrogens is facilitated by the spherical distribution inherent to the 1s electron. Here we demonstrate how topological analysis of the electron density of molecules with bridging hydrogens can inform a deeper appreciation of the character and complexity of the chemical bond. DFT calculations are performed to generate the electron density for the experimental structures of a range of complexes with bridging hydrogens. Analysis using both the Atoms in Molecules (AIM) perspective and a range of electron indicators and localization functions demonstrates the utility of topological analysis for the detection and characterization of multi‐center bonding.

Comprehensive study on thermal decomposition mechanism and interaction of 3-Nitro-1,2,4-Triazol-5-One/Poly-3-nitromethyl-3-methyloxetane plastic bonded explosives

In this paper, the thermal decomposition process of 3-Nitro-1,2,4-Triazol-5-One (NTO)/Poly-3-nitromethyl-3-methyloxetane (Poly-NIMMO) based Plastic Bonded Explosives (PBXs) at five temperatures from 2500 K to 3500 K was simulated based on the reactive molecular dynamics, and some related analysis contents were supplemented and verified by first-principles and quantum chemistry methods. In particular, given the strong acidity of NTO explosive, the interaction between NTO and Poly-NIMMO was analyzed. The analysis results of the atoms in molecules (AIM) method and Independent gradient model based on Hirshfeld partition (IGMH) method show that there are some relatively strong hydrogen bonds between them. The activation energies of the initial decomposition stage and the intermediate decomposition stage of the mixed system are 60.37 kJ∙mol−1 and 98.37 kJ∙mol−1. Compared with the pure NTO system, the activation energies of the two stages decrease to a different extent. Poly-NIMMO in the mixed system brings a lot of NO2 and OH groups, these molecular fragments and groups will have chemical reactions with NTO and decomposition products of NTO, resulting in the reduction of the number of hydrogen transfer reactions between NTO molecules. By comparing the quantity of products, it can be found that the content of H2O is greatly increased. The curve reaches the peak in a shorter time, and the decomposition reaction rate of the system is faster. The amount of CO2 did not increase too much, and more C atoms gathered to form clusters. The changes of the number of bonds verify the above analysis. In addition, in a certain temperature range, the relationship between the maximum number of clusters and temperature is positively correlated, but the excessive temperature can inhibit the maximum number of clusters. The ratio of O, N, H atoms to C atoms in the cluster after equilibrium at five temperatures is H/C > N/C > O/C. There is no doubt that Poly-NIMMO will reduce the acidity of the system, but it will promote the thermal decomposition of NTO and reduce the insensitivity of PBXs to thermal stimulation.

Spectroscopic, reactivity analysis and docking studies of 3-(adamantan-1-yl)-4-(4-fluorophenyl)-1-[(4-phenylpiperazin-1-yl)methyl]-4,5-dihdyro-1H-1,2,4-triazole—5-thione: DFT and MD simulations

An adamantane-thione derivative, 3-(adamantan-1-yl)-4-(4-fluorophenyl)-1-[(4-phenylpiperazin-1-yl)methyl]-4,5-dihdyro-1H-1,2,4-triazole—5-thione (ATT) is investigated experimentally and theoretically to predict its various chemical and electronic properties. The solvation energies are predicted in acetone, DMSO, ethanol and water and acetone is a better solvent due to high value of solvation energy. When compared to the gas phase, the chemical descriptors of ATT decreased in the solution phase. The adamantane cage breathing mode is assigned at 785 (theoretical) and 784 cm−1 (IR). Topological study of the atom in molecules (AIM) shows the ring critical points corresponding to the phenyl, pyrazine, triazole and 4-fluorophenyl rings.From molecular dynamics (MD) simulations, solvent accessible surface area (SASA) values are from 656 to 736 and 289 to 294 (Å2) for unbound and bound structures.

Intramolecular Interactions in Derivatives of Uracil Tautomers.

The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using the polarizable continuum model (PCM) of solvation. The substituents were characterized by electronic (charge of the substituent active region, cSAR) and geometric parameters. Intramolecular interactions between non-covalently bonded atoms were investigated using the theory of atoms in molecules (AIM) and the non-covalent interaction index (NCI) method, which allowed discussion of possible interactions between the substituents and N/NH endocyclic as well as =O/-OH exocyclic groups. The nitro group was more electron-withdrawing in the 5 than in the 6 position, while the opposite effect was observed in the case of electron donation of the amino group. These properties of both groups were enhanced in polar solvents; the enhancement depended on the ortho interactions. Substitution or solvation did not change tautomeric preferences of uracil significantly. However, the formation of a strong NO∙∙∙HO intramolecular hydrogen bond in the 5-NO2 derivative stabilized the dienol tautomer from +17.9 (unsubstituted) to +5.4 kcal/mol (substituted, energy relative to the most stable diketo tautomer).

Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules.

Graphene oxide (GO), a nanomaterial with promising applications that range from water purification to enzyme immobilization, is actively present in scientific research since its discovery. GO studies with computational methodologies such as molecular dynamics are frequently reported in the literature; however, the models used often rely on approximations, such as randomly placing functional groups and the use of generalized force fields. Therefore, it is important to develop new MD models that provide a more accurate description of GO structures and their interaction with an aqueous solvent and other adsorbate molecules. In this paper, we derived new force field non-bonded parameters from linear-scaling density functional theory calculations of nanoscale GO sheets with more than 10,000 atoms through an atoms-in-molecules (AIM) partitioning scheme. The resulting GAFF2-AIM force field, derived from the bonded terms of GAFF2 parameterization, reproduces the solvent structure reported in ab initio MD simulations better than the force field nowadays widely used in the literature. Additionally, we analyzed the effect of the ionic strength of the medium and of the C/O ratio on the distribution of charges surrounding the GO sheets. Finally, we simulated the adsorption of natural amino acid molecules to a GO sheet and estimated their free energy of binding, which compared very favorably to their respective experimental values, validating the force field presented in this work.

Insight into the effect of anions on cycloaddition of CO2 catalyzed by carboxylate anion-based ionic liquids: A theoretical study by QM and MD

Elucidating the mechanism of carbon dioxide (CO2) cycloaddition reaction catalyzed by ionic liquid (ILs) facilitates the rational design of efficient IL catalysts at the molecular level. To date, a great deal of research has been devoted to the halogen-containing ILs, however, the catalytic mechanism of halogen-free ILs remains unclear. In this contribution, an exhaustive theoretical study of the coupling reaction of CO2 with epichlorohydrin (ECH) catalyzed by three halogen-free ILs has been carried out for the first time by combining density functional theory (DFT) calculations with molecular dynamics (MD) simulations. Meanwhile, the effect of carboxylate anion structure on catalytic activity is deeply investigated. The final results provide a comprehensive catalytic mechanism of carboxylate anion-based ILs. The most favorable mechanism involves three steps, i.e., ring-opening of ECH, CO2 insertion, and ring-closure to form the product. Among them, the ring-opening of ECH is the rate-determining step (RDS). Additionally, the analytical results of the independent gradient model based on Hirshfeld partition (IGMH) and atoms in molecules (AIM) suggest that the electrophilic activation from carboxylate anions plays a critical role in promoting the ECH ring-opening process. The electrophilic activation of anions is investigated for the first time in this work. The results indicate that incorporating electrophilic groups into anions is a promising pathway to develop new robust and efficient halogen-free ILs.

Superstrong Chemical Bonding of Noble Gases with Oxidoboron (BO+) and Sulfidoboron (BS+).

Inspired by the overwhelming exploration of noble gas-boron (Ng-B) bond containing chemical compounds, the stability of the Ng bound BY+ and AlY+ (Y = O and S) has been investigated by using various ab initio based quantum chemical methods. Ng atoms are found to form exceptionally strong bonds with BO+ species in the predicted NgBO+ (Ng = He-Rn) complexes with remarkably high Ng-B dissociation energies ranging from 138.0 to 462.2 kJ mol-1 for the He-Rn series. It is the highest ever Ng-B binding energy in conjunction with the smallest Ng-B bond length for any of the cationic species involving a Ng-B bond as reported until today. More importantly, the calculated Ng-B bond lengths have been found to be much lower than the respective covalent limits in both NgBO+ and NgBS+ ions. The electronegativity difference between O and S atoms has been reflected nicely in the Ng-B and Ng-Al binding energies, which are found to be 91.9-346.5, 9.6-169.2, and 6.8-142.1 kJ mol-1 in NgBS+, NgAlO+, and NgAlS+, respectively. The strong covalent bonding between Ng and B/Al atoms in the predicted chemical systems has also been supported by the natural bonding orbital (NBO) and electron density based atoms-in-molecule (AIM) analysis. In addition, the energy decomposition analysis (EDA) in combination with the natural bond orbital for chemical valence (NOCV) indicates that the orbital interaction term is the prime contributor to the total attraction energy in the Ng-B and Ng-Al bonds. Furthermore, Ng-B and Ng-Al bonding can be assessed using the donor-acceptor model where the σ-electron donation that takes place from Ng (HOMO) → XY+ (LUMO) (X = B and Al; Y = O and S) is the major contributor to the orbital interaction energy. All the computational results along with the very recent experimental observation of ArOH+ and NgMX (Ng = Ar-Xe; M = Cu, Ag, Au; X = F, Cl) clearly indicate that it might be possible to synthesize and characterize these superstrong complexes, NgXY+ (Ng = He-Rn; X = B and Al; Y = O and S), under suitable experimental technique(s).