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.     

Adsorption of NH(3) and H(2)O in acidic chabazite. Comparison of ONIOM approach with periodic calculations

The adsorption of NH(3) and H(2)O in acidic chabazite has been studied with the B3LYP method within the cluster approach (5T, 48T clusters) and the periodic approach adopting a Si/Al = 11/1 chabazite and a basis set of polarized double-zeta quality. The 5T cluster has been treated fully ab initio at the B3LYP level whereas the 48T cluster has been treated with the ONIOM2 scheme using B3LYP as the high level of theory and the MNDO, AM1, and HF/3-21G methods as low levels of theory. Periodic calculations show that the adsorption of NH(3) in acidic chabazite takes place through an ion pair (NH(4)(+)-CHA(-)) structure, the computed adsorption energy being -32 kcal/mol. The adsorption of H(2)O leads to a hydrogen bonded (H(2)O-HCHA) complex with the computed adsorption energy of -20 kcal/mol. All ONIOM combinations provide similar structures to those obtained with periodic calculations. Adsorption energies, however, are sensitive to the low level used, especially for NH(3). The ONIOM B3LYP:HF/3-21G method is the one that provides more satisfactory results. Present results show that, for larger zeolites, the ONIOM scheme can be successfully applied while drastically reducing the cost of a fully ab initio treatment.     

Theoretical study of M(PH3)2 complexes of C60, corannulene (C20H10), and sumanene (C21H12) (M = Pd or Pt). Unexpectedly large binding energy of M(PH3)2(C60)

DFT and MP2 to MP4(SDQ) methods were applied to M(PH3)2(C60), Pt(PH3)2(C20H10), and Pt(PH3)2(C21H12) (M = Pd or Pt, C20H10 = corannulene, and C21H12 = sumanene). The binding energy considerably fluctuates around MP2 and MP3 levels but much less upon going from MP3 to MP4(SDQ) in Pt(PH3)2(C2H4), Pt(PH3)2(C20H10), and Pt(PH3)2(C21H12). Also, the MP4(SDQ) method presents a binding energy similar to that of the CCSD(T) method in Pt(PH3)2(C2H4). Thus, it is likely that the MP4(SDQ) method is useful to evaluate binding energies of these complexes. The binding energies of Pt(PH3)2(C20H10) and Pt(PH3)2(C21H12) are evaluated to be 24.9 and 26.1 kcal/mol, respectively, by the MP4(SDQ) method and only +5.8 and -2.6 kcal/mol, respectively, by the DFT(B3LYP) method. These MP4(SDQ)-calculated binding energies of Pt(PH3)2(C20H10) and Pt(PH3)2(C21H12) are similar to that of Pt(PH3)2(C2H4), which strongly suggests that these complexes can be successfully synthesized. The binding energy of Pt(PH3)2(C60) is evaluated to be 44.8 and 45.5 kcal/mol with the ONIOM(MP4(SDQ):UFF) and ONIOM(MP4(SDQ):B3LYP) methods, respectively, and that of the Pd analogue is evaluated to be 39.9 kcal/mol with the ONIOM(MP4(SDQ):UFF) method, whereas the DFT(B3LYP), DFT(BVP86), and DFT(BPW91) methods provide much smaller binding energies. It is noted that these binding energies are much larger than those of the ethylene, corannulene, and sumanene analogues. This difference is reasonably interpreted in terms that the LUMO of C60 is at much lower energy than those of ethylene, corannulene, and sumanene. We investigated also how to separate the high level and the low level regions in the ONIOM calculation of M(PH3)2(C60) and proposed here the reasonable way to evaluate the binding energy of transition-metal complexes of C60.     

Intermolecular Interaction of HMX： an Application of ONIOM Methodology

IntroductionExtensive studies on intermolecular interac-tions have been made in the past decades due totheir importance in a wide range of physical,chem-ical and biological fields.Researches on the weakintermolecular interactions began with hydrogenbonds.Scheiner summarized the ab initio investiga-tions on hydrogen bonding in detail[1] .With the abinitio method supermolecular structures and bind-ing energies can be predicted notonly for H- bondedsystems but also for other systems[2 _ 5] when …     

Solvent effects on the excited state properties of 2-aminopurine—a theoretical study by the ONIOM and Supramolecular method

In this paper, the micro-solvated effects on the lowest-energy vertical transition state and adiabatic excited states of 2-aminopurine (2Ap) were studied by Supramolecular method (B3LYP/6-31++G(d)) and ONIOM (B3LYP/6-31++G(d):PM3) method. The results are as follows: (1) In 2Ap molecule surrounded by six water molecules the pyramidalization of amino group in 2Ap almost disappears, and the hex-atomic ring is obviously buckled. The adiabatic lowest-energy valence excitation of gaseous 2Ap also causes the disappearance of amino pyramidalization. (2) The energy for lowest-energy singlet π→π^* vertical transition in water is predicted as 3.99 and 4.29 eV by Supramolecular and ONIOM method, respectively. Both values are in good agreement with the reported experimental result, 4.11 eV. The energy for the second lowest-energy n→π^* transition, 4.72 eV, by the Supramolecular method is obviously deviated from the reported experimental value 4.46 eV. The corresponding value given by the two-layer ONIOM method, 4.43 eV, is in good agreement with the experimental value. (3) The optimized energy of the fluorescent emission state (S₁ state) are 3.61 and 3.87 eV by Supramolecular and ONIOM methods, respectively. The calculated oscillator strengths, in both gas and water clusters, were compared with reported experimental and theoretical results. These results indicated that both Supramolecular and ONIOM methods, combined with TD DFT B3LYP/6311++G(d), can provide good results of calculating excited state and spectra properties of 2Ap in condensed phase. This fact encouraged us to extend our study to 2Ap-T base pair and its solvated model so as to obtain the spectra properties of 2Ap in real DNA environment.     

Characterization of acidity in [B], [Al], and [Ga] isomorphously substituted ZSM‐5: Embedded DFT/UFF approach

The structure and electronic properties of the Brønsted acid site in B, Al or Ga isomorphously substituted ZSM‐5 zeolites were studied by using quantum cluster and embedded ONIOM approaches. In the former approach, zeolites are modeled by 5T and 12T quantum clusters, where T represents a Si or Al atom. In the latter model, called “Embedded ONIOM”, the long‐range interactions of the zeolite lattice beyond the 12T quantum cluster is included via optimized point charges added to the ONIOM(B3LYP/6‐31G(d,p):UFF). Inclusion of the extended zeolitic framework covering the nanocavity has an effect on the structure and adsorption properties. We found that the OH distances and v OH of the acidic proton in zeolite obtained from both models can predict the trend of acid strength as: B‐ZSM‐5 < Ga‐ZSM‐5 < Al‐ZSM‐5, which is in very good agreement with the experimental sequence. Furthermore, the PA data calculated from E‐ONIOM is also consistent with the experimental trend: B‐ZSM‐5 < Ga‐ZSM‐5 < Al‐ZSM‐5. It has, therefore, been demonstrated that our embedded ONIOM model provides accurate performance and can be one of the useful and affordable methods for future mechanistic studies involving petrochemical reactions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study of the SN2 reaction of Cl−(H2O)+CH3Cl using our own N-layered integrated molecular orbital and molecular mechanics polarizable continuum model method (ONIOM, PCM)

The effects of solvation in the S_N2 reaction Cl^–(H₂O)+CH₃Cl were investigated using our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) polarizable continuum model (PCM) method [Vreven T, Mennucci B, da Silva CO, Morokuma K, Tomasi J (2001) J Chem Phys 115:62–72], which surrounds the microsolvated ONIOM system with a polarizable continuum. The microsolvating water molecule tends to stay in the vicinity of the original chloride ion. In the ONIOM calculations, Cl^–+CH₃Cl was considered as the model system and was handled with the high-level method, while the explicit water molecule in the microsolvated complex was treated at the low-level. The molecular orbital (MO) and ONIOM(MO:MO) calculations allow us to assess the errors introduced by the ONIOM extrapolation, as well as the effects of microsolvation on the potential-energy surfaces. We find that ONIOM[B3LYP/6-31+G(d,p):HF/6-31+G(d,p)] and ONIOM[B3LYP/6-31+G(d,p):HF/6-31+G(d,p)]-PCM methods are good approximations to the target B3LYP/6-31+G(d,p) and B3LYP/6-31+G(d,p)-PCM methods. In addition, several approximate (computationally less expensive) schemes in the ONIOM-PCM method have been compared to the exact scheme, and all are shown to perform well.Contribution to the Jacopo Tomasi Honorary Issue     

Adsorption of Methanol,Formaldehyde and Formic Acid on the Si(100)-2×1 Surface:A Theoretical Study

Small organic molecules on Si surface serve model systems in studies of the process of SiC, SiO and thin diamond films formation on the surfaces. We have applied the hybrid density functional B3LYP method in conjunction with cluster model approach and the ONIOM method1 to the study of methanol, formaldehyde and formic acid adsorption on the Si(100)-2×l surface.     

Quantum chemical calculations based on ONIOM and the DFT methods in the inclusion complex: doxycycline/2-O-Me-β-cyclodextrin

A computational study of inclusion complexes of 2-methyl-βCD with Doxycycline tautomeric (enol and keto form) has been performed with several combinations of ONIOM hybrid calculations. The reliability of the ONIOM2 calculations at the integrated level, ONIOM2 (M05-2X/6-31G(d): M05-2X/3-21G*), ONIOM2 (M05-2X/6-31G(d):HF/3-21G*), ONIOM2 (B3LYP/6-31G(d):HF/3-21G*), ONIOM2 (B3LYP/6-31G(d):B3LYP/3-21G*) and ONIOM2 (B3PW91/6-31G(d):B3PW91/3-21G*) was examined. Their complexation, binding, deformation and stabilization energies, and geometrical data were compared with those of the target geometry structure optimized at the M05-2X/6-31G(d) level of theory. Mixed combinations ONIOM2 (M05-2X 6-31G(d):HF 3-21G*) and ONIOM2 (B3LYP 6-31G(d):HF 3-21G*) reproduces nearly the target geometry structure and provides realistic energetic results at a relatively low computational cost.     

Host-guest inclusion complex between β-cyclodextrin and paeonol: A theoretical approach

Host-guest interactions of β-cyclodextrin (β-CD) with paeonol (PAE) were simulated using semi-empirical PM3 and both ONIOM2 [(B3LYP/6-31G*:PM3), (HF/6-31G*:PM3)] methods. The results obtained with PM3 method clearly indicate that the complexes formed are energetically favored with or without solvent, the model 1 (PAE entering into the cavity of β-CD from its wide side by OCH3 group) is found more favored than the model 2 (PAE entering into the cavity of β-CD from its wide side by COCH3 group). Finally, natural bonding orbital (NBO) analysis was performed based on ONIOM2 optimized complexes to quantify the donor–acceptor interactions between PAE and β-CD.     

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.     

Structures and reaction mechanisms of cumene formation via benzene alkylation with propylene in a newly synthesized ITQ-24 zeolite: an embedded ONIOM study

The cumene formation via benzene alkylation with propylene on the new three-dimensional nanoporous catalyst, ITQ-24 zeolite, has been investigated by using the ONIOM2(B3LYP/6-31G(d,p):UFF) method. Both consecutive and associative reaction pathways are examined. The contributions of the short-range van der Waals interactions, which are explicitly included in the ONIOM2 model, and an additional long-range electrostatic potential from the extended zeolite framework to the energy profile are taken into consideration. It is found that benzene alkylation with propylene in the ITQ-24 zeolite prefers to occur through the consecutive reaction mechanism. The benzene alkylation step is the reaction rate-determining step with an estimated activation energy of 35.70 kcal/mol, comparable with an experimental report in beta-zeolite of 34.9 kcal/mol. The electrostatic potential from the extended zeolite framework shows a much more significant contribution to the transition state selectivity than the van der Waals interactions.     

Molecular structures of 8,8′-dithioureido-2,2′-binaphthalene derivatives and their anions recognition: an ONIOM investigation

The structures of 8,8′-bis(3-phenylthioureidomethyl)-2,2′-binaphthalene (1), 8,8′-bis(3-butylthioureidomethyl)-2,2′-binaphthalene (2) and their complexes with anionic guests such as carboxylate ions (acetate, oxalate, malonate, succinate, glutarate, adipate, pimelate, suberate, and azelate), inorganic oxygen-containing anions (nitrate, sulfate, bicarbonate, hydrogen phosphate, and dihydrogen phosphate), and halide ions (fluoride, chloride, and bromide) were obtained using the ONIOM approach. The binding abilities of receptors 1 and 2 to anionic species in terms of binding energy, thermodynamic properties, and selectivity coefficient were obtained at the ONIOM(B3LYP/6-31G(d):AM1) and BSSE-corrected B3LYP/6-31G(d)//ONIOM(B3LYP/6-31G(d):AM1) levels of theory. The multipoint hydrogen bonding between receptors (either the receptor 1 or 2) and anionic guests were found. The hydrogen phosphate is the most preferable ion to bind with either the receptor 1 or 2.     

苯在Si(111)-7*7表面化学吸附的理论研究

采用两种大小不同的原子簇模型Si_(30)H_(28)和Si_(13)H_(16),分别用两层 ONIOM方法（对较大原子簇）和普通量子化学方法（对较小原子族）考察了苯分子 在Si(111)-7 * 7表面的化学吸附。对三种可能的吸附物种分别用DFT或HF方法进行 了计算。通过大小原子簇吸附物种的吸附能以及几何构型优化参数的比较发现,对 于稳定的吸附物种,较小的原子簇基本上可以代替较大的原子簇进行计算,而对于 不太稳定的吸附物种,就不得不考虑周边原子的影响。计算结果表明苯在Si(111)- 7 * 7表面的主要吸附种是双σ成键的1,4加成产物,不稳定的单吸附物种可能是 1,4加成物种的前驱态。     

用密度泛函方法研究质子化苯基丙酮-水团簇

The structure and growth trend of the protonated acetophenone-water clusters have been investigated using the DFT-B3LYP method combined with the standard 6-31+G(d,p) basis set. In order to obtain more accurate single-point energy the B3LYP/6-311++G(3df,2p) method was adapted. The results show that the formation of H+C8H8O-H2O is a barrierless reaction process and the equilibrium distance between the proton and the O atom in C8H8O molecule is 1.015 A. For H+C8H8O-(H2O)n(n=1,2,3) clusters, the proton lies between the acetophenone molecule C8H8O and the water molecule H2O. The distance between the proton and the O atom of the C8H8O molecule increased from n=1 to n=3; C8H8O-H+-H2O can be regarded as an solvation shell. For H+C8H8O (H2O)n (n=4,5,6,7,8) clusters, the proton lies between the two H2O molecules forming a H5O2+ structure, C8H8O-H5O2+ is an important structure, which the other H2O molecules will attack from different sides.     

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.     

气体分子对甲烷水合物稳定性的影响

通过B3LYP方法, 在6-31G(d,p)水平下, 分别优化了结构I型甲烷水合物十二面体和十四面体晶穴结构. 结果表明, CH4分子使晶穴的相互作用能降低, 增强了晶穴的稳定性. 计算了晶穴中甲烷分子C—H键的对称伸缩振动频率, 计算结果与实验值相符合. 研究发现CH4分子影响晶穴中氧原子的电荷分布, 从而增强了氢键的稳定性. 通过分子动力学方法研究水合物晶胞中气体分子的占有率对水合物稳定性的影响, 进一步说明气体分子对水合物晶穴稳定性的重要作用.     

Different phosphorescent excited states of tetra- and octanuclear dendritic-like phosphine gold(I) thiolate complexes: photophysical and theoretical studies

The study of the photophysical properties of dendritic-like phosphinothiolate gold(I) complexes has been carried out. The studied complexes are two series of analogous compounds bearing 4 or 8 metal centers: the tetranuclear [Au(4)(S-C(6)H(4)-X)(4){DAB-G0-(PPh(2))(4)}] (X = F (3), MeO (4), Me (5) and NO(2) (6)) and the octanuclear [Au(8)(S-C(6)H(4)-X)(8){DAB-G1-(PPh(2))(8)}] (X = F (9), MeO (10), Me (11) and NO(2) (12)) complexes. All compounds are brightly luminescent in solid state at 77 K displaying lifetimes in the microsecond range. The correlation between the substituent in position four of the benzenethiolate ligand and the emission energy shows that the emissions arise from (3)[pπ(S)→pσ(Au)] or from intra-ligand (3)[π(S)→π*(C(6)H(4)X)] charge transfer transitions, depending on the substituents. Theoretical DFT-B3LYP, ONIOM (DFT-B3LYP/UFF) and ONIOM (MP2/UFF) calculations on mononuclear and dinuclear model systems permit evaluation of both the structural distortions upon excitation to the lowest triplet excited state T(1) and the shape of the orbitals involved in the charge transfer transitions. These calculations also allow us to evaluate the influence of the substituent in position four of the benzenethiolate ligand and the presence of Au···Au interactions.