Semiconducting Clathrates Meet Gas Hydrates: Xe24[Sn136]

Semiconducting Group 14 clathrates are inorganic host–guest materials with a close structural relationship to gas hydrates. Here we utilize this inherent structural relationship to derive a new class of porous semiconductor materials: noble gas filled Group 14 clathrates (Ng_x[M₁₃₆], Ng=Ar, Kr, Xe and M=Si, Ge, Sn). We have carried out high‐level quantum chemical studies using periodic Local‐MP2 (LMP2) and dispersion‐corrected density functional methods (DFT‐B3LYP‐D3) to properly describe the dispersive host–guest interactions. The adsorption of noble gas atoms within clathrate‐II framework turned out to be energetically clearly favorable for several host–guest systems. For the energetically most favorable noble gas filled clathrate, Xe₂₄[Sn₁₃₆], the adsorption energy is ?52 kJ mol^?1 per guest atom at the LMP2/TZVPP level of theory, corresponding to ?9.2 kJ mol^?1 per framework Sn atom. Considering that a hypothetical guest‐free Sn clathrate‐II host framework is only 2.6 kJ mol^?1 per Sn atom less stable than diamond‐like α‐Sn, the stabilization resulting from the noble gas adsorption is very significant.     

Structural,Vibrational and Electronic Properties of Defective Single‐Walled Carbon Nanotubes Functionalised with Carboxyl Groups: Theoretical Studies

Covalent sidewall functionalisation of defective zigzag single‐walled carbon nanotubes [SWCNTs(10,0)] with COOH groups is investigated by using DFT. Four types of point defects are considered: vacancy (V), divacancy [V₂(5‐8‐5), V₂(555‐777)], adatom (AA) and Stone–Wales (SW). The energetic, structural, electronic and vibrational properties of these systems are analysed. Decreasing reactivity is observed in the following order: AA>V>V₂(555‐777)>V₂(5‐8‐5)>SW. These studies also demonstrate that the position in which a carboxyl group is attached to a defective SWCNT is of primary importance. Saturation of two‐coordinate carbon atoms in systems with the vacancy V‐7 and with the adatom AA‐1(2) is 3.5–4 times more energetically favourable than saturation of three‐coordinate carbon atoms for all studied systems. Vibrational analysis for these two systems shows significant redshifts of the ν(C?O) stretching vibration of 96 and 123 cm^?1 compared to that for carboxylated pristine systems. Detailed electronic‐structure analysis of the most stable carboxylated systems is also presented.     

Probing the Chemical Functionalization of Single‐Walled Carbon Nanotubes with Multiple Carbon Ad‐Dimer Defects

Drying‐tube‐shaped single‐walled carbon nanotubes (SWCNTs) with multiple carbon ad‐dimer (CD) defects are obtained from armchair (n,n,m) SWCNTs (n=4, 5, 6, 7, 8; m=7, 13). According to the isolated‐pentagon rule (IPR) the drying‐tube‐shaped SWCNTs are unstable non‐IPR species, and their hydrogenated, fluorinated, and chlorinated derivatives are investigated. Interestingly, chemisorptions of hydrogen, fluorine, and chlorine atoms on the drying tube‐shaped SWCNTs are exothermic processes. Compared to the reaction energies for binding of H, F, and Cl atoms to perfect and Stone–Wales‐defective armchair (5,5) nanotubes, binding of F with the multiply CD defective SWCNTs is stronger than with perfect and Stone–Wales‐defective nanotubes. The reaction energy for per F₂ addition is between 85 and 88 kcal mol^?1 more negative than that per H₂ addition. Electronic structure analysis of their energy gaps shows that the CD defects have a tendency to decrease the energy gap from 1.98–2.52 to 0.80–1.17 eV. After hydrogenation, fluorination, and chlorination, the energy gaps of the drying‐tube‐shaped SWCNTs with multiple CD defects are substantially increased to 1.65–3.85 eV. Furthermore, analyses of thermodynamic stability and nucleus‐independent chemical shifts (NICS) are performed to analyze the stability of these molecules.     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.     

金刚石（111）清洁／附氢表面与甲基的相互作用

利用Ａｍｌ分子轨道法计算了金刚石（１１１）清洁／附氢表面与甲基相互作用的特殊势能曲线，深入研究了清洁、附氢表面与甲基相互作用下基底弛豫重建、四甲基构型及成键能的差别，进而得到附氢表面较清洁表面更适合于甲基吸附，是更好的金刚石薄膜生长址的结论。在距基底表面０．５ｎｍ内，甲基与清洁、附氢表面皆有强烈的相互作用。     

Study of the temperature‐dependent conformational averaging of 1H NMR resonances in vinylcyclopropane through the use of ab initio methodology and Boltzmann statistics

The temperature dependence of the ¹ H NMR resonance of the C‐4 olefinic proton in vinylcyclopropane was investigated through a combination of ab initio calculations and Boltzmann statistics. A torsional energy profile as a function of the 〈?〉 dihedral angle was obtained using HF methodology with a 6–311G** basis set, while the corresponding ¹ H chemical shift profiles for the C‐4 proton were computed using the GIAO approach and either HF, DFT (B3LYP) or MP2 methods at the 6–311G** level of theory. Chemical shifts at different temperatures calculated as canonical ensemble averages in which the different ab initio ¹ H chemical shift profiles and a Boltzmann factor defined by the HF/ 6–311G** energy function are employed reproduce remarkably well the temperature dependence observed experimentally. Attempts to perform a similar study using only the GIAO‐MP2 ¹ H chemical shift profile and 〈?〉 dihedral angle trajectories obtained from molecular dynamics simulations at different temperatures failed to reproduce the experimental trends. This shortcoming was attributed to the inability of the force fields employed, Tripos 6.0 and MMFF94, to reproduce properly the three‐well torsional potential of vinylcyclopropane. The application of both methodologies to the calculation of population‐dependent chemical shifts in other systems is discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Reassessment of methyl rotation barriers and conformations by correlated quantum chemistry methods

Internal rotations of the methyl group in ortho‐substituted and 2,6‐disubstituted toluenes in their ground state have been investigated by means of various ab initio quantum chemistry methods. Computed barriers at the Hartree‐Fock (HF) level using medium sized basis sets agreed reasonably with experimental results in the case of the studied ortho‐substituted toluenes. However, this agreement worsens when using very large basis sets. Furthermore, the determination of the conformation and barriers of more weakly hindered methyl groups, that is, for 2,6‐dihalogenotoluenes or toluene itself, necessitates high level correlated computations, because of a possible failure of HF calculations in this case. Density functional theory (DFT) techniques required, in several cases, much more extended basis sets than the post‐HF Møller‐Plesset perturbation (MP2, MP4) ones, to insure the convergence of the computed barriers. Non‐negligible variations of the computed barriers when using different DFT functionals are observed for some systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2093–2100, 2003     

Structural Characteristics of Hydrogenated Carbon and Boron Nitride Nanotubes: Impact of H?H Interactions

The structural characteristics of perhydrogenated carbon and boron nitride nanotubes are determined by means of quantum chemical calculations. Two families of nanotubes are systematically studied for both carbon and boron nitride, the nanotubes being derived from the perhydrogenated (110) and (111) sheets of diamond and cubic boron nitride. Single‐walled perhydrogenated carbon nanotubes prefer structures analogous to the (111) sheet. In clear contrast, the single‐walled perhydrogenated boron nitride nanotubes prefer structures analogous to the (110) sheet. The significantly different structural characteristics are due to the polarization of hydrogen atoms in the perhydrogenated boron nitride nanotubes. The presence of attractive electrostatic H? H interactions leads to a strong preference for multilayering of the boron nitride sheets and nanotubes. The results are expected to provide new insights into the structural characteristics of main‐group binary hydrides.     

Ab initio calculations for absorption and emission energies of alkali halide crystals doped with thallium

We calculate transition energies associated with optical properties of thallium doping in alkali halide crystals via an atomic cluster of minimal size where an sp‐valence‐shell impurity enters as a substitutional defect in the model crystal. Hartree–Fock (HF), density functional theory (DFT), and configuration interaction (CI) [CIS (CI with single excitation) and QCISD (single plus double and quadruple excitation)] calculations are performed to theoretically obtain the absorption and emission energies as vertical transitions evaluated at the ground and first excited‐state optimized geometries, respectively, where the optimization is carried out separately with the HF and DFT methods. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 785–790, 2000     

Comparison of ab initio and density functional methods for vibrational analysis of TeCl4

Vibrational analysis of tellurium tetrachloride, TeCl₄, was performed with Hartree–Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6–31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A₂ (ν₄) fundamental, where the results of the best methods were within 4 cm⁻¹. The best force fields were obtained with the following methods: Becke3–Lee–Yang–Parr and Becke3–Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl₄; however, it provides poor results with correlated methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 308–318, 1998     

Highly Accurate CCSD(T) and DFT–SAPT Stabilization Energies of H‐Bonded and Stacked Structures of the Uracil Dimer

The CCSD(T) interaction energies for the H‐bonded and stacked structures of the uracil dimer are determined at the aug‐cc‐pVDZ and aug‐cc‐pVTZ levels. On the basis of these calculations we can construct the CCSD(T) interaction energies at the complete basis set (CBS) limit. The most accurate energies, based either on direct extrapolation of the CCSD(T) correlation energies obtained with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets or on the sum of extrapolated MP2 interaction energies (from aug‐cc‐pVTZ and aug‐cc‐pVQZ basis sets) and extrapolated ΔCCSD(T) correction terms [difference between CCSD(T) and MP2 interaction energies] differ only slightly, which demonstrates the reliability and robustness of both techniques. The latter values, which represent new standards for the H‐bonding and stacking structures of the uracil dimer, differ from the previously published data for the S22 set by a small amount. This suggests that interaction energies of the S22 set are generated with chemical accuracy. The most accurate CCSD(T)/CBS interaction energies are compared with interaction energies obtained from various computational procedures, namely the SCS–MP2 (SCS: spin‐component‐scaled), SCS(MI)–MP2 (MI: molecular interaction), MP3, dispersion‐augmented DFT (DFT–D), M06–2X, and DFT–SAPT (SAPT: symmetry‐adapted perturbation theory) methods. Among these techniques, the best results are obtained with the SCS(MI)–MP2 method. Remarkably good binding energies are also obtained with the DFT–SAPT method. Both DFT techniques tested yield similarly good interaction energies. The large magnitude of the stacking energy for the uracil dimer, compared to that of the benzene dimer, is explained by attractive electrostatic interactions present in the stacked uracil dimer. These interactions force both subsystems to approach each other and the dispersion energy benefits from a shorter intersystem separation.     

Structure Sensitivity of CO Oxidation on Co3O4: A DFT Study

The reaction mechanism of CO oxidation on the Co₃O₄ (110) and Co₃O₄ (111) surfaces is investigated by means of spin‐polarized density functional theory (DFT) within the GGA+U framework. Adsorption situation and complete reaction cycles for CO oxidation are clarified. The results indicate that 1) the U value can affect the calculated energetic result significantly, not only the absolute adsorption energy but also the trend in adsorption energy; 2) CO can directly react with surface lattice oxygen atoms (O_2f/O_3f) to form CO₂ via the Mars–van Krevelen reaction mechanism on both (110)‐B and (111)‐B; 3) pre‐adsorbed molecular O₂ can enhance CO oxidation through the channel in which it directly reacts with molecular CO to form CO₂ [O₂(a)+CO(g)→CO₂(g)+O(a)] on (110)‐A/(111)‐A; 4) CO oxidation is a structure‐sensitive reaction, and the activation energy of CO oxidation follows the order of Co₃O₄ (111)‐A(0.78 eV)>Co₃O₄ (111)‐B (0.68 eV)>Co₃O₄ (110)‐A (0.51 eV)>Co₃O₄ (110)‐B (0.41 eV), that is, the (110) surface shows higher reactivity for CO oxidation than the (111) surface; 5) in addition to the O_2f, it was also found that Co³⁺ is more active than Co²⁺, so both O_2f and Co³⁺ control the catalytic activity of CO oxidation on Co₃O₄, as opposed to a previous DFT study which concluded that either Co³⁺ or O_2f is the active site.     

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala–Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono‐ and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2‐TZVP and CCSD(T)/aug‐cc‐pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI‐)DFT, (RI‐)MP2, and SCS‐MP2, were referenced. It was shown that deviations of 3–5 kcal mol^?1 (translating to 2–3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave‐function methods, both MP2 and SCS‐MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06‐2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave‐function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.     

Water Adsorption and Dissociation on Ceria‐Supported Single‐Atom Catalysts: A First‐Principles DFT+U Investigation

Single‐atom catalysts have attracted wide attention owing to their extremely high atom efficiency and activities. In this paper, we applied density functional theory with the inclusion of the on‐site Coulomb interaction (DFT+U) to investigate water adsorption and dissociation on clean CeO₂(111) surfaces and single transition metal atoms (STMAs) adsorbed on the CeO₂(111) surface. It is found that the most stable water configuration is molecular adsorption on the clean CeO₂(111) surface and dissociative adsorption on STMA/CeO₂(111) surfaces, respectively. In addition, our results indicate that the more the electrons that transfer from STMA to the ceria substrate, the stronger the binding energies between the STMA and ceria surfaces. A linear relationship is identified between the water dissociation barriers and the d band centers of STMA, known as the generalized Brønsted–Evans–Polanyi principle. By combining the oxygen spillovers, single‐atom dispersion stabilities, and water dissociation barriers, Zn, Cr, and V are identified as potential candidates for the future design of ceria‐supported single‐atom catalysts for reactions in which the dissociation of water plays an important role, such as the water–gas shift reaction.     

Interactions between hydrogenated diamond surface and adsorbates with different concentration of NO2 molecules: A first‐principles study

To elucidate the effects of NO₂ and H₂O molecules on the surface conductivity of hydrogenated diamond film, models of various adsorbates containing different molecular ratio of NO₂ and H₂O on hydrogenated diamond (100) surfaces were constructed. The adsorption energies, equilibrium geometries of adsorbates, density of states, and atomic Mulliken populations were studied by using first‐principles method. The results showed that H₂O molecule in the adsorbate could weaken the interactions between the adsorbates and hydrogenated diamond surface significantly. Compared with H₂O molecule, NO₂ molecule relaxes more dramatically when adsorbed on hydrogenated diamond surface. In addition, density of states for C(100):H–2NO₂, C(100):H–NO₂, and C(100):H–NO₂ + H₂O systems are very similar to each other, which indicates an obvious peak at valence band maximum level for all the three samples. It can be attributed to mainly single occupied molecule orbital of NO₂ molecule and slightly C–H bond of C(100):H substrate. When the adsorbates contain one NO₂ and two H₂O molecules, the peak shifts slightly into valence band, but its intensity increases significantly. All the samples exhibit p‐type surface conductivity when adsorbed with pure NO₂ molecules, and the surface conductivity remains as H₂O molecules added into the NO₂ adsorbate layer. However, for oxygenated diamond surface, very week interactions generate between diamond surface and various adsorbates. All the oxygenated diamond (100) surfaces with various adsorbates containing different NO₂ and H₂O molecules on it exhibit an insulating property.     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010