An interface between the universal force field and the effective fragment potential method

In order to properly describe reactions in heterogeneous catalyst systems, the reactants, solvent, and bulk effects of the surface must be taken into account. Embedded-cluster QM (quantum mechanics)/MM (molecular mechanics) methods can treat reactions on surfaces (the gas-surface interface), and the effective fragment potential method (EFP) can accurately treat the solvent effects on reactions (the gas-liquid interface). In order to create a QM/MM/EFP hybrid method for treatment of heterogeneous catalytic systems in the presence of a solvent (the liquid-surface interface), an EFP-MM interaction potential has been developed. Example calculations on small clusters of silica and water have been carried out.     

QM/MM studies of Ni-Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states

The catalytically active (Ni-SI and Ni-R) and inactive states (Ni-A and Ni-B) of Ni-Fe hydrogenases have been studied using density functional theory (DFT) methods. Both isolated clusters and clusters embedded in the enzyme have been used to model the Ni-A, Ni-B, Ni-SI and Ni-R states. The BP86 and B3LYP functionals were employed, and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods were used for the embedded calculations. The QM/MM studies, rather than the isolated cluster calculations, were generally found to give structures which correlated better with X-ray data. The structure of the unready state (Ni-A), was correctly predicted by the QM/MM, but not by the isolated cluster calculation. Comparison with the observed crystal structure favoured the catalytically active state, Ni-SI, to be the protonated (Ni-SI(II)), rather than the unprotonated state (Ni-SI(I)). In the QM/MM studies, the binding of H(2) to Ni-SI(II) is preferred at the Ni (Ni-R(Ni)), rather than at the Fe centre (Ni-R(Fe)), in agreement with xenon binding studies, and in contrast to isolated cluster studies. These calculations cannot say with certainty which functional should be favoured, nor the preferred spin state of the catalytically active species. However, the lack of any predicted structure in which H(2) binds to the Fe centre, does favour a low spin state for Ni-SI(II), and the use of the BP86 functional. This is in agreement with recent high level ab initio calculations of a model of the Ni-SI(I) state.     

氮掺杂石墨烯负载单原子Zr催化CO2加氢的密度泛函理论研究

基于密度泛函理论计算,研究了H2和CO2在氮掺杂石墨烯负载单原子Zr催化剂(Zr Nx-Gr)上的吸附和CO2催化加氢反应. H2和CO2在Zr N3-Gr上单独吸附的吸附能分别为-0.49和-2.17 e V,在H2和CO2共吸附状态下,吸附能为-2.24 e V,均高于在Zr N4-Gr表面的吸附能,表明Zr N3-Gr表面更利于CO2加氢反应的发生.在Zr N3-Gr表面, CO2在共吸附后保持了其单独吸附时的特性,削弱了H2分子的吸附. CO2在Zr Nx-Gr表面催化加氢反应起始于H2和CO2的共吸附构型,沿反式HCOOH路径形成甲酸盐(HCOO*)中间体,然后HCOO*基团吸附H原子形成反式甲酸,在Zr N3-Gr和Zr N4-Gr表面该路径的反应能垒分别为1.85和2.48 e V.另一路径为产生CO与H2O的反应,在Zr N3-Gr和Zr N4-Gr表面的反应能垒分别为1.86和1.73 e V,表明Zr N3-Gr更利于CO2加氢生成甲酸反应的发生,而Zr N4-Gr表面更利于CO的产生.     

Quantum chemical prediction of reaction pathways and rate constants for dissociative adsorption of CO(x) and NO(x) on the graphite (0001) surface

We present predictions of reaction rate constants for dissociative adsorption reactions of CO(x) (x = 1, 2) and NO(x) (x = 1, 2) molecules on the basal graphite (0001) surface based on potential energy surfaces (PES) obtained by the integrated ONIOM(B3LYP:DFTB-D) quantum chemical hybrid approach with dispersion-augmented density functional tight binding (DFTB-D) as low level method. Following an a priori methodology developed in a previous investigation of water dissociative adsorption reactions on graphite, we used a C(94)H(24) dicircumcoronene graphene slab as model system for the graphite surface in finite-size molecular structure investigations, and single adsorbate molecules reacting with the pristine graphene sheet. By employing the ONIOM PES information in RRKM theory we predict reaction rate constants in the temperature range between 1,000 and 5,000 K. We find that among CO(x) and NO(x) adsorbate species, the dissociative adsorption reactions of CO(2) and both radical species NO and NO(2) are likely candidates as a cause for high temperature oxidation and erosion of graphite (0001) surfaces, whereas reaction with CO is not likely to lead to long-lived surface defects. High temperature quantum chemical molecular dynamics simulations (QM/MD) at T = 5,000 K using on-the-fly DFTB-D energies and gradients confirm the results of our PES study.     

Theoretical study of N2O reduction by CO in Fe-BEA Zeolite.

Quantum mechanical (QM) and QM/molecular mechanics (MM) studies of the full catalytic cycle of N(2)O reduction by CO in Fe-BEA zeolite, that is, oxidation of BEA-Fe by N(2)O and reduction of BEA-Fe-alphaO by CO, is presented. A large QM cluster, representing half of the channel of the BEA zeolite, is used. The contribution of the MM embedding to the calculated activation energies is found to be negligible. The minimum-energy paths for N(2)O decomposition and reduction with CO are calculated using the nudged elastic band (NEB) method. Calculated and experimental activation energies are in good agreement. The two possible orientations for the gaseous molecules adsorbing on the Fe site that are found lead to different activation energies.     

QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface

We present a new software to easily perform QM:MM and QM:QM' calculations called QMX. It follows the subtraction scheme and it is implemented in the Atomic Simulation Environment (ASE). Special attention is paid to couple molecular calculations with periodic boundaries approaches. QMX inherits the flexibility and versatility of the ASE package: any combination of methods namely force field, semiempirical, first principle, and ab initio, can be used as hybrid potential energy surface (PES). Its ease of use is demonstrated by considering the adsorption of Al₂Cl₃Me₃ on silica surface and by combining different levels of theory (from standard DFT to MP2 calculations) for the so‐called High Level cluster with standard PW91 density functional theory calculations for the Low Level environment. It is shown that the High Level cluster must contain the silanol group close to the aluminum atoms. The bridging adsorption is favored by 58 kJ mol^?1 at the MP2:PW91 level with respect to the terminal position. Using large clusters at the MP2:PW91 level, it is shown that PW91 calculations are sufficient for structure optimization but that embedded methods are required for accurate energy profiles. © 2013 Wiley Periodicals, Inc.     

Chemisorption of CO and mechanism of CO oxidation on supported platinum nanoclusters

Kinetic, isotopic, and infrared studies on well-defined dispersed Pt clusters are combined here with first-principle theoretical methods on model cluster surfaces to probe the mechanism and structural requirements for CO oxidation catalysis at conditions typical of its industrial practice. CO oxidation turnover rates and the dynamics and thermodynamics of adsorption-desorption processes on cluster surfaces saturated with chemisorbed CO were measured on 1-20 nm Pt clusters under conditions of strict kinetic control. Turnover rates are proportional to O(2) pressure and inversely proportional to CO pressure, consistent with kinetically relevant irreversible O(2) activation steps on vacant sites present within saturated CO monolayers. These conclusions are consistent with the lack of isotopic scrambling in C(16)O-(18)O(2)-(16)O(2) reactions, and with infrared bands for chemisorbed CO that did not change within a CO pressure range that strongly influenced CO oxidation turnover rates. Density functional theory estimates of rate and equilibrium constants show that the kinetically relevant O(2) activation steps involve direct O(2)* (or O(2)) reactions with CO* to form reactive O*-O-C*=O intermediates that decompose to form CO(2) and chemisorbed O*, instead of unassisted activation steps involving molecular adsorption and subsequent dissociation of O(2). These CO-assisted O(2) dissociation pathways avoid the higher barriers imposed by the spin-forbidden transitions required for unassisted O(2) dissociation on surfaces saturated with chemisorbed CO. Measured rate parameters for CO oxidation were independent of Pt cluster size; these parameters depend on the ratio of rate constants for O(2) reactions with CO* and CO adsorption equilibrium constants, which reflect the respective activation barriers and reaction enthalpies for these two steps. Infrared spectra during isotopic displacement and thermal desorption with (12)CO-(13)CO mixtures showed that the binding, dynamics, and thermodynamics of CO chemisorbed at saturation coverages do not depend on Pt cluster size in a range that strongly affects the coordination of Pt atoms exposed at cluster surfaces. These data and their theoretical and mechanistic interpretations indicate that the remarkable structure insensitivity observed for CO oxidation reactions reflects average CO binding properties that are essentially independent of cluster size. Theoretical estimates of rate and equilibrium constants for surface reactions and CO adsorption show that both parameters increase as the coordination of exposed Pt atoms decreases in Pt(201) cluster surfaces; such compensation dampens but does not eliminate coordination and cluster size effects on measured rate constants. The structural features and intrinsic non-uniformity of cluster surfaces weaken when CO forms saturated monolayers on such surfaces, apparently because surfaces and adsorbates restructure to balance CO surface binding and CO-CO interaction energies.     

Absorption and emission spectra of fluorescent silica nanoparticles from TD-DFT/MM/PCM calculations

A multi-scale computational protocol, which combines Quantum Mechanics and Molecular Mechanics (QM/MM) calculations with the polarisable continuum model (PCM), has been used to study the tetramethylrhodamine isothiocyanate (TRITC) fluorophore, embedded in three different environments, namely in water, on an amorphous silica surface and covalently encapsulated in a silica nanoparticle (C dot). Absorption and emission spectra have been simulated by using TD-B3LYP/PCM calculations, performed on the TRITC ground and excited state geometries, optimized at the QM/MM level. The results are in good agreement with experimental data confirming the caging effect played by the silica shell on the mobility of the TRITC molecule when covalently encapsulated in silica nanoparticles. This could result in a decrease of the nonradiative decay rate and thus an increase of the quantum yield of the molecule.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

CO hydrogenation on stepped Cu and CuZn alloy surfaces: Competition between methanol synthesis and methanation pathways

Comprehensive fundamental understanding of CO hydrogenation reactions over Cu and ZnCu alloy surfaces is of great importance. Herein, we report a comparative DFT calculation study of elementary surface reaction network of CO hydrogenation reactions on stepped Cu(211), Cu(611), ZnCu(211) and ZnCu(611) surfaces. On ZnCu(211) and ZnCu(611) surfaces, the energetic favorable reaction path of CO hydrogenation reaction follows CO* → HCO* → H₂CO* → H₃CO* → CH₃OH* → CH₃OH with H₃CO* hydrogenation as the rate-limiting step and proceeds more facilely on ZnCu(611) surface than on ZnCu(211) surface. On Cu(211) and Cu(611) surfaces, the energetic favorable reaction path of CO hydrogenation reaction follows CO* → HCO* → HCOH* → H₂COH* → H₃COH* → CH₃* → CH₄* → CH₄ with H₂COH* hydrogenation as the rate-limiting step and proceeds more facilely on Cu(611) than on Cu(211). The key difference of CO hydrogenation reaction on ZnCu alloy surface and Cu is that the resulting CH₃OH* species desorbs to produce CH₃OH on ZnCu alloy but undergoes H*-assisted decomposition to CH₃* and eventually to CH₄ on Cu surface. These results successfully unveil elementary surface reaction networks and structure sensitivity of Cu and ZnCu alloy-catalyzed CO hydrogenation reactions.     

In situ SERS and SHINERS study of electrochemical hydrogenation of p-ethynylaniline in nonaqueous solvents

Surface-enhanced Raman spectroscopy (SERS) studies of electrode/solution interfaces are important for understanding electrochemical processes. However, revealing the nature of reactions at well-defined single crystal electrode surfaces, which are SERS-inactive, remains challenging. In this work, shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) was used for the first time to study electrochemical adsorption and hydrogenation reactions at single crystal surfaces in nonaqueous solvents. A roughened Au surface was also studied for comparison. The experimental results show that the hydrogenation of adsorbed p-ethynylaniline (PEAN) on roughened Au electrode surfaces occurred at very negative potentials in methanol because of the catalytic effect of surface plasmon resonance (SPR). However, because “hot electrons” were blocked by the silica shell of Au@SiO₂ nanoparticles and aprotic acetonitrile was an ineffective hydrogen source, surface reactions at Au(111) were inhibited in the systems studied. Density functional theory (DFT) calculations revealed that the PEAN triple bond opened, allowing adsorption in a flat configuration on the Au(111) surface via two carbon atoms. This work provides an advanced understanding of electrochemical interfacial processes at single crystal surfaces in nonaqueous systems.     

Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach

Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.     

担体对Fe-MnO催化剂CO加氢合成烯烃性能影响的TPSR表征

考察了不同担体担载的Ｆｅ－ＭｎＯ催化剂上ＣＯ加氢合成烯烃的反应。结果表明担体直接影响低碳烯烃选择性。通过对催化剂的ＣＯ，ＣＯ／Ｈ２，Ｃ２Ｈ４等吸附的ＴＰＳＲ表征及催化剂表面ＣＯ加氢微观反应的研究，证明以碱性担体为基质的ＰＢＣ催化剂具有强吸附ＣＯ能力，且生成的烯烃不易发生二次反应，因而ＰＢＣ催化剂具有较高的烯烃选择性；以酸性担体为基质的ＰＡＣ催化剂对ＣＯ为弱吸附，对Ｈ２为较强吸附，且烯烃会发生强烈的     

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface

To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the classical SN2 reaction of Cl-+CH3Cl in solution and the second proton transfer step of the reaction catalyzed by the enzyme 4-oxalocrotonate tautomerase. The activation free energies calculated with this new sequential sampling and optimization approach to the QM/MM-MFEP method agree well with results from other simulation approaches such as the umbrella sampling technique with direct QM/MM dynamics sampling, demonstrating the accuracy of the iterative QM/MM-MFEP method.     

Quantum study of the active sites of the γ alumina surface (II): QM/MM (LSCF) approach to water, hydrogen disulfide and carbon monoxide adsorption

The mixed quantum mechanics/molecular mechanics (QM/MM) local self consistent field (LSCF) method is applied to study the adsorption of water, hydrogen sulfide, and carbon monoxide molecules on γ alumina surfaces. The effect of the long-range contributions included in the LSCF adsorption/dissociation energies are compared to cluster results. For the carbon monoxide, the long-range contributions do not change the adsorption energies in comparison with the cluster approach. In opposition, the long-range contributions lower the adsorption and dissociation energies of water and hydrogen disulfide. Cautions to be taken on the application of the LSCF method to γ alumina are also discussed.     

Hydrophobic monolayer preparation by Langmuir-Blodgett and chemical adsorption techniques

Alkylsiloxane and perfluoroalkylsiloxane monolayers are prepared on siliceous surfaces using the techniques of Langmuir-Blodgett deposition and solid-liquid chemical adsorption. Acid-catalyzed hydrolysis and polycondensation reactions provide two-dimensional siloxane networks at the liquid-vapor interface, which can be compressed to mean molecular areas of approximately 22 and approximately 32 A(2) for pendent hydrocarbon and fluorocarbon chains, respectively. Subsequent Langmuir-Blodgett transfer onto glass substrates at moderate surface pressures leads to compact monolayers for single-component precursors, while mixed alkyl- and perfluoroalkylsilanes produce nonhomogeneous films characterized by transfer ratios greater than unity. As an alternate monolayer preparation technique, silane polymerization was performed directly on siliceous surfaces via a chemical adsorption mechanism. XPS analysis of a chemically adsorbed 1H,1H,2H,2H-perfluorodecylsiloxane film confirms a single adsorbed monolayer thickness in which the pendent fluoroalkyl chains align nonperpendicularly with respect to the surface. The surface free energy was determined to be 11.4 dyn cm(-1) based on static contact angle measurements. AFM imaging shows the presence of surface defects due to oligomer deposition during the drying process. The use of solubilized trichloro-based silane coupling agents under anhydrous conditions is shown to produce surfaces with a minimal number of surface defects. The presence of undissolved silane material in the bulk solution significantly increases the number of surface defects.     

The effect of alloying on the H-atom adsorption on the (100) surfaces of Pd-Ag,Pd-Pt,Pd-Au,Pt-Ag,and Pt-Au. A theoretical study

The effect of alloying on the adsorption of atomic hydrogen was studied using density functional theory (DFT). In the study the (100) surfaces of Pd-Ag, Pd-Pt, Pd-Au, Pt-Ag, and Pt-Au alloys were considered by means of a cluster model. The structural and energetic properties of the H atom adsorbed on the Pd₄Me (Me = Ag, Pt, Au) and Pt₄Me (Me = Pd, Ag, Au) clusters were calculated and compared with the H-atom adsorption on monometallic clusters. The effect of alloying on the H-atom adsorption is evident for all the investigated bimetallic systems. However, it strongly depends on the second metal atom, Me, is placed in the surface layer or in the subsurface one. In general, the H atom adsorbed in a site containing the second metal exhibits different properties from those characteristic of its adsorption on Pd(100) and Pt(100). Hence, the modified interaction between atomic hydrogen and the alloyed surfaces may increase the selectivity of the catalytic hydrogenation reactions on such surfaces.     

金属氧化物表面化学吸附和反应的量子化学簇模型方法研究

综述了本研究小组利用量子化学簇模型方法研究金属氧化物表面化学吸附和反应的工作.提出了选簇的三个原则,即电中性原则、化学配比原则和配位原则.发现在符合前两个原则的基础上,一个具有最饱和配位、或最少悬空键的簇往往是一个用于化学吸附研究的好的簇模型.与此同时,探讨了如何恰当地考虑大块固体本底的长程影响,提出了用球电荷模拟簇模型的环境、环境与簇体进行电荷自洽的SPC簇模型方法.利用该模型研究了一系列具有催化背景的重要体系,包括H2/ZnO、O/MgO、NO/MgO、N2O/MgO、N2O/Li/MgO、CO/MgO、CO/NiO等.