Transannular Diels-Alder reactivities of 14-membered macrocylic trienes and their relationship with the conformational preferences of the reactants: a combined quantum chemical and molecular dynamics study

Transannular Diels-Alder (TADA) reactions that occur between the diene and dienophile moieties located on a single macrocyclic triene molecule have been recognized as effective synthetic routes toward realizing complex tricyclic molecules in a single step. In this paper, we report a comprehensive study on the TADA reactions of 14-membered cyclic triene macrocycles to yield A.B.C[6.6.6] tricycles using quantum chemical methods and using classical molecular dynamics simulations. A benchmark study has been performed to examine the reliability of the commonly used ab initio methods and hybrid density functional levels of theory in comparison with results from CCSD(T) calculations to accurately model TADA reactions. The energy barriers obtained using the M06-2X functional were found to be in quantitative agreement with the CCSD(T) level of theory using a reasonably large basis set. Conformational properties of the reactants have been systematically studied using extensive molecular dynamics (MD) simulations. For this purpose, model systems were conceived, and force field parameters corresponding to the dihedral terms in the potential energy function were obtained. Linear relationship between the activation energies corresponding to the TADA reactions and the probability of finding the reactant in certain conformational states was obtained. A clustering method along with optimizations at the molecular mechanics and density functional M06-2X levels has been used to locate the most stable conformation of each of the trienes.     

DFT computational study towards investigating Cladribine anticancer drug adsorption on the graphene and functionalized graphene

Structural Chemistry - Density functional theory calculations at the M06-2X/6-31G** level have been carried out to examine the adsorption behavior of Cladribine drug on the graphene and graphene...     

The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree-Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene-M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene-M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene-M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene-M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems.     

Theoretical study on alkaloid encapsulating via cyclopentano-cucurbit[n]uril (n = 8, 10)/graphene oxide heterojunction

Here, physical chemistry properties of the inclusion complexes of some alkaloids and cyclopentano-cucurbit[8, 10]urils (Cy-CB[8, 10]) were investigated via molecular dynamic (MD) simulations and density functional theory (DFT) calculations. The possibility of the heterojunction formation between cyclopentano-cucurbit[8, 10]urils and graphene oxide was investigated via MD simulation. Based on the results, an effective role of graphene oxide on the encapsulation complex formation, especially in the presence of codeine and morphine was confirmed. DFT (M06-2X) and DFT-D3 (M06-2X-D3) functionals were applied for geometry optimization of the complexes. To have an insight into the atomic level, different analyses, such as natural bond orbital and quantum theory of atoms in molecule analyses were applied and discussed. DFT results confirm that Cy-CB[8] makes a stronger interaction with alkaloids in comparison with Cy-CB[10]. Thermodynamic studies show that the complexation process of codeine inside Cy-CB[n] is more favorable than other complexes. Moreover, energy analysis showed that the van der Walls part plays an important role in alkaloid stabilization inside the Cy-CB[n] cavity.     

A simple molecular mechanics potential for μm scale graphene simulations from the adaptive force matching method

A simple molecular mechanics force field for graphene (PPBE-G) was created by force matching the density functional theory Perdew-Burke-Ernzerhof forces using the adaptive force matching method recently developed in our group. The PPBE-G potential was found to provide significantly more accurate forces than other existing force fields. Several properties of graphene, such as Young's modulus, bending rigidity, and thermal conductivity, have been studied with our potential. The calculated properties are in good agreement with corresponding density functional theory and experimental values. The thermal conductivity calculated with reverse non-equilibrium molecular dynamics depends sensitively on graphene size thus requiring the simulation of large sheets for convergence. Since the PPBE-G potential only contains simple additive energy expressions, it is very computationally efficient and is capable of modeling large graphene sheets in the μm length scale.     

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.     

The Structure of 2-Methylphenylcyanamide in the Solid State

The structure of 2-methylphenylcyanamide NCNH(C₆H₄Me-2) is established in the solid state using single crystal X-ray diffraction data. The contribution of various intermolecular contacts to the crystal packing is studied using the Hirshfeld surface analysis and quantum chemical calculations within the density functional (DFT) M06-2X/6-311++G(d,p) level of theory.     

Probing the bent bonds in cyclopropane systems for gas storage and separation process: A computational study

The hydrogen, carbon dioxide, and carbon monoxide gas adsorption and storage capacity of lithium-decorated cyclopropane ring systems were examined with quantum chemical calculations at density functional theory, DFT M06-2X functional using 6-31G(d) and cc-pVDZ basis sets. To examine the reliability of M06-2X DFT functional, a few representative systems are also examined with complete basis set CBS-QB3 method and CCSD-aug-cc-pVTZ level of theory. The cyclopropane systems can bind to one Li⁺ ion; however, the corresponding the methylated systems can bind with two Li⁺ ions. The cyclopropane systems can adsorb six hydrogen molecules with an average binding energy of 3.8 kcal/mol. The binding free energy (ΔG) values suggest that the hydrogen adsorption process is feasible at 273.15 K. The calculation of desorption energies indicates the recyclable property of gas adsorbed complexes. The same number of CO₂ and CO gas molecules can also be adsorbed with an average binding energy of −14.4 kcal/mol and −10.7 kcal/mol, respectively. The carbon dioxide showed ~3–4 kcal/mol better binding energy as compared to carbon monoxide and hence such designed systems can function as a potential candidate for the separation of these flue gas molecules. The nature of interactions in complexes was examined with atoms in molecules analysis revealed the electrostatic nature for the interaction of Li⁺ ion with cyclopropane rings. The chemical hardness and electrophilicity calculations showed that the gas adsorbed complexes are rigid and therefore robust as gas storage materials.     

The calculations of phonon dispersion relations for single-wall carbon armchair and zigzag nanotubes

A 3D single-wall carbon nanotube can be viewed as a 2D graphite sheet rolled into a 3D cylinder. In the study of dispersion relations of carbon nanotubes, the consistent force parameters for 2D graphite sheets have to be modified to include the curvature effect. The present paper reports a series of calculations of phonon dispersion relations for single-wall carbon armchair, zigzag nanotube in which the curvature effect has been properly treated. The symmetry of crystal vibration mode at the centre of Brillouin zone is analyzed based on our numeric results and the structure symmetry of the nanotubes.     

Perchlorination of Coronene Enhances its Propensity for Self‐Assembly on Graphene

Providing a quantitative understanding of the thermodynamics involved in molecular adsorption and self‐assembly at a nanostructured carbon material is of fundamental importance and finds outstanding applications in the graphene era. Here, we study the effect of edge perchlorination of coronene, which is a prototypical polyaromatic hydrocarbon, on the binding affinity for the basal planes of graphite. First, by comparing the desorption barrier of hydrogenated versus perchlorinated coronene measured by temperature‐programmed desorption, we quantify the enhancement of the strength of physisorption at the single‐molecule level though chlorine substitution. Then, by a thermodynamic analysis of the corresponding monolayers based on force‐field calculations and statistical mechanics, we show that perchlorination decreases the free energy of self‐assembly, not only enthalpically (by enhancing the strength of surface binding), but also entropically (by decreasing the surface concentration). The functional advantage of a chemically modulated 2D self‐assembly is demonstrated in the context of the molecule‐assisted liquid‐phase exfoliation of graphite into graphene.     

微波固相法快速制备氮掺杂石墨烯

以鳞片石墨为原料,首先通过Hummers法制备氧化石墨,再将洗涤至中性的氧化石墨分散液与乙二胺反应得到功能化石墨烯。干燥后的功能化石墨烯在微波辐照下能瞬间产生高热,促使接枝的乙二胺分子分解并实现对石墨烯原位掺杂制备出氮掺杂石墨烯。利用扫描电子显微镜(SEM)、透射电子显微镜(TEM)、傅里叶变换红外光谱(FTIR)、X射线光电子能谱(XPS)、X射线衍射(XRD)、X射线能谱(EDS)对样品的形貌、结构和组成进行了表征。结果表明:该合成途径能成功实现对氧化石墨烯的还原和掺杂,所合成的氮掺杂石墨烯呈现透明绢丝状结构。     

微波固相法快速制备氮掺杂石墨烯

以鳞片石墨为原料, 首先通过Hummers法制备氧化石墨, 再将洗涤至中性的氧化石墨分散液与乙二胺反应得到功能化石墨烯。干燥后的功能化石墨烯在微波辐照下能瞬间产生高热, 促使接枝的乙二胺分子分解并实现对石墨烯原位掺杂制备出氮掺杂石墨烯。利用扫描电子显微镜(SEM)、透射电子显微镜(TEM)、傅里叶变换红外光谱(FTIR)、X射线光电子能谱(XPS)、X射线衍射(XRD)、X射线能谱(EDS)对样品的形貌、结构和组成进行了表征。结果表明:该合成途径能成功实现对氧化石墨烯的还原和掺杂, 所合成的氮掺杂石墨烯呈现透明绢丝状结构。     

Assessment of density functionals and force field methods on anion–π interaction in heterocyclic calix complexes

The performance of ten density functionals and four force field methods in describing non-covalent interactions have been assessed by studying the interaction energies and structures of the four anion–π complexes involving tetraoxacalix[2]arene[2]triazine and various anions. Their structures are optimized at MP2/6-311++G(d,p) level, and interaction energies are obtained at DF-MP2-F12/aug-cc-pVDZ level. The result shows that the functional M06-2X predicts the most reliable interaction energy, followed by wB97XD and BHandH. B97D slightly overestimates the interaction energy. Other functionals and force field methods seriously overestimate the interaction energy. For the structures, three functionals M06-2X, wB97XD and BH and H predict the most reliable results, followed by B97D. The force field methods predict the largest deviations. The present work suggests that the functional M06-2X is a reliable method to describe energies and structural properties of the large molecules involving the anion–π interactions.     

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution

We are presenting a theoretical study of the hydrolysis of a β‐lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06‐2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substrate implies the existence of a huge number of possible conformers, some of them implying formation of intramolecular hydrogen bond interaction that can determine the energetics of the conformers defining the different states along the reaction profile. The results show PM3 provides results that are in qualitative agreement with DFT calculations. The free energy profiles show a step‐wise mechanism that is kinetically determined by the nucleophilic attack of a water molecule activated by the proton transfer to the carboxylate group of the substrate (the first step). However, since the main role of the β‐lactamase would be reducing the free energy barrier of the first step, and keeping in mind the barrier obtained from second intermediate to products, population of this second intermediate could be significant and consequently experimentally detected in β‐lactamases, as shown in the literature. © 2012 Wiley Periodicals, Inc.     

Aqueous Dispersions of Graphene from Electrochemically Exfoliated Graphite

A facile and environmentally friendly synthetic strategy for the production of stable and easily processable dispersions of graphene in water is presented. This strategy represents an alternative to classical chemical exfoliation methods (for example the Hummers method) that are more complex, harmful, and dangerous. The process is based on the electrochemical exfoliation of graphite and includes three simple steps: 1) the anodic exfoliation of graphite in (NH₄)₂SO₄, 2) sonication to separate the oxidized graphene sheets, and 3) reduction of oxidized graphene to graphene. The procedure makes it possible to convert around 30 wt % of the initial graphite into graphene with short processing times and high yields. The graphene sheets are well dispersed in water, have a carbon/oxygen atomic ratio of 11.7, a lateral size of about 0.5–1 μm, and contain only a few graphene layers, most of which are bilayer sheets. The processability of this type of aqueous dispersion has been demonstrated in the fabrication of macroscopic graphene structures, such as graphene aerogels and graphene films, which have been successfully employed as absorbents or as electrodes in supercapacitors, respectively.     

Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations

Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential.     

Improved polyvinylpyrrolidone (PVP)/graphite nanocomposites by solution compounding and spray drying

In order to evaluate the roles of graphite dispersion on the functional properties of the composites, PVP/graphite nanocomposites were prepared by blending the aqueous suspension of expanded graphite sheets and polyvinylpyrrolidone (PVP) aqueous solution by ultrasonic treatment, followed by spray drying and direct drying as a comparison individually. The effects of graphite loading and drying method on the dispersion of graphite and the resultant properties of the composites such as electrical and thermal conductivity, friction, and dynamic mechanical properties were studied. The results from transmission electron microscopy (TEM), scanning electron microscopy (SEM), and X‐ray diffraction showed that the composites prepared by fast spray drying exhibited a higher degree of exfoliation and a better dispersion of graphite sheets in the PVP matrix than the corresponding composites prepared by direct drying, leading to a conclusion that fast spray drying can effectively prevent from re‐stacking of the exfoliated graphite sheets as illustrated. As a result, dynamic mechanical thermal analysis showed significant increases in the storage modulus and glass transition temperature for the composites prepared by spray drying. Besides, the spray drying as well greatly improved the electrical and thermal conductivity of the composites. It was also found that the electrical and thermal conductivity of the composites strongly depended on the graphite dispersion, while the friction coefficient unexpectedly does not. Increasing graphite loading level might enhance the probability of graphite sheets re‐stacking, resulting in poor graphite dispersion. Copyright © 2011 John Wiley & Sons, Ltd.     

Molecular modeling of phenothiazine derivatives: self-assembling properties

This study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π-π stacking phenothiazine derivatives and between different alkane chains varying from propane to decane. Second-order M?ller-Plesset perturbation (MP2), coupled cluster (CC), and density functional (DFT) theories were the quantum chemistry methods used in our calculation. For MP2 and CC methods, the density-fitting and local approximations were taken into account, while in the case of DFT, the M06 and M06-2x hybrid meta-GGA exchange-correlation functionals as well as the semiempirical correction to the DFT functional for dispersion (BLYP-D) was considered. The results obtained with the aforementioned methods were compared with the potential energy curve given by the DF-SCSN-LMP2 theory considered as benchmark. For all these calculations, the correlation-consistent basis sets of cc-pVNZ (where N = D, T, Q) were used. In addition, potential energy curves built using the semiempirical PM6-D2 and the MM3 molecular force field methods were also compared with the benchmark curve and their efficiency was discussed. As the next step, several geometry conformations were investigated for both phenothiazine derivatives and alkane chain dimers. It was found that the conformational stability of these molecular systems is exclusively given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures was compared with the results obtained by the higher level local perturbation theory method, and based on these conclusions larger phenothiazine derivative oligomers structures were investigated. Finally, the optimal configuration of the complex molecular systems built by phenothiazine derivative, alkane chain fragments, and thiol groups was determined, and their self-assembling properties were discussed.     

Determination of Graphene Sheets Content in Carbon Materials by Raman Spectroscopy

Graphene layer is a monolayer of graphite. Graphene single layer has confirmed to have a higher electron and hole mobility than silicon and has high heat conduction and special optical properties. And un‐perfect graphene sheets exist in any carbon materials. In our previous result to determine the graphene sheets content in any carbon material can be determined by X‐ray spectrum combination with a peak decomposition method. In this study, we have prepared two serious carbon materials from wood wastes, with and without MnO₂ catalytic pyrolysis processes. Results show that all the G band intensity of all synthesized samples including a commercial graphene powder in Raman spectrum has a proportional relation with the graphene sheets content in these carbon materials.     

Thermal Disproportionation of Oxo-Functionalized Graphene

Graphene production by wet chemistry is an ongoing scientific challenge. Controlled oxidation of graphite introduces oxo functional groups; this material can be processed and converted back to graphene by reductive defunctionalization. Although thermal processing yields conductive carbon, a ruptured and undefined carbon lattice is produced as a consequence of CO₂ formation. This thermal process is not understood, but it is believed that graphene is not accessible. Here, we thermally process oxo-functionalized graphene (oxo-G) with a low (4–6 %) and high degree of functionalization (50–60 %) and find on the basis of Raman spectroscopy and transmission electron microscopy performed at atomic resolution (HRTEM) that thermal processing leads predominantly to an intact carbon framework with a density of lattice defects as low as 0.8 %. We attribute this finding to reorganization effects of oxo groups. This finding holds out the prospect of thermal graphene formation from oxo-G derivatives.