Treating dispersion effects in extended systems by hybrid MP2:DFT calculations--protonation of isobutene in zeolite ferrierite

We propose use of a hybrid method to study problems that involve both bond rearrangements and van-der-Waals interactions. The method combines second-order M?ller-Plesset perturbation theory (MP2) calculations for the reaction site with density functional theory (DFT) calculations for a large system under periodic boundary conditions. Hybrid MP2:DFT structure optimisation for a cluster embedded in the periodic model is the first of three steps in a multi-level approach. The second step is extrapolation of the MP2 energy to the complete basis set limit. The third step is extrapolating the high-level (MP2) correction to the limiting case of the full periodic structure. This is done by calculating the MP2 correction for a series of cluster models of increasing size, fitting an analytic expression to these energy corrections, and applying the fitted expression to the full periodic structure. We assume that, up to a constant, the high-level correction is described by a damped dispersion expression. Combining the results of all three steps yields an estimate of the MP2 reaction energy for the full periodic system at the complete basis set level. The method is designed for a reaction between a small or medium sized substrate molecule and a very large chemical system. For adsorption of isobutene in zeolite H-ferrierite, the energies obtained for the formation of different structures, the pi-complex, the isobutoxide, the tert-butoxide, and the tert-butyl carbenium ion, are -78, -73, -48, and -21 kJ mol(-1), respectively. This corresponds to corrections of the pure DFT (PBE functional) results by -62, -70, -67, and -29 kJ mol(-1), respectively. Hence, the MP2 corrections are substantial and, perhaps more importantly, not the same for the different hydrocarbon species in the zeolite. Coupled-cluster (CCSD(T)) calculations change the MP2 energies by -4 kJ mol(-1) (tert-butyl cation) or less (below +/-1 kJ mol(-1) for the other species).     

On the dynamics of H2 adsorption on the Pt(111) surface

The dynamics and kinetics of the dissociation of hydrogen over the hexagonal close packed platinum (Pt(111)) surface are investigated using Car–Parrinello molecular dynamics and static density functional theory calculations of the potential energy surfaces. The calculations model the reference energy‐resolved molecular beam experiments, considering the degrees of freedom of the catalytic surface. Two‐dimensional potential energy surfaces above the main sites on Pt(111) are determined. Combined with Car–Parrinello trajectories, they confirm the dissociative adsorption of H₂ as the only adsorption pathway on this surface at H₂ incindence energies above 5 kJ/mol. A direct determination of energy‐resolved sticking coefficients from molecular dynamics is also performed, showing an excellent agreement with the experimental data at incidence energies in the 5–30 kJ/mol range. Application of dispersion corrections does not lead to an improvement in the prediction of the H₂ sticking coefficient. The adsorption reaction rate obtained from the calculated sticking coefficients is consistent with experimentally derived literature values.     

CO2 capture by metal-organic frameworks with van der Waals density functionals

We use density functional theory calculations with van der Waals corrections to study the role of dispersive interactions on the structure and binding of CO(2) within two distinct metal-organic frameworks (MOFs): Mg-MOF74 and Ca-BTT. For both classes of MOFs, we report calculations with standard gradient-corrected (PBE) and five van der Waals density functionals (vdW-DFs), also comparing with semiempirical pairwise corrections. The vdW-DFs explored here yield a large spread in CO(2)-MOF binding energies, about 50% (around 20 kJ/mol), depending on the choice of exchange functional, which is significantly larger than our computed zero-point energies and thermal contributions (around 5 kJ/mol). However, two specific vdW-DFs result in excellent agreement with experiments within a few kilojoules per mole, at a reduced computational cost compared to quantum chemistry or many-body approaches. For Mg-MOF74, PBE underestimates adsorption enthalpies by about 50%, but enthalpies computed with vdW-DF, PBE+D2, and vdW-DF2 (40.5, 38.5, and 37.4 kJ/mol, respectively) compare extremely well with the experimental value of 40 kJ/mol. vdW-DF and vdW-DF2 CO(2)-MOF bond lengths are in the best agreement with experiments, while vdW-C09(x) results in the best agreement with lattice parameters. On the basis of the similar behavior of the reduced density gradients around CO(2) for the two MOFs studied, comparable results can be expected for CO(2) adsorption in BTT-type MOFs. Our work demonstrates for this broad class of molecular adsorbate-periodic MOF systems that parameter-free and computationally efficient vdW-DF and vdW-DF2 approaches can predict adsorption enthalpies with chemical accuracy.     

Accurate quantum chemical energies for the interaction of hydrocarbons with oxide surfaces: CH(4)/MgO(001)

We examine the adsorption of CH(4) on the MgO(001) surface by a hybrid approach. It combines MP2 calculations with extrapolation to the complete basis set limit for the adsorption site and the CH(4)-CH(4) pair interactions in the adsorbate layer, with DFT+dispersion calculations under periodic boundary conditions for the whole system. To the total binding energy of 10.7 kJ mol(-1), the DFT+D(ispersion) correction contributes 0.7 kJ mol(-1) only, showing that the Mg(9)O(9) two-layer surface model is an excellent choice and that the interaction between the CH(4) molecules in the adsorbate layer is dominated by pair interactions. Contributions due to relaxation of the atom positions of 0.6 kJ mol(-1) (evaluated at DFT+dispersion) and of higher order correlation effects of 2.0 kJ mol(-1) (evaluated by CCSD(T)) yield a final estimate of 13.3 kJ mol(-1). To this total adsorption energy, the lateral interactions between the CH(4) molecules in the adsorbate layer contribute substantially, 4.1 kJ mol(-1)."Observed" desorption energies of 15.3 and 16.0 kJ mol(-1) have been derived from the observed Arrhenius desorption barriers (12.6 and 13.1 kJ mol(-1)) using thermal enthalpy contributions and a substantial zero-point energy (4.2 kJ mol(-1)) calculated from DFT+D vibrational frequencies. The comparison shows that our final hybrid MP2?:?PBE+D+ΔCCSD(T) estimate has reached chemical accuracy. It misses 2-3 kJ mol(-1) of binding only, which is most likely due to missing higher order correlation effects.PBE+D(ispersion) itself yields an adsorption energy that agrees within 1 kJ mol(-1) with our final hybrid MP2?:?PBE+D+ΔCCSD(T) estimate.     

Ammonia IRMS-TPD measurements and DFT calculation on acidic hydroxyl groups in CHA-type zeolites

Br?nsted acidity of H-chabazite (CHA) zeolites (Si : Al(2) = 4.2) was investigated by means of ammonia infrared-mass spectrometry/temperature-programmed desorption (IRMS-TPD) methods and density functional calculations. Four IR bands were observed at 3644, 3616, 3575 and 3538 cm(-1), and they were ascribable to the acidic OH groups on four nonequivalent oxygen sites in the CHA structure. The absorption band at 3538 cm(-1) was attributed to the O(4)H in the 6-membered ring (MR), and ammonia adsorption energy (DeltaU) of this OH group was the lowest among the 4 kinds of OH groups. The other 3 bands were assigned to the acidic OH groups in 8MR. It was observed that the DeltaU in 8 and 6MR were 131 (+/-3) and 101 kJ mol(-1), respectively. On the other hand, the density functional theory (DFT) calculations within periodic boundary conditions yielded the adsorption energies on these OH groups in 8 and 6MR to be ca. 130 and 110 kJ mol(-1), respectively, in good agreement with the experimentally-observed values.     

Ab initio and microcalorimetric investigations of alkene adsorption on phosphotungstic acid

The adsorption of ethene, propene, 1-butene, trans-2-butene, and isobutene on phosphotungstic acid has been characterized by density functional theory (DFT) calculations and microcalorimetric experiments. The DFT-calculated chemisorption energies to form the corresponding alkoxides for ethene, propene, 1-butene, trans-2-butene, and isobutene were -86.8, -90.3, -102.6, -79.9, and -91.4 kJ mol(-1), respectively (for their most-favorable binding modes). The relative chemisorption energies to form the alkoxides are dictated by the strength of interaction of the acidic proton with the carbon atom of the double bond that becomes protonated. The activation barrier for chemisorption was greatest for alkenes with primary (1 degrees) carbenium-like transition states followed by secondary (2 degrees) and tertiary (3 degrees) transition states. The adsorption enthalpy established from microcalorimetric experiments with propene and isobutene was approximately -100 kJ mol(-1), which is close to the DFT-calculated values. Chemisorption of ethene on phosphotungstic acid during microcalorimetric experiments was minimal, presumably because of the large activation barrier associated with a 1 degrees carbenium-like transition state. The results from this study are compared with those in the literature for the adsorption of alkenes on zeolites, which have a similar adsorption mechanism. Our results suggest that alkene adsorption is stronger on phosphotungstic acid than on zeolites, as supported by the more exothermic chemisorption energies. Additionally, activation barriers for alkene adsorption are lower over phosphotungstic acid than over zeolites.     

苯与铂化学吸附作用及其溶剂效应的量子化学研究

The chemical adsorption of Benzene on Pt under the effect of water has been full optimally computed with density functional B3LYP/LanL2DZ from Gaussian 98(A.9 version). The result showed the adsorption of benzene on Pt is a spontaneous process. The adsorption energies are -149.6535 and -202.1635 kJ/mol respectively in two cases, without water and in water. The adsorption energy is decreased in water solvent and the effect of water solvent is shown. The transition state of the transfer Pt on benzene was found by QST2 computation, and corresponding transfer active energies are 61.2537 and 70.8356 kJ/mol without water and in water respectively.     

甲烷与含氮有机杂环化合物吸附作用的DFT研究

根据煤中氮的存在形式,提炼出11种具有不同杂化方式及含氮量的有机环状化合物.应用密度泛函理论(DFT)模拟方法对甲烷在这11种含氮化合物上的吸附模型进行结构优化,并结合吸附能、电荷分布及静电势能面的分析,从微观角度考察了甲烷与这些化合物之间的相互作用.计算结果表明:甲烷与含氮化合物的相互作用能在3.81-6.82kJ·mol-1范围内,且通过氢键和静电力相互作用;当化合物中氮的杂化方式为sp2时,其与甲烷的作用能大于sp3杂化方式的;当化合物中的氮含量增加时,可以提供更多的甲烷吸附位点.     

Prediction of activation energies for aromatic oxidation by cytochrome P450

We have estimated the activation energy for aromatic oxidation by compound I in cytochrome P450 for a diverse set of 17 substrates using state-of-the-art density functional theory (B3LYP) with large basis sets. The activation energies vary from 60 to 87 kJ/mol. We then test if these results can be reproduced by computationally less demanding methods. The best methods (a B3LYP calculation of the activation energy of a methoxy-radical model or a partial least-squares model of the semiempirical AM1 bond dissociation energies and spin densities of the tetrahedral intermediate for both a hydroxyl-cation and a hydroxyl-radical model) give correlations with r(2) of 0.8 and mean absolute deviations of 3 kJ/mol. Finally, we apply these simpler methods on several sets of reactions for which experimental data are available and show that we can predict the reactive sites by combining calculations of the activation energies with the solvent-accessible surface area of each site.     

System-dependent dispersion coefficients for the DFT-D3 treatment of adsorption processes on ionic surfaces

Dispersion-corrected density functional theory calculations (DFT-D3) were performed for the adsorption of CO on MgO and C(2) H(2) on NaCl surfaces. An extension of our non-empirical scheme for the computation of atom-in-molecules dispersion coefficients is proposed. It is based on electrostatically embedded M(4)X(4) (M=Na, Mg) clusters that are used in TDDFT calculations of dynamic dipole polarizabilities. We find that the C(MM)(6) dispersion coefficients for bulk NaCl and MgO are reduced by factors of about 100 and 35 for Na and Mg, respectively, compared to the values of the free atoms. These are used in periodic DFT calculations with the revPBE semi-local density functional. As demonstrated by calculations of adsorption potential energy curves, the new C(6) coefficients lead to much more accurate energies (E(ads)) and molecule-surface distances than with previous DFT-D schemes. For NaCl/C(2) H(2) we obtained at the revPBE-D3(BJ) level a value of E(ads) =-7.4 kcal mol(-1) in good agreement with experimental data (-5.7 to -7.1 kcal mol(-1)). Dispersion-uncorrected DFT yields an unbound surface state. For the MgO/CO system, the computed revPBE-D3(BJ) value of E(ads) =-4.1 kcal mol(-1) is also in reasonable agreement with experimental results (-3.0 kcal mol(-1)) when thermal corrections are taken into account. Our new dispersion correction also improves computed lattice constants of the bulk systems significantly compared to plain DFT or previous DFT-D results. The extended DFT-D3 scheme also provides accurate non-covalent interactions for ionic systems without empirical adjustments and is suggested as a general tool in surface science.     

Hydrogen adsorption on graphite (0001) surface: a combined spectroscopy-density-functional-theory study

The adsorption of H/D atoms on the graphite (0001) surface is investigated by means of both high-resolution electron-energy loss spectroscopy (HREELS) and periodic first-principle density-functional theory. The two methods converge towards two modes of adsorption: adsorption in clusters of about four hydrogen atoms and adsorption in pairs of atoms on contiguous carbon sites. The desorption energies estimated from the calculated dissociation energies range from 8 to 185 kJ mol(-1) leading to an estimated surface coverage at saturations of 30-44 at. %. These results are compared with previous thermal desorption spectroscopy results. New HREEL signal assignments are proposed based on quantum calculations.     

Substituent effects on heats of formation, group interactions, and detonation properties of polyazidocubanes

We have calculated the heats of formation (HOFs) for a series of polyazidocubanes by using the density functional theory (DFT), Hartree-Fock, and MP2 methods with 6-31G* basis set as well as semiempirical methods. The cubane skeleton was chosen for a reference compound, that is, the cubane skeleton was not broken in the process of designing isodesmic reactions. There exists group additivity for the HOF with respect to the azido group. The semiempirical AM1 method also produced reliable results for the HOFs of the title compounds, but the semiempirical MINDO3 did not. The relationship between HOFs and molecular structures was discussed. It was found that the HOF increases 330-360 kJ/mol for each additional number of the azido group being added to the cubane skeleton. The distance between azido groups slightly influences the values of HOFs. The interacting energies of neighbor azido groups in polyazidocubanes are in the range of 2.3 approximately 6.6 kJ/mol, which are so small and less related to the substituent numbers. The average interaction energy between nearest neighbor --N3 groups in the most stable conformer of octaazidocubane is 2.29 kJ/mol at the B3LYP/6-31G* level. The relative stability related to the number of azido groups of the title compounds was assessed based on the calculated HOFs, the energy gaps between the frontier orbitals, and the bond orders of the C--N3 and C--C bonds. The predicted detonation velocity of hepta- and octa-derivatives is over 9 km/s, and the detonation pressure of them is ca. 40 GPa or over.     

Quantum mechanical investigation of the inner-sphere reorganization energy of cyclooctatetraene/cyclooctatetraene radical anion. Part I

The inner-sphere reorganization energy of the electron self-exchange of the couple cyclooctatetraene/cyclooctatetraene radical anion has been investigated by quantum mechanical calculations. The more stable Jahn Teller distorted B2g conformation of the radical anion has been used in this study. Two different theories have been applied in this first part. The harmonic approximation in the classical Marcus scheme has been modified by using projected force constants, which are obtained from the complete force constant matrix and the geometry changes of the molecule during the ET (introduced by Mikkelsen). A different approach (introduced by Nelsen) combines the different energies of the neutral and radical anion with and without relaxation corresponding to the vertical ionization potential and the vertical electron affinity. The electronic energies of the neutral molecule and the radical anion differ dramatically applying three different levels of quantum mechanical calculations (UAM1, UB3LYP, PMP2 with three different basis sets with and without diffuse functions). Nevertheless the Nelsen method gives almost consistent results for the inner-sphere reorganization energies: 120.1 kJ/mol for semiempirical UAM1 method, 159.3 kJ/mol, 156.4 kJ/mol and 158.3 kJ/mol for density functional UB3LYP/6-31G*, UB3LYP/6-31++G* and UB3LYP/AUG-cc-pVDZ calculations and 192.5 kJ/mol for ab-initio PMP2/6-31G* investigations, respectively. These values are in agreement with earlier experimental work supposing the total reorganization energy to be larger than 38 kcal/mol assuming an electron self-exchange rate of 10(4) M(-1) s(-1). The simple harmonic approximation of Marcus relation has not yet been applied for a molecule like cyclooctatetraene with large torsional geometry changes. Using the projected force constants after scaling, considerably different results for the inner-sphere reorganization energy have been calculated: 738.1 kJ/mol for the UB3LYP/6-31G*, 743.3 kJ/mol for UB3LYP/6-31++G* and 759.1 kJ/mol for UB3LYP/AUG-cc-pVDZ level of theory. Comparison with our concentration dependent EPR experiments are controversial to the earlier experimental results, but the latter supports the assumption that the electron self-exchange occurs in a time scale so that the molecules cannot complete their vibrational motions. Therefore the projected Marcus relation is not valid for cyclooctatetraene/cyclooctatetraene radical anion including a large torsional change during the electron transfer.     

Predicting adsorption enthalpies on silicalite and HZSM‐5: A benchmark study on DFT strategies addressing dispersion interactions

We evaluated the accuracy of periodic density functional calculations for adsorption enthalpies of water, alkanes, and alcohols in silicalite and HZSM‐5 zeolites using a gradient‐corrected density functional with empirical dispersion corrections (PBE‐D) as well as a nonlocal correlation functional (vdW‐DF2). Results of both approaches agree in acceptable fashion with experimental adsorption energies of alcohols in silicalite, but the adsorption energies for n‐alkanes in both zeolite models are overestimated, by 21?46 kJ mol^?1. For PBE‐D calculations, the adsorption of alkanes is exclusively determined by the empirical dispersion term, while the generalized gradient approximation‐DFT part is purely repulsive, preventing the molecule to come too close to the zeolite walls. The vdW‐DF2 results are comparable to those of PBE‐D calculations, but the latter values are slightly closer to the experiment in most cases. Thus, both computational approaches are unable to reproduce available experimental adsorption energies of alkanes in silicalite and HZSM‐5 zeolite with chemical accuracy. © 2014 Wiley Periodicals, Inc.     

Validation of dispersion-corrected density functional theory approaches for ionic liquid systems

The performance of several general gradient approximation, meta general gradient approximation, and hybrid functionals is tested against M?ller-Plesset perturbation theory second-order for ionic liquid systems. Additionally, two dispersion-corrected approaches (addition of van der Waals forces by a 1/r(6) term and employing a dispersion-corrected atom-center dispersion pseudopotential) were studied. For the 1-butyl-3-methylimidazolium cation neglecting dispersion results in different trends for structural stabilities. The two applied correction schemes for density functional theory improve the results tremendously. Investigating several 1-butyl-3-methylimidazolium dicianamide ion pairs shows a mean absolute deviation from M?ller-Plesset perturbation theory of 35.7 kJ/mol for Hartree-Fock and up to 33.2 kJ/mol for the density functional theory methods. The dispersion-corrected methods reduce the mean absolute deviation to less than 10 kJ/mol. Comparing adducts of the 1-ethyl-3-methylimidazolium dicianamide ion pair with Diels-Alder educts (cyclopentadiene and methylacrylate) shows similar energetic differences as for the ion pairs. Furthermore large deviations in geometries for the intermolecular distances were found for the Hartree-Fock approach (mean absolute deviation: 190 pm) and density functional theory (mean absolute deviation up to 178 pm) while for the dispersion-corrected methods the mean absolute deviation is less than 50 pm.     

高能体系分子间相互作用研究: 含NNO~2和NH~2混合物

以abinitioHF/6-31G^*计算求得NH~3+NH~2NO~2的两种优化构型,经MP4电子相关能校正和Boys-Bernardi方案校正基组叠加误差求得精确的分子间相互作用能。还用PM3方法计算研究TATB(均三氨基三硝基苯)分别与HMX(奥克托金)和RDX(黑索金)的混合体系,经色散能校正电子相关近似地求得分子间相互作用能。结果表明,NH~3与NH~2NO~2之间的最大结合能为-38.32kJ/mol;分子间相互作用增强了N-NO~2键强度;TATB与HMX,RDX的结合能远大于石墨与HMX或RDX的结合能,表明TATB对HMX和RDX的润湿和钝感作用较石墨更强。     

Computational methods in organic thermochemistry. 1. Hydrocarbon enthalpies and free energies of formation

Standard state enthalpies and free energies of formation can be computed with reasonable accuracy (usually within 4 and often 2 kJ/mol) using high level model chemistries. A comparison set of nearly 300 organic compounds ranging from 1 to 10 carbon atoms having a variety of functional groups for which enthalpy and free energy literature values are available has been examined using G2, G2MP2, G3, G3MP2, G3B3, G3MP2B3, CBS-QB3, and density functional (B3LYP/6-311+G(3df,2p)) model chemistries. G3 gives an average mean absolute deviation of 3.0 and 13.4 kJ/mol for the enthalpies and free energies, respectively, using the atomization method and 3.1 and 3.7 kJ/mol when bond separation reactions are employed. G3 and G3B3 are the most accurate overall; the related G3MP2 and G3MP2B3 are nearly as accurate and can compute larger molecules. CBS-QB3 was also found to be accurate but is more limited in the size of molecules that can be computed. The density functional energies were found to have large deviations from the literature values using either the atomization or the bond separation method. Regardless of the model employed, the free energies are increasingly underestimated by computation as the size of the molecule increases. A series of corrections applied to the aliphatic hydrocarbons is presented, which usually reduces the deviations to less than 4 kJ/mol regardless of the size of the molecule.     

ADSORPTION OF MACROPOROUS PHOSPHONIC ACID RESIN FOR INDIUM

The adsorption kinetics and mechanism of a nrovel chelate resin, macroporous phosphonic acid resin (PAR) for In(Ill) were investigated Tile statically saturated adsorption capacity is 216mg·g^-1resin at 298K in HAc-NaAc medium. Tire apparent adsorption rate constant is k298=4.84×10^-5 s^-1. Tile adsorption behavior of PAR for In(Ill) obeys the Freundlich isotherm. The thermodynamic adsorption parameters, enthalpy change △H, free energy change △G and entropychange △S of PAR for In(Ⅲ) are 11.5kmol, -12.6kJmol and 80.8Jmol.K, respectively. The apparent activation energy is Ea=3.5k.l/mol. Tire molar coordination ratio of the functional group of PAR to In(Ⅲ) is about 3:1.