The H and H2 interaction with Pd3Cu,Pd4, and Cu4 fcc (111) clusters: A DFT comparative study

A comparative study of adsorption of H atoms and H₂ molecules on Pd₃Cu, Cu₄, and Pd₄ clusters has been performed through density functional calculations, using the hybrid B3LYP exchange‐correlation functional as implemented in the Gaussian98 program. For Pd atoms the relativistic small‐core effective core potential LANL and LANL2DZ basis set was used and for hydrogen a 6‐31G** basis set was used. The main emphasis is set in the reaction behavior of the different clusters with hydrogen atoms and molecules. We find that full geometry optimization does not appreciably change the metal cluster geometry either for certain reaction modes or the H and H₂ capture parameters, but increases the number of reactive sites of the metal clusters. Also, we found that there is charge transfer competition between H and Cu atoms, which drastically diminishes H₂ adsorption energy, related to the Pd cluster observed value. Edges and threefold sites are the principal hydrogen adsorption sites. Hydrogen has a great mobility over the metal clusters for different minima, especially when Cu is present; many initial pathways end in the same adsorption site. The observed hydrogen adsorption and binding energies are well reproduced by the calculations. Also, the adsorption mechanisms were determined. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Geometry,basis set,and correlation energy dependence of computed protonation energies of imino bases

The nitrogen protonation energies of the imino bases HN?CHR, where R is H, CH₃, NH₂, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree–Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree–Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree–Fock nitrogen protonation energies of the imino bases HN?CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O?CHR.     

Geometry,basis set,and correlation energy dependence of computed protonation energies of carbonyl bases

The protonation energies of H₂CO and its monosubstituted derivatives RCHO, where R is CH₃, NH₂, OH, and F, have been evaluated at various levels of theory to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require at least a basis set as large as 6-31G7, the inclusion of correlation, and optimized Hartree—Fock 6-31G1 geometries. Consistent relative protonation energies can be obtained at the Hartree—Fock level with smaller basis sets.     

Competition between chalcogen bond and halogen bond interactions in YOX<Subscript>4</Subscript>:NH<Subscript>3</Subscript> (Y = S,Se; X = F,Cl, Br) complexes: An ab initio investigation

Using ab initio calculations, the geometries, interaction energies and bonding properties of chalcogen bond and halogen bond interactions between YOX₄ (Y = S, Se; X = F, Cl, Br) and NH₃ molecules are studied. These binary complexes are formed through the interaction of a positive electrostatic potential region (σ-hole) on the YOX₄ with the negative region in the NH₃. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level, through analysis of molecular electrostatic potentials, quantum theory of atoms in molecules and natural bond orbital methods. Our results indicate that even though the chalcogen and halogen bonds are mainly dominated by electrostatic effects, but the polarization and dispersion effects also make important contributions to the total interaction energy of these complexes. The examination of interaction energies suggests that the chalcogen bond is always favored over the halogen bond for all of the binary YOX₄:NH₃ complexes.     

Theoretical study of the adsorption of ethylene on alkali‐exchanged zeolites

The structures of alkali‐exchanged faujasite (X–FAU, X = Li⁺ or Na⁺ ion) and ZSM‐5 (Li–ZSM‐5) zeolites and their interactions with ethylene have been investigated by means of quantum cluster and embedded cluster approaches at the B3LYP/6‐31G(d, p) level of theory. Inclusion of the Madelung potential from the zeolite framework has a significant effect on the structure and interaction energies of the adsorption complexes and leads to differentiation of different types of zeolites (ZSM‐5 and FAU) that cannot be drawn from a typical quantum cluster model, H₃SiO(X)Al(OH)₂OSiH₃. The Li–ZSM‐5 zeolite is predicted to have a higher Lewis acidity and thus higher ethylene adsorption energy than the Li–FAU zeolites (16.4 vs. 14.4 kcal/mol), in good agreement with the known acidity trend of these two zeolites. On the other hand, the cluster models give virtually the same adsorption energies for both zeolite complexes (8.9 vs. 9.1 kcal/mol). For the larger cation‐exchanged Na–FAU complex, the adsorption energy (11.6 kcal/mol) is predicted to be lower than that of Li–FAU zeolites, which compares well with the experimental estimate of about 9.6 kcal/mol for ethylene adsorption on a less acidic Na–X zeolite. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 333–340, 2003     

Adsorption of NO,NH<Subscript>3</Subscript> and H<Subscript>2</Subscript>O on V<Subscript>2</Subscript>O<Subscript>5</Subscript>/TiO<Subscript>2</Subscript> catalysts

The adsorption of small molecules NO, NH₃ and H₂O on V₂O₅/TiO₂ catalysts is studied with the semiempirical SCF MO method MSINDO as pre-stage for the selective catalytic reduction of NO. The mixed catalyst is represented by hydrogen-terminated cluster models. The local arrangement of the cluster atoms is in accordance with available experimental information. Partial relaxation of cluster atoms near the adsorption sites is taken into account. Calculated adsorption energies are compared with experimental literature data. Rapid convergence of computed properties with cluster size is observed. A possible reaction mechanism for the catalytic reduction of NO with NH₃ and O₂ is outlined.     

Complexes of ammonia with propane and cyclopropane: electrostatic guidelines for ab initio treatment

A model based on the molecular electrostatic potential (MESP) is employed for the investigation of structures and energies of complexes of ammonia with propane and cyclopropane. The electrostatic model geometries are employed as starting points for an ab initio investigation at the self-consistent field and second-order M?ller-Plesset (MP2) levels. The most stable structures of C₃H₆..NH₃ and C₃H₈..NH₃ complexes have the interaction energies of 10.07 kJ/mol and 8.15 kJ/mol, respectively, at the MP2/6-31G(d,p) level. The energy rank order of the structures is not altered with the use of the 6-31++G(d,p) basis set, and the basis␣set superposition error has little effect. The interaction energy decomposition analysis shows that the electrostatic component is dominant over the other ones. MESP topography thus seems to offer valuable hints for predicting the structures of weakly bonded complexes. Received: 8 July 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Density Functional Theory Studies on the Adsorption of NH2NO2 on Al13 Cluster

Density functional theory method with full geometry optimization was used to study the adsorption of nitroamine (NH₂NO₂) on Al₁₃ cluster. Both dissociative and nondissociative adsorption structures were predicted with different NH₂NO₂ molecule orientations on Al₁₃ cluster surfaces. In dissociative chemisorption, the main decomposition products of NH₂NO₂ are O atom(s) and NH₂NO or NH₂N species. The O atoms being ruptured from the N?CO bond form strong Al?CO bonds with the neighboring Al around the adsorbed sites. In addition, the species obtained as a result of O atom elimination remains bonded to the surface. The largest adsorption energy is ?737.66?kJ/mol when the NH₂NO₂ molecule decomposes into two O atoms and a NH₂N fragment. For nondissociative adsorption, the seriously deformed nitroamine forms various N?CO?CAl bonding configurations with Al. The significant charge transfer occurs for all adsorption configurations. The most charge transfer is 2.068 e from the Al cluster surface to the fragments of the decomposed NH₂NO₂. The change of the electronic structures is obvious due to the adsorption or dissociation of NH₂NO₂ molecule. Nitroamine readily oxidizes the aluminum surface of the Al₁₃ cluster.     

On the interaction of palladium with olefinic systems

We have performed all electron Hartree–Fock gradient calculations and geometry optimizations on systems composed of one to three palladium atoms and: CH₃ cation and anion, C₂H₄, C₂H₃NH₂, C₄H₄, NH₃, and (NH₃) + (C₂H₄). Several basis set considerations are discussed and the binding energies of Pd to these small molecules are reported. We find the counterpoise correction to the binding energies of these systems to be large. We also present MP2 calculations of the palladium binding energy with a large uncontracted palladium spd basis set in the PdC₂H₄ and PdNH₃ systems. The binding interaction between ethylene and palladium results in a mixing of the 4d–π* and 5s–π orbitals, and, is dissociative to the ethylene. The palladium-butadiene and palladium-cyclobutene relative stabilites and structures are interesting since these molecules could form from acetylene on a palladium surface. We find the Pd-butadiene cyclic structure to be 43 kcal/mol more stable than the Pd-cyclobutene product.     

Theoretical study on intermolecular interactions in BrF/HnX adducts

Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and H_nX (HF, H₂O, and NH₃) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions.     

Comparison of embedded cluster models to study zeolite catalysis: Proton transfer reactions in acidic chabazite

A number of cluster models used to study the interaction of NH₃ and NH⁻₄ with the Bronsted sites of the acidic zeolite, chabazite, are assessed by comparison with the results from full periodic Hartree-Fock calculations. Corrections to bare cluster models to take account of the electrostatic environment due to the periodic zeolite are found to agree well with periodic calculations, and appear to be more successful than a more sophisticated embedding procedure. © 1997 by John Wiley & Sons, Inc.     

3-硝基-1,2,4-三唑-5-酮与NH3及H2O分子间相互作用的理论研究

在DFT-B3LYP/6-311＋＋G**水平上, 求得3-硝基-1,2,4-三唑-5-酮(NTO)/NH₃和NTO/H₂O两种超分子体系势能面上5种全优化构型. 经基组叠加误差(BSSE)和零点能(ZPE)校正, 求得NTO与NH₃和H₂O的分子间最大相互作用能依次为－37.58和－30.14 kJ/mol, 表明NTO与NH₃的分子间相互作用强于与H₂O的作用. 超分子体系中电子均由NH₃或H₂O向NTO转移, 相互作用能主要由强氢键所贡献, 由自然键轨道分析揭示了相互作用的本质. 对优化构型进行振动分析, 并基于统计热力学求得200.0～800.0 K温度范围从单体形成超分子的热力学性质变化. 发现由NTO和NH₃形成超分子II和III在常温下可自发进行; 而NTO和H₂O只在低温下才能自发形成IV, V和VI超分子.     

Computational models for proton transfer in biological systems

A computational scheme based on a “mixed basis set” approach is applied to the study of the structure and the energetics in proton transfer systems. Five hydrogen-bonded systems of the type (CH₃H_nA ‥ H ‥ BH_mCH₃)⁺, where A and B can be N, O, or S, have been investigated with various minimal and extended basis sets. Calculations with the extended basis set yield double-well potential energy curves, which the minimal basis set is unable to reproduce. Calculations with the mixed basis set, constructed from an extended basis set on the atoms engaged in the hydrogen transfer part and a minimal basis set on the rest of the molecule, give predictions of geometries, potential energy curves, and relative energies similar to the results from the extended basis set. Inclusion of polarization functions in the mixed basis set becomes essential in systems that contain third row atoms. This scheme should become useful in studies of large molecules in which different parts can be represented at different levels of computational complexity.     

Ab initio valence-bond calculations of H2O

The first and second bond dissociation energies for H₂O have been calculated in anab initio manner using a multistructure valence-bond scheme. The basis set consisted of a minimal number of non-orthogonal atomic orbitals expressed in terms of gaussian-lobe functions. The valence-bond structures considered properly described the change in the molecular system as the hydrogen atoms were individually removed to infinity. The calculated equilibrium geometry for the H₂O molecule has an O-H bond length of 1.83 Bohrs and an HOH bond angle of 106.5°. With 49 valence-bond structures the energy of H₂O at this geometry was ?76.0202 Hartrees. The calculated equilibrium bond length for the OH radical was 1.86 Bohrs and the energy, using the same basis set, was ?75.3875 Hartrees. After correction for zero point energies the calculated bond dissociation energies are: H₂O → OH + H, D₁=75.38 kcal/mole and OH → O+H, D₂=54.79 kcal/mole.     

Density functional theory study of the interaction between 3‐nitro‐1,2,4‐triazole‐5‐one and ammonia

Two fully optimized geometries of 3‐nitro‐1,2,4‐triazol‐5‐one (NTO)–NH₃ complexes have been obtained with the density function theory (DFT) method at the B3LYP/6‐311++G** level. The intermolecular interaction energy is calculated with zero point energy (ZPE) correction and basis set superposition error (BSSE) correction. The greatest corrected intermolecular interaction of the NTO–NH₃ complexes is ?37.58 kJ/mol. Electrons in complex systems transfer from NH₃ to NTO. The strong hydrogen bonds contribute to the interaction energies dominantly. Natural bond orbital (NBO) analysis is performed to reveal the origin of the interaction. Based on vibrational analysis, the changes of thermodynamic properties from the monomer to complexes with the temperature ranging from 200 K to 800 K have been obtained using the statistical thermodynamic method. It is found that two NTO–NH₃ complexes can be produced spontaneously from NTO and NH₃ at normal temperature. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

An assessment of density functional methods for studying molecular adsorption in cluster models of zeolites

The performance of six density functional theory (DFT) methods has been tested for a zeolite cluster containing three tetrahedral atoms (3T) and the complexes it forms with water and methanol molecules. The DFT methods (BLYP, BP86, BPW91, B3LYP, B3P86, B3PW91) give results in good agreement with second-order perturbation theory (MP2). The results in this paper provide evidence of the suitability of DFT methods for studying hydrogen-bonded adsorption complexes in zeolites. Generally, the hybrid DFT methods are in closer agreement with experiment and MP2 than the pure DFT methods for geometrical parameters. The only exception is the Z⁻ geometry, perhaps due to its anionic character. All DFT methods give results in good overall agreement with MP2 for intramolecular geometrical parameters of the adsorption complexes, intramolecular vibrational frequencies, and adsorption energies. The B3LYP method gives intermolecular geometries and intermolecular vibrational frequencies which are closest to those obtained from the MP2 method. Thus, the B3LYP method seems to be the best choice for a density functional treatment of molecular adsorption in zeolite systems.     

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 geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Hydrogen bond vs proton transfer in HZSM5 zeolite. A theoretical study

The interaction of a large set of bases covering a wide range of the basicity scale with HZSM5 medium-size zeolites has been investigated through the use of two model clusters, namely 5T and 7T:63T. The 5T cluster has been treated fully ab initio at the B3LYP level, whereas the 63T cluster has been treated with the ONIOM2 scheme using the B3LYP:MNDO combination for geometry optimizations and B3LYP:HF/3-21G for adsorption energies. The optimized geometries of the different hydrogen bond (HB) and ion pair (IP) complexes obtained with both models are rather similar. However, there are significant dissimilarities as far as the adsorption energies are concerned, in particular when dealing with IP clusters whose intrinsic stability is largely underestimated when the simpler 5T model is used. 5T clusters could be used to obtain reasonable estimates of adsorption energies provided these are scaled by a factor of 1.1 for HB complexes and 1.4 for IP complexes. The zeolite cavity favors the proton transfer process, similarly to that found by third polar partners in gas-phase HB trimers. The intrinsic basicity of the base and its adsorption energy within the zeolite are correlated. From this correlation, is possible to conclude that, in general, bases with proton affinities (PA) larger than 200 kcal mol(-1) should lead to the formation of IPs, whereas bases with PA smaller than this value should form HB complexes.