Massively parallel direct SCF calculations on large metal clusters: Ni5-Ni481

Summary The convergence of the cluster model with respect to excitation energies, ionization potentials and hydrogen chemisorption energy in the four-fold hollow site of the Ni(100) surface is studied for a sequence of cluster models from Ni₅ up to Ni₁₈₁. For the largest, Ni₄₈₁, cluster studied, only the structure of the occupied levels for one state is obtained. The concept of bond-preparation is found to be essential for the evaluation of chemisorption energies also for clusters with more than 100 atoms. The cluster excitation energies show a slow decrease such that even for Ni₁₈₁ the step between the lower excited states is still 0.1–0.2 eV. The effect ofp-functions on surrounding cluster atoms is found to be 3–4 kcal/mol independent of cluster-size. The direct SCF program DISCO was parallelized using the TCGMSG toolkit in order to perform the calculations. The easy strategy utilized is analysed and exhaustive timings on the Alliant Campus/800 MPP system with 200 CPU's are presented.     

Interaction energy of a water molecule with a single-layer graphitic surface modeled by hydrogen- and fluorine-terminated clusters

In ab initio calculations a finite graphitic cluster model is often used to approximate the interaction energy of a water molecule with an infinite single-layer graphitic surface (graphene). In previous studies, the graphitic cluster model is a collection of fused benzene rings terminated by hydrogen atoms. In this study, the effect of using fluorine instead of hydrogen atoms for terminating the cluster model is examined to clarify the role of the boundary. The interaction energy of a water molecule with the graphitic cluster was computed using ab initio methods at the MP2 level of theory and with the 6-31G(d = 0.25) basis set. The interaction energy of a water molecule with graphene is estimated by extrapolation of two series of increasing size graphitic cluster models (C(6n2)H(6n) and C(6n2)F(6n), n = 1-3). Two fixed orientations of water molecule are considered: (a) both hydrogen atoms of water pointing toward the cluster (mode A) and (b) both hydrogen atoms of water pointing away from the cluster (mode B). The interaction energies for water mode A are found to be -2.39 and -2.49 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively. For water mode B, the interaction energies are -2.32 and -2.44 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively.     

N_2H_4-CH_3OH氢键团簇体系的从头计算

用从头计算法研究了 (N2 H4-CH3OH)氢键团簇体系。分别在HF/6 31G 和HF/6 31G 水平上对它们的中性和离子团簇进行几何全优化 ,得到了 3种中性混合团簇稳定构型和离子混合团簇稳定构型 ,并对其能量和稳定性进行了比较。讨论了 3种不同构型离子团簇可能的解离通道。给出了质子化混合团簇的稳定构型 ,并对其可能的解离通道进行了讨论。文中最后计算出N2 H4,CH3OH ,(N2 H4-CH3OH)团簇的质子亲和能 (PA) ,分别为 :2 0 6.7kcal/mol,1 78.3kcal/mol,2 2 7.5kcal/mol,其中质子亲和能PAcalc[N2 H4]与实验值PAexp[N2 H4]=2 0 4 .8kcal/mol符合得很好。     

Theoretical calculation of the dehydrogenation of ethanol on a Rh/CeO2(111) surface

We applied periodic density-functional theory (DFT) to investigate the dehydrogenation of ethanol on a Rh/CeO2 (111) surface. Ethanol is calculated to have the greatest energy of adsorption when the oxygen atom of the molecule is adsorbed onto a Ce atom in the surface, relative to other surface atoms (Rh or O). Before forming a six-membered ring of an oxametallacyclic compound (Rh-CH2CH2O-Ce(a)), two hydrogen atoms from ethanol are first eliminated; the barriers for dissociation of the O-H and the beta-carbon (CH2-H) hydrogens are calculated to be 12.00 and 28.57 kcal/mol, respectively. The dehydrogenated H atom has the greatest adsorption energy (E(ads) = 101.59 kcal/mol) when it is adsorbed onto an oxygen atom of the surface. The dehydrogenation continues with the loss of two hydrogens from the alpha-carbon, forming an intermediate species Rh-CH2CO-Ce(a), for which the successive barriers are 34.26 and 40.84 kcal/mol. Scission of the C-C bond occurs at this stage with a dissociation barrier Ea = 49.54 kcal/mol, to form Rh-CH(2(a)) + 4H(a) + CO(g). At high temperatures, these adsorbates desorb to yield the final products CH(4(g)), H(2(g)), and CO(g).     

A theoretical study of atomic oxygen chemisorption on the Ni(100) and Ni(111) surfaces

Atomic oxygen chemisorption has been studied for the fourfold hollow site of the Ni(100) surface and for the threefold hollow site of the Ni(111) surface. To model the Ni(100) surface, 10 different clusters in the range Ni₅ to Ni₄₁ were used, and for the Ni(111) surface, 11 different clusters in the range Ni₁₃ to Ni₄₃ were used. A detailed analysis of the orbital occupations of the cluster with and without oxygen for the different clusters shows that there are three different possible bonding mechanisms. In two of these, the basic feature is that a₁ electrons of the cluster are kicked out by the oxygen 2p_z orbital and moved to holes in the 2p_{x, y} orbitals. A picture where the oxygen electrons fit into the electronic structure of the cluster is emphasized. The third mechanism, which is applicable for only one cluster, can be described as the formation of two covalent bonds of E symmetry. The final best estimate of the oxygen chemisorption energy for the Ni(100) surface is about 130 kcal/mol, and for the Ni(111) surface, about 115 kcal/mol. In particular for the Ni(111) surface, an excited oxygen state with radical character is identified, which might be a catalytically important species. The excitation energy to reach this state should be on the order of 10 kcal/mol for the Ni(111) surface.     

Convergence in the QM‐only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

We report systematic quantum mechanics‐only (QM‐only) and QM/molecular mechanics (MM) calculations on an enzyme‐catalyzed reaction to assess the convergence behavior of QM‐only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2‐SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single‐point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model ( M3a , with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4 . QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a , but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate‐limiting in the QM/MM calculations with M3a ( M4 ). QM‐only gas‐phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM‐only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single‐point QM‐only and QM/MM calculations (MAD typically about 1–2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1–2 kcal/mol.Copyright © 2013 Wiley Periodicals, Inc.     

Reactivity of isobutane on zeolites: a first principles study

In this work, ab initio and density functional theory methods are used to study isobutane protolytic cracking, primary hydrogen exchange, tertiary hydrogen exchange, and dehydrogenation reactions catalyzed by zeolites. The reactants, products, and transition-state structures are optimized at the B3LYP/6-31G* level, and the final energies are calculated using the CBS-QB3 composite energy method. The computed activation barriers are 52.3 kcal/mol for cracking, 29.4 kcal/mol for primary hydrogen exchange, 29.9 kcal/mol for tertiary hydrogen exchange, and 59.4 kcal/mol for dehydrogenation. The zeolite acidity effects on the reaction barriers are also investigated by changing the cluster terminal Si-H bond lengths. The analytical expressions between activation barriers and zeolite deprotonation energies for each reaction are proposed so that accurate activation barriers can be obtained when using different zeolites as catalysts.     

Mechanisms of and effect of coadsorption on water dissociation on an oxygen vacancy of the MgO(100) surface

The dissociation mechanism of a water molecule at an oxygen vacancy on the MgO(100) surface was studied by using the embedded cluster method at the DFT/B3 LYP level, while the energetic information was refined by using the IMOMO method at the CCSD level. We found that a water molecule initially adsorbs on one of the magnesium ions surrounding the vacancy site with a binding energy of 15.98 kcal mol(-1). It then can dissociate on the MgO(100) surface along two possible dissociation pathways. One pathway produces a hydroxyl group bonded to the original magnesium with a proton filling the vacancy via a transition state with a barrier of 4.67 kcal mol(-1) relative to the adsorbed water configuration. The other pathway yields two hydroxy groups; the hydroxy group originally belonging to the water molecule fills the vacancy, while the hydrogen atom binds with the surface oxygen to form the other hydroxy group. Hydrogen atoms of these hydroxy groups can recombine to form a hydrogen molecule and the surface is healed. Although the barrier (14.09 kcal mol(-1)) of the rate-controlling step of the latter pathway is higher than that of the former one, the energies of all of its stationary points are lower than that of the separated reactants (H(2)O+cluster). The effects of water coadsorption are modeled by placing an additional water molecule near the active center, which suggests that the more coadsorbed water molecules further stabilize the hydroxy species and prevent the hydrogen molecule formation through the latter pathway. The results support the photoemission spectral evidence of water dissociation on the defective MgO(100) surface at low water coverage.     

The benzene+OH potential energy surface: intermediates and transition states

The potential energy surface for the interaction between benzene and hydroxyl radical is studied in detail using quantum mechanical methods, with a particular focus on the hydrogen abstraction pathway. Geometric parameters are optimized using a variety of density functional methods as well as perturbation theory. Energies are refined using coupled cluster singles and doubles with perturbative triples [CCSD(T)] extrapolated to the complete basis set limit. At our most reliable level of theory, complexation energies are found to be (with zero-point corrected energies in parentheses) 3.7 (2.8) kcal/mol for the benzene-hydroxyl radical complex and 2.9 (-1.7) kcal/mol for the phenyl radical-water complex. The barrier to H abstraction lies 6.5 (4.2) kcal/mol above the infinitely separated benzene and hydroxyl radical monomers.     

First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface

Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from ?22.9 to ?33.9 kcal/mol for formaldehyde, and from ?44.3 to ?66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde → HCO + H, HCO → H + CO, and CO → C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST‐based rates are consistent with HREELS observation. © 2013 Wiley Periodicals, Inc.     

Cooperative enhancement of water binding to crownophane by multiple hydrogen bonds: analysis by high level ab initio calculations.

The intermolecular interaction energy of the model system of the water-crownophane complex was analyzed. The water molecule has four hydrogen bonds, with the two hydrogen-donating phenolic hydroxy groups and two hydrogen-accepting oxygen atoms of the poly-oxyethylene chain of the crownophane in the complex. The MP2/6-311G(2d,2p) level calculations of the model system of the complex (hydrogen donating unit + hydrogen accepting unit + water) indicate that the binding energy of the water is 21.85 kcal/mol and that the hydrogen bond cooperativity increases the binding energy as much as 3.67 kcal/mol. The calculated interaction energies depend on the basis set, while the basis set dependence of the cooperative increment is negligible. Most of the cooperative increment is covered by the HF level calculation, which suggests that the major source of the hydrogen bond cooperativity in this system has its origin in induction. The BLYP/6-311G** and PW91/6-311G** level interaction energies of the model system are close to the MP2/6-311G** interaction energies, which suggests that the DFT calculations with these functionals are useful methods to evaluated the interactions of hydrogen bonded systems.     

Reactivity of alkyl versus silyl peroxides. The consequences of 1, 2-silicon bridging on the epoxidation of alkenes with silyl hydroperoxides and bis(trialkylsilyl)peroxides

The bond dissociation energies for a series of silyl peroxides have been calculated at the G2 and CBS-Q levels of theory. A comparison is made with the O-O BDE of the corresponding dialkyl peroxides, and the effect of the O-O bond strength on the activation barrier for oxygen atom transfer is discussed. The O-O bond dissociation enthalpies (DeltaH(298)) for bis (trimethylsilyl) peroxide (1) and trimethylsilyl hydroperoxide (2) are 54.8 and 53.1 kcal/mol, respectively at the G2 (MP2) and CBS-Q levels of theory. The O-O bond dissociation energies computed at G2 and G2(MP2) levels for bis(tert-butyl) peroxide and tert-butyl hydroperoxide are 45.2 and 48.3 kcal/mol, respectively. The barrier height for 1,2-methyl migration from silicon to oxygen in trimethylsilyl hydroperoxide is 47.9 kcal/mol (MP4//MP2/6-31G). The activation energy for the oxidation of trimethylamine to its N-oxide by bis(trimethylsilyl) peroxide is 28.2 kcal/mol (B3LYP/6-311+G(3df,2p)// B3LYP/6-31G(d)). 1,2-Silicon bridging in the transition state for oxygen atom transfer to a nucleophilic amine results in a significant reduction in the barrier height. The barrier for the epoxidation of E-2-butene with bis(dimethyl(trifluoromethyl))silyl peroxide is 25.8 kcal/mol; a reduction of 7.5 kcal/mol relative to epoxidation with 1. The activation energy calculated for the epoxidation of E-2-butene with F(3)SiOOSiF(3) is reduced to only 2.2 kcal/mol reflecting the inductive effect of the electronegative fluorine atoms.     

A new alligator-clip compound for molecular electronics

We used the B3LYP flavor of density functional calculations to study new alligator-clip compounds for molecular electronics with platinum electrodes. First, with commonly used S-based linkage molecule 3-methyl-1,2-dithiolane (MDTL) we find that after chemisorption on Pt(1 1 1) the most stable structure is ring-opened with a binding energy of 32.44 kcal/mol. Among several alternative alligator-clip compounds we find that P-based molecules lead to much higher binding energies. For the ring-closed structure of 3-methyl-1,2-diphospholane (MDPL) a binding energy of 47.72 kcal/mol was calculated and even 54.88 kcal/mol for the ring-opened molecule. Thus, MDPL provides a more stable link to the metal surface and might increase the conductance.     

Calculation of solvation free energies of charged solutes using mixed cluster/continuum models

We derive a consistent approach for predicting the solvation free energies of charged solutes in the presence of implicit and explicit solvents. We find that some published methodologies make systematic errors in the computed free energies because of the incorrect accounting of the standard state corrections for water molecules or water clusters present in the thermodynamic cycle. This problem can be avoided by using the same standard state for each species involved in the reaction under consideration. We analyze two different thermodynamic cycles for calculating the solvation free energies of ionic solutes: (1) the cluster cycle with an n water cluster as a reagent and (2) the monomer cycle with n distinct water molecules as reagents. The use of the cluster cycle gives solvation free energies that are in excellent agreement with the experimental values obtained from studies of ion-water clusters. The mean absolute errors are 0.8 kcal/mol for H(+) and 2.0 kcal/mol for Cu(2+). Conversely, calculations using the monomer cycle lead to mean absolute errors that are >10 kcal/mol for H(+) and >30 kcal/mol for Cu(2+). The presence of hydrogen-bonded clusters of similar size on the left- and right-hand sides of the reaction cycle results in the cancellation of the systematic errors in the calculated free energies. Using the cluster cycle with 1 solvation shell leads to errors of 5 kcal/mol for H(+) (6 waters) and 27 kcal/mol for Cu(2+) (6 waters), whereas using 2 solvation shells leads to accuracies of 2 kcal/mol for Cu(2+) (18 waters) and 1 kcal/mol for H(+) (10 waters).     

An adsorption and calorimetric study of the interaction of hydrogen with chromium oxide

The chemisorption of hydrogen on porous chromium oxide was studied at temperatures up to 723 K under the conditions of controlled oxygen, hydrogen, and water contents in the samples. The molar heats of chemisorption were measured at temperatures up to 473 K. Hydrogen was found to be chemisorbed (310 kJ/mol) in the form of water and absorbed into oxide volume (165 kJ/mol) in the form of coordination bound atoms. Changes in the molar heat of the processes during chemisorption were caused by changes in the ratio between chemisorption and sorption. The phenomena observed and quantitative results could be explained by simple Langmuir concepts without assumptions of surface heterogeneity.     

Periodic density functional theory study of methane activation over La(2)O(3): activity of O(2-), O(-), O(2)(2-), oxygen point defect,and Sr(2+)-doped surface sites

Results of gradient-corrected periodic density functional theory calculations are reported for hydrogen abstraction from methane at O(s)(2-), O(s)(-), O(2)(s)(2-) point defect, and Sr(2+)-doped surface sites on La(2)O(3)(001). The results show that the anionic O(s)(-) species is the most active surface oxygen site. The overall reaction energy to activate methane at an O(s)(-) site to form a surface hydroxyl group and gas-phase (*)CH(3) radical is 8.2 kcal/mol, with an activation barrier of 10.1 kcal/mol. The binding energy of hydrogen at an site O(s)(-) is -102 kcal/mol. An oxygen site with similar activity can be generated by doping strontium into the oxide by a direct Sr(2+)/La(3+) exchange at the surface. The O(-)-like nature of the surface site is reflected in a calculated hydrogen binding energy of -109.7 kcal/mol. Calculations indicate that surface peroxide (O(2(s))(2-)) sites can be generated by adsorption of O(2) at surface oxygen vacancies, as well as by dissociative adsorption of O(2) across the closed-shell oxide surface of La(2)O(3)(001). The overall reaction energy and apparent activation barrier for the latter pathway are calculated to be only 12.1 and 33.0 kcal/mol, respectively. Irrespective of the route to peroxide formation, the O(2)(s)(2-) intermediate is characterized by a bent orientation with respect to the surface and an O-O bond length of 1.47 A; both attributes are consistent with structural features characteristic of classical peroxides. We found surface peroxide sites to be slightly less favorable for H-abstraction from methane than the O(s)(-) species, with DeltaE(rxn)(CH(4)) = 39.3 kcal/mol, E(act) = 47.3 kcal/mol, and DeltaE(ads)(H) = -71.5 kcal/mol. A possible mechanism for oxidative coupling of methane over La(2)O(3)(001) involving surface peroxides as the active oxygen source is suggested.     

An ab initio benchmark study of hydrogen bonded formamide dimers

The five singly and doubly hydrogen bonded dimers of formamide are calculated at the correlated level by using resolution of identity M?ller-Plesset second-order perturbation theory (RIMP2) and the coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] method. All structures are optimized with the Dunning aug-cc-pVTZ and aug-cc-pVQZ basis sets. The binding energies are extrapolated to the complete basis set (CBS) limit by using the aug-cc-pVXZ (X = D, T, Q) basis set series. The effect of extending the basis set to aug-cc-pV5Z on the geometries and binding energies is studied for the centrosymmetric doubly N-H...O bonded dimer FA1 and the doubly C-H...O bonded dimer FA5. The MP2 CBS limits range from -5.19 kcal/mol for FA5 to -14.80 kcal/mol for the FA1 dimer. The DeltaCCSD(T) corrections to the MP2 CBS limit binding energies calculated with the 6-31+G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are mutually consistent to within < or =0.03 kcal/mol. The DeltaCCSD(T) correction increases the binding energy of the C-H...O bonded FA5 dimer by 0.4 kcal/mol or approximately 9% over the distance range +/-0.5 Angstrom relative to the potential minimum. This implies that the ubiquitous long-range C-H...O interactions in proteins are stronger than hitherto calculated.     

Cepa calculations of potential energy surfaces for open-shell systems. I. The reaction of O(3P) with H2(1Σg+)

Ab initio calculations including electron correlation effects (mainly on CEPA-PNO level) have been performed for the potential energy surface of the reaction of ³P oxygen atoms with molecular hydrogen. The collinear abstraction reaction (C_∞v symmetry) and the vertical insertion reaction (C_2v) have been investigated with particular emphasis.The influence of the orbital basis size and of electron correlation both on the reaction energy and on the barrier height and location for the abstraction reaction has been studied in some detail. Our extrapolated value for the barrier for this reaction is 13.4 ± 1.0 kcal/mol, in fair agreement with the experimental activation energy, while the insertion reaction has to pass over a barrier of =48 kcal/mol. The analysis of electron correlation effects reveals that it is compulsory to include all singly and doubly substituted configurations, to correct for unlinked cluster contributions and to use fairly large basis sets if one wants to get accurate ab initio potential surfaces for the reactions of triplet oxygen atoms.     

Ab initio pair potentials for the ionic lithium-formate system

The potential energy surfaces for the interatomic interaction in the Li⁺HCOO^– system have been investigated byab initio methods within the rigid-molecule approximation. Analytical potential expressions were fitted to 133 calculated SCF energies for the Li⁺-HCOO^– interaction, 42 SCF energies for the Li⁺-Li⁺ interaction, and 332 SCF energies for the HCOO^–-HCOO^– interaction. The global minimum on the Li⁺-HCOO^– surface is –170 kcal/mol and corresponds to the lithium ion lying on the C₂ axis of the formate ion at 2.2 Å from the carbon atom on the oxygen side. The cation-cation and anion-anion interactions are repulsive everywhere, although the potential surface is markedly anisotropic for the HCOO^–-HCOO^– interaction.