The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections

Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added dispersion correction have been used to study stabilising carbohydrate-aromatic and amino acid-aromatic interactions. The interaction energy for three simple sugars in different conformations with benzene, all give interaction energies close to 5 kcal mol(-1). Our original parameterization of PM3 (PM3-D) seriously overestimates this value, and has prompted a reparametrization which includes a modified core-core interaction term. With two additional parameters, the carbohydrate complexes, as well as the S22 data set, are well reproduced. The new PM3 scheme (PM3-D*) is found to describe the peptide bond-aromatic ring interactions accurately and, together with the DFT-D method, it is used to investigate the interaction of six amino acids with pyrene. Whilst the peptide backbone can adopt both stacked and T-shaped structures in the complexes with similar interaction energies, there is a preference for the unsaturated ring to adopt a stacked structure. Thus, peptides in which the latter interactions are maximised are likely to be the most effective for the functionalisation of carbon nanotubes.     

胺基功能化的炭材料上二氧化碳吸附的密度泛函理论研究

本文利用色散作用校正的密度泛函理论研究了炭材料上含氮官能团对CO₂吸附的作用。通过计算比较了不同含氮官能团炭材料结构片段吸附二氧化碳后的结构参数和能量,由于较强的静电作用和形成弱氢键,含单个苯环的酰胺和吡啶类的吸附剂吸附二氧化碳的作用强于单个苯胺和吡咯类吸附剂。但当增加苯环数时,色散作用主导的吡咯型吸附剂的吸附能力显著增强。以上结果预示着酰胺和吡咯类将是大π体系中具有良好CO₂吸附性能的吸附剂。因而,色散作用在CO₂吸附过程中也占据着重要地位。计算得到的结果与我们之前的实验结果一致,并且将有利于筛选更有效的二氧化碳吸附剂。     

Predicting whether aromatic molecules would prefer to enter a carbon nanotube: A density functional theory study

The interaction of a carbon nanotube (CNT) with various aromatic molecules, such as aniline, benzophenone, and diphenylamine, was studied using density functional theory able to compute intermolecular weak interactions (B3LYP-D3). CNTs of varying lengths were used, such as 4-CNT, 6-CNT, and 8-CNT (the numbers denoting relative lengths), with the lengths being chosen appropriately to save computation times. All aromatic molecules were found to exhibit strong intermolecular binding energies with the inner surface of the CNT, rather than the outer surface. Hydrogen bonding between two aromatic molecules that include N and O atoms is shown to further stabilize the intermolecular adsorption process. Therefore, when benzophenone and diphenylamine were simultaneously allowed to interact with a CNT, the aromatic molecules were expected to preferably enter the CNT. Furthermore, additional calculations of the intermolecular adsorption energy for aniline adsorbed on a graphene surface showed that the concavity of graphene-like carbon sheet is in proportion to the intermolecular binding energy between the graphene-like carbon sheet and the aromatic molecule.     

Effect of carbon nanotubes’ crystal structure on adsorption kinetics of small molecules An experimental study utilizing ultra-high vacuum thermal analysis techniques

The effect of carbon nanotubes’ (CNT) crystal structure on chemical reactivity has been studied in much detail in the liquid phase using CNT suspension. This type of information is pertinent for developing CNT separation strategies. However, few experimental studies are available providing data for gas–CNT interactions utilizing ultra-high vacuum (UHV) surface science techniques. Structure–activity relationships (SAR) for gas–surface interactions are important for sensor designs and heterogeneous catalysis exploring, for example, CNT’s potential as a support for fuel cell catalysts. We report on UHV kinetics experiments with single-wall metallic, semiconducting, and mixed CNTs in order to provide the experimental basis to correlate CNT’s crystal structure and chemical activity. Thermal desorption spectroscopy (TDS), a simple temperature ramping technique, has been used to determine the binding energies of a number of probe molecules including alkanes, alcohols, thiophene, benzene, and water on CNTs at UHV conditions. TDS allows for the identification of adsorption sites of probe molecules in CNT bundles, using gold foil or silica as a support for the drop-and-dry technique. A weak and probe molecule dependent SAR is present for adsorption inside the CNTs but not for the population of external sites by the probe molecules. The experimental data are in part consistent with current theoretical predictions by other groups. In addition, the effect of different solvents (methanol, SDS, and NMP) and cleaning procedures will briefly be discussed using results of spectroscopic (Auger electron spectroscopy) and kinetic techniques. Furthermore, molecular beam scattering techniques were utilized to characterize the adsorption dynamics, i.e., the gas-to-surface energy transfer processes of alkanes on CNTs. For example, opening the CNT tube ends by high temperature annealing, increases the so-called initial adsorption probability, that is, the probability for adsorption in the limit of zero surface concentration (coverage). This result directly illustrates the effect of large surface areas of CNTs, using internal and external surfaces, for gas adsorption.     

Endohedral and exohedral complexes of 1-benzene with carbon nanotubes and high-density assembly of multiple benzenes inside of a carbon nanotube

The 1-benzene was put on the inside and surface of various armchair (n, n) (n = 6-12, 14) and zigzag (n, 0) (n = 10-17, 20) nanotubes of different diameters. The binding structure, binding energy, and effects on binding energy were analyzed. All interaction structures and the properties of the assembled complexes were investigated via density functional tight-binding method. Furthermore, we put multiple benzene molecules (2-18 benzenes) inside the armchair (10, 10), (9, 9), and (8, 8) carbon nanotubes (CNTs) and found that two types of structures were formed for the endohedral complexes of multiple benzenes-spiral symmetrical polygon and criss-crossed types, respectively. The detail of the binding energies and structure properties for (10, 10)/kBen (k = 1-6, 18), (9, 9)/kBen (k = 4, 5, 15), and (8, 8)/kBen (k = 1-8) were discussed. Furthermore, the HOMOs and LUMOs of the representative complexes were also studied to illustrate the interactions. This article offers a new assembly method to prepare a high density of benzenes inside of CNTs and offers a method for benzene adsorption by CNT.     

Nerve agents interacting with single wall carbon nanotubes: Density functional calculations

First-principles calculations based on density functional theory (DFT) method are used to investigate the adsorption properties of nerve agent DMMP on typical zigzag (semiconducting) and armchair (metallic) single wall carbon nanotubes (SWCNTs). The adsorption energies for DMMP molecule on different adsorption sites on SWCNTs are obtained. The results indicate that DMMP is weakly bound to the outer surface of both the considered SWCNTs and the obtained adsorption energy values and binding distances are typical for the physisorption. We find that DMMP adsorptive capability of metallic CNTs is about twofold that of semiconducting one. The adsorption of DMMP on the higher chiral angle nanotubes was also investigated and the results indicate that nanotube’s chirality increases the adsorption capability of the tube but however the adsorption characteristic is typical for the physisorption. Furthermore, co-adsorption of two DMMP molecules on the SWCNTs as a single-layer/bi-layer of adsorbed molecules as well as the adsorption of one DMMP molecule on the CNT bundles consisting of three SWCNTs has also been examined. The obtained results reveal that for both the considered systems the binding energy was increased for the DMMP adsorption but it’s still typical for the physisorption, consistent with the recent experimental result. The study of the electronic structures and charge analysis indicate that no significant hybridization between the respective orbital takes place and the small interaction obtained quantitatively in terms of binding energies.     

Adsorption structures of benzene on a Si(5 5 12)-2x1 surface: a combined scanning tunneling microscopy and theoretical study

In the first ever attempt to study the adsorption of organic molecules on high-index Si surfaces, we investigated the adsorption of benzene on Si(5 5 12)-(2x1) by using variable-low-temperature scanning tunneling microscopy and density-functional theory (DFT) calculations. Several distinct adsorption structures of the benzene molecule were found. In one structure, the benzene molecule binds to two adatoms between the dimers of D3 and D2 units in a tilted butterfly configuration. This structure is produced by the formation of di-sigma bonds with the substrate and of two C[Double Bond]C double bonds in the benzene molecule. In another structure, the molecule adsorbs on honeycomb chains with a low adsorption energy because of strain effects. Our DFT calculations predict that the adsorption energies of benzene are 1.03-1.20 eV on the adatoms and 0.22 eV on the honeycomb chains.     

Computational studies of boron‐ and nitrogen‐doped single‐walled carbon nanotubes as potential sensor materials of hydrogen halide molecules HX (X = F,Cl, Br)

Potential applicability of undoped, B‐, and N‐doped carbon nanotubes (CNTs) for elaboration of the working materials of gas sensors of hydrogen halide molecules HX (X = F, Cl, Br) is analyzed in computational studies of molecular adsorption on the CNTs surfaces. Density Functional Theory (DFT)‐based geometry‐optimized calculations of the electronic structure of undoped, B‐, and N‐doped CNTs of (3,3) and (5,5) chiralities with adsorbed HX (X = F, Cl, Br) molecules are performed within molecular cluster approach. Relaxed geometries, binding energies between the adsorbates and the nanotubes, charge states of the adsorbates and the electronic wave function contours are calculated and analyzed in the context of gas sensing applications. Obtained results are supplemented by calculations of adsorption of hydrogen halides on B(N)‐doped graphene sheets which are considered as model approximation for large‐diameter CNTs. It is found that the B‐doped CNTs are perspective for elaboration of sensing materials for detection of HCl and HBr molecules. The undoped and the N‐doped CNTs are predicted to be less suitable materials for detection of hydrogen halide gases HX (X = F, Cl, Br). © 2015 Wiley Periodicals, Inc.     

Density functional theory modeling of the adsorption of small analyte and indicator dye 9-(diphenylamino)acridine molecules on the surface of amorphous silica nanoparticles

The adsorption of small analyte molecules (H(2)O, NH(3), C(2)H(5)OH, and (CH(3))(2)CO) and an indicator dye, 9-(diphenylamino)acridine (DPAA), on the surface of amorphous silica particles is studied using electronic structure calculations at the DFT-D level of theory taking into account explicit corrections for van der Waals forces. Cluster models of three different types are used; two of them have been constructed using classical MD methods. The effect of particle size, local environment, and the choice of the exchange-correlation functional and basis set on the adsorption energies is studied, and adsorption energies are extrapolated to nanosized clusters. It is shown that the dye is more strongly bound to amorphous silica particles than the studied analyte molecules and that the energy of DPAA adsorption increases with the particle size, being at least twice as high as the energy of analyte adsorption for nanosized clusters. Electrostatic interactions play an important role in the adsorption of acridine dyes on the surface of silica nanoparticles.     

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.     

Enhancement of hydrogen physisorption on graphene and carbon nanotubes by Li doping

Density-functional calculations of the adsorption of molecular hydrogen on a planar graphene layer and on the external surface of a (4,4) carbon nanotube, undoped and doped with lithium, have been carried out. Hydrogen molecules are physisorbed on pure graphene and on the nanotube with binding energies about 80-90 meV/molecule. However, the binding energies increase to 160-180 meV/molecule for many adsorption configurations of the molecule near a Li atom in the doped systems. A charge-density analysis shows that the origin of the increase in binding energy is the electronic charge transfer from the Li atom to graphene and the nanotube. The results support and explain qualitatively the enhancement of the hydrogen storage capacity observed in some experiments of hydrogen adsorption on carbon nanotubes doped with alkali atoms.     

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.     

SAMPL6 host–guest challenge: binding free energies via a multistep approach

In this effort in the SAMPL6 host–guest binding challenge, a combination of molecular dynamics and quantum mechanical methods were used to blindly predict the host–guest binding free energies of a series of cucurbit[8]uril (CB8), octa-acid (OA), and tetramethyl octa-acid (TEMOA) hosts bound to various guest molecules in aqueous solution. Poses for host–guest systems were generated via molecular dynamics (MD) simulations and clustering analyses. The binding free energies for the structures obtained via cluster analyses of MD trajectories were calculated using the MMPBSA method and density functional theory (DFT) with the inclusion of Grimme’s dispersion correction, an implicit solvation model to model the aqueous solution, and the resolution-of-the-identity (RI) approximation (MMPBSA, RI-B3PW91-D3, and RI-B3PW91, respectively). Among these three methods tested, the results for OA and TEMOA systems showed MMPBSA and RI-B3PW91-D3 methods can be used to qualitatively rank binding energies of small molecules with an overbinding by 7 and 37 kcal/mol respectively, and RI-B3PW91 gave the poorest quality results, indicating the importance of dispersion correction for the binding free energy calculations. Due to the complexity of the CB8 systems, all of the methods tested show poor correlation with the experimental results. Other quantum mechanical approaches used for the calculation of binding free energies included DFT without the RI approximation, utilizing truncated basis sets to reduce the computational cost (memory, disk space, CPU time), and a corrected dielectric constant to account for ionic strength within the implicit solvation model.     

密度泛函理论研究Al在丝光沸石骨架中的取代位置和NH3的吸附

采用色散校正密度泛函方法（DFT-D2）计算了Al同晶取代进入H-[Al]MOR丝光沸石骨架中可能的位置及其对NH₃分子吸附表征Brönsted酸性。热力学上,Al优先取代位是T2O5位,接着是T4O2、T1O7和T3O1位,能量差仅在0.03~0.07 eV,表明Al可能分布在四种非等价晶体T位。同时,电荷平衡质子的位置影响Al取代位的稳定性,数据表明电荷平衡质子与O5位结合的可能性最大。另外,用DFT和 DFT-D2方法计算了NH₃分子在每一个Al取代的T位的吸附能,通过比较,DFT低估了NH₃吸附能0.41 eV,表明色散校正DFT-D2方法对于NH₃吸附是很有必要的,T2O5位的Brönsted酸性最强。     

Impact of the Chirality and Curvature of Carbon Nanostructures on Their Interaction with Aromatics and Amino Acids

Understanding noncovalent interactions on the surfaces of carbon nanostructures (CNSs) is of fundamental importance and also has implications in nano‐ and biotechnology. The interactions of aromatic compounds such as benzene, naphthalene, and aromatic amino acids with CNSs of varying diameter, chirality, and curvature were systematically explored by using density functional theory. Planar graphene exhibits stronger binding affinity than curved carbon nanotubes (CNTs), whereas zigzag CNTs appear to show stronger binding affinity than armchair CNTs. For hydrocarbons, there exist two competing modes, namely, π–π stacking interactions and CH ??? π interactions, which bring the aromatic motifs into parallel and perpendicular dispositions with respect to the CNSs, respectively. Our results reveal that π–π stacking interactions override CH ??? π interactions in such cases. However, in the case of aromatic amino acids, π–π interactions can exist simultaneously along with a range of other interactions, including CH ??? π. The polarizability and HOMO energy of the CNSs were found to be the key factors that determine the binding energies. The HOMO–LUMO energy gaps of the CNSs were found to be undisturbed by the noncovalent functionalization of the aromatic molecules.     

Adsorption of functionalized benzoic acids on MgSO4.H2O (100).

Using a combination of ab initio and semiempirical methods, adsorption problems on surfaces with large unit cells and low symmetry can still be studied. Here, a hybrid approach of density functional theory (DFT) and Hartree-Fock (HF) was used. As an example, we determined the geometry and the electronic properties of benzoic acid (BA), salicylic acid (SA) and para-salicylic acid (p-SA) adsorbed on MgSO(4).H(2)O (100), which are used as conditioner molecules for the electrostatic separation of minerals. Contrary to general expectations, these molecules are chemisorbed, with binding energies around 1.9 eV, forming bonds through the carboxylic O atom of the COOH groups in a nonplanar geometry, although the surface is a stoichiometric wide-band-gap insulator and the molecules stay intact. In contrast, a planar adsorption geometry turned out to be nonbonding. Bonding takes place by means of surface-molecule resonances due to the overlap of the valence band with molecular orbitals, assisted by a small charge-transfer molecule to the surface of around 0.15e. These combined interactions cause an intramolecular twist between the COOH group and the benzene ring.     

碳纳米管内P—Ylide反应的理论研究

碳纳米管空腔不仅可以改变填充到其内部分子的性质,而且对其内部的SN2取代反应有促进或抑制作用,因而被视为一种新型的“固体溶剂”．本文通过密度泛函理论研究了CH2O和PH3CH2在气相、苯溶液和碳纳米管空腔内的[2＋2]加成反应．结果表明,与气相相比,碳纳米管空腔对于[2＋2]环加成反应影响不大,这是因为所研究的[2＋2]环加成反应中,反应物并不是轴对称的,不同于SN2取代反应的一维线性排列,所以具有较大轴向极化率的碳纳米管对[2＋2]环加成反应影响较小．     

Benchmarking density functional methods against the S66 and S66x8 datasets for non-covalent interactions

Dispersion-corrected density functional theory is assessed on the new S66 and S66x8 benchmark sets for non-covalent interactions. In total, 17 different density functionals are evaluated. Two flavors of our latest additive London-dispersion correction DFT-D3 and DFT-D3(BJ), which differ in their short-range damping functions, are tested. In general, dispersion corrections are again shown to be crucial to obtain reliable non-covalent interaction energies and equilibrium distances. The corrections strongly diminish the performance differences between the functionals, and in summary most dispersion-corrected methods can be recommended. DFT-D3 and DFT-D3(BJ) also yield similar results but for most functionals and intermolecular distances, the rational Becke-Johnson scheme performs slightly better. Particularly, the statistical analysis for S66x8, which covers also non-equilibrium complex geometries, shows that the Minnesota class of functionals is also improved by the D3 scheme. The best methods on the (meta-)GGA or hybrid- (meta-)GGA level are B97-D3, BLYP-D3(BJ), PW6B95-D3, MPW1B95-D3 and LC-ωPBE-D3. Double-hybrid functionals are the most accurate and robust methods, and in particular PWPB95-D3 and B2-PLYP-D3(BJ) can be recommended. The best DFT-D3 and DFT-D3(BJ) approaches are competitive to specially adapted perturbation methods and clearly outperform standard MP2. Comparisons between S66, S22 and parts of the GMTKN30 database show that the S66 set provides statistically well-behaved data and can serve as a valuable tool for, for example, fitting purposes or cross-validation of other benchmark databases.     

Theoretical study of the P-Ylide reaction in the carbon nanotube

Recent studies have shown that the inner phase of carbon nanotubes (CNTs) can not only change the properties of molecules inside the tube, but also enhance or restrain the S_N2 reactions. Thus, the CNTs can be considered a form of solid solvent. In this paper, we study the [2+2] cycloaddition reaction between CH₂O and PH₃CH₂ in the gas phase, benzene solution and inner phase of CNT using the density functional theory (DFT). The results indicate that the inner phase of CNT has little effect on the [2+2] cycloaddition reaction. This can be explained as that while taking the linear arrangement for S_N2 reaction, the reactants do not possess the axial symmetry for the studied [2+2] cycloaddition reaction. Therefore, although the CNT has large axial polarizability, it can exert little influence on the [2+2] cycloaddition reaction. Our studies will be helpful for further understanding of the inner phase chemistry of CNTs.     

Dispersion-corrected density functional theory calculations of the molecular binding of n-alkanes on Pd(111) and PdO(101)

We investigated the molecular binding of n-alkanes on Pd(111) and PdO(101) using conventional density functional theory (DFT) and the dispersion-corrected DFT-D3 method. In agreement with experimental findings, DFT-D3 predicts that the n-alkane desorption energies scale linearly with the molecule chain length on both surfaces, and that n-alkanes bind more strongly on PdO(101) than on Pd(111). The desorption energies computed using DFT-D3 are slightly higher than the measured values for n-alkanes on Pd(111), though the agreement between computation and experiment is a significant improvement over conventional DFT. The measured desorption energies of n-alkanes on PdO(101) and the energies computed using DFT-D3 agree to within better than 2.5 kJ/mol (< 5%) for chain lengths up to n-butane. The DFT-D3 calculations predict that the molecule-surface dispersion energy for a given n-alkane is similar in magnitude on Pd(111) and PdO(101), and that dative bonding between the alkanes and coordinatively unsaturated Pd atoms is primarily responsible for the enhanced binding of n-alkanes on PdO(101). From analysis of the DFT-D3 results, we estimate that the strength of an alkane η(2)(H, H) interaction on PdO(101) is ~16 kJ/mol, while a single η(1) H-Pd dative bond is worth about 10 kJ/mol.