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Abstract: In order to describe the structural and energetic properties of Al-MCM-22 zeolite effectively and reasonably, ONIOM2 and ONIOM3 models as well as full B3LYP/6-31G(d) optimization on different sized clusters have been tested. On the basis of the computed bond lengths, substitution energies, proton affinities and O–H stretching frequencies for the Al1–O3H–Si4 and Al2–O9H–Si5 acid sites, three-layered ONIOM schemes (B3LYP/6-311G(d,p):HF/3-21G(d):MNDO) with 8T high-layer up to cluster sizes of 10 Å have the nearly same results as compared with those obtained from full B3LYP/6-31G(d) optimizations on 8 Å clusters. The computed O–H stretching frequencies, adsorption energy of ammonia, and Al···H1 distances agree well with the available experimental data. [Copyright &y& Elsevier]

Abstract: Geometry optimizations of Venlafaxine/β-Cyclodextrin complex were carried out using MM2, PM3, ONIOM2 and ONIOM3 methods. The binding and complexation energies for both orientations considered in this research are reported. The geometry of the most stable complex shows that the aromatic ring is deeply self-included inside the hydrophobic cavity of β-CD also an intermolecular hydrogen bond is established between host and guest molecules. This suggests that hydrophobic effect and hydrogen bond play an important role in the complexation process. Additional information about binding in the complexes (C1) and (D1) was obtained by NBO analysis, the stabilization energy E (2) calculated with ONIOM3 method is more significant. [Copyright &y& Elsevier]

Abstract: The purpose of this study is to compare solvent effects of the polarizable continuum model (PCM) and ONIOM (our Own N-layered Integrated molecular Orbital molecular Mechanics) model. The test was performed by calculating Gibbs energies of reaction and activation for the Z/E thermal isomerization reaction of acetaldehyde N,N-dimethylhydrazone at 298.15K in the solvent of cyclohexane. Four density functional theory typed methods, B3LYP, BB1K, MPW1B95 and MPWB1K with the 6-311++G(3df,2p)//6-31G(2df,p) basis sets were employed to give estimates of Gibbs energies. We compared the calculated results with the available experimental observation (established by Clarke et al. [Clarke et al., J. Chem. Soc. Perkin Trans II 11 (1991) 1649.]). As a result of the calculations, it is found that with the ONIOM model the four density functional theory typed computations gave estimates of Gibbs energy of activation in agreement with the experimental observation while the PCM calculated values overestimated the energy of activation by about 3 or 4kcal/mol. For the calculated free energies of reaction, the four density functional theory typed computations with the PCM and the ONIOM models gave very close results with a range of about 1kcal/mol. [Copyright &y& Elsevier]

Abstract: The performance of the mixed basis set and the ONIOM methods on the activation energy of the ring opening pericyclic reaction of substituted cyclobutenes was reported. The B3LYP, BB1K and MPWB1K functionals with several basis sets were used in this investigation. The study indicates that the B3LYP functional is more appropriate for predicting the activation energy of the ring opening reaction than the BB1K and MPWB1K functionals. However, the BB1K and MPWB1K functionals can represent the substituent effect on the activation energy as accurately as the B3LYP functional. In general, the mixed basis set yields less root mean square error but takes significantly more computational time than the ONIOM method. The results suggest that the 6-31G(d):CEP-31G mixed basis set is the method of choice for this system judging from the least root mean square error and the least maximum absolute error, whereas the MPWB1K functional with the 6-311+G(2d,2p):6-31G(d) mixed basis set is the method of choice for calculating the relative activation energy. [Copyright &y& Elsevier]

Abstract: The molecular structures of 3,4-dichloro-2,5-diamidopyrrole LH, its deprotonated species L −, self-assembly dimeric species and its complexes with fluoride, chloride and hydroxide ions were obtained using the B3LYP/6-31G(d) calculations. The optimized structures at the B3LYP/6-31G(d) and ONIOM(B3LYP/6-31G(d):PM3) levels of the self-assembly dimer co-existing with TBA (tetrabutylammonium) as [L 2.2TBA] were obtained and their geometrical data show good agreement with the X-ray crystallographic structure. In the presence of hydroxide (as TBA.OH), deprotonation of LH and dimerization of L − are the most favorable reaction as compared to systems in the presence of fluoride and chloride ions. The hydroxide ion is able to draw a pyrrole proton from the LH and afford one water molecule via proton-transfer process. [Copyright &y& Elsevier]

Abstract: Structures of hydrated A–U base pair were investigated by using DFT and hybrid ONIOM methods in order to examine the efficacy of the ONIOM (QM:MM) approach in describing the structure of the hydrated RNA base pair. Comparison of these results reveals that the ONIOM (DFT:AMBER) approach, in which the nucleic acid base pair is treated quantum chemically by DFT and ambient water molecules treated by AMBER molecular mechanics, maintains the structures of the hydrated A–U base pair optimized by full DFT quantum chemical methods. [Copyright &y& Elsevier]

Abstract: A performance evaluation of Density Functional Tight Binding (DFTB) in the two-layer ONIOM method is presented in an effort to estimate DFTB effectiveness as an inexpensive low level quantum mechanical layer. Ground state geometries, geometry error, S-values and energy error for: (H2O) x (MeOH) y , [(η5-C5Me n H5−n )2Ti]2(μ2, η2,η2-N2), n =4, and complexes of Cu+ with tyrosine, were compared to target calculations at B3LYP level of theory for all three of the systems and second order Moller-Plesset (MP2) target level of theory for the first two systems. The calculated root-mean-square errors (RMS) of the ONIOM optimized geometries relative to the target are found to be small. The DFTB level of theory was unable to reproduce the target geometry structure for one of the isomers of tyrosine–Cu+ complex, while the ONIOM combinations were able to reproduce all target structures. The absolute value of the geometry error was determined to be smaller then the corresponding energy error except for the (H2O) x (MeOH) y system at the ONIOM(MP2/6-31G(d,p):DFTB) level of theory. The S-values were relatively small and close in value contributing to relatively small energy errors. Both method combinations ONIOM(MP2:DFTB) and ONIOM(DFT:DFTB) show similar performance compared to the corresponding target level of theory. The results also suggest that it is safe to use ONIOM(DFT:DFTB) for investigations of [(η5-C5Me n H5−n )2Ti]2(μ2, η2,η2-N2) complexes. [Copyright &y& Elsevier]

Abstract: Quantum mechanical calculations have been performed on faujasite and silicalite models to investigate reported experimental differences in yields of two key catalytic products (propionitrile and acrylonitrile) formed from the reaction of acetonitrile with either methanol or formaldehyde, respectively. The calculations were performed using 12T and 10T cluster representations of faujasite and silicalite, respectively, and the results are in good overall agreement with experimental observations. Both reactions are predicted to proceed in a concerted manner, with the transfer of a proton to the basic zeolite oxygen atom in conjunction with the methyl group migration to form a reaction intermediate. The stationary points found on the reaction surface in both zeolites have been systematically assessed using principal components analysis to give us an insight into the correlated nature of the structural/electronic changes that occur on the reaction surfaces. [Copyright &y& Elsevier]

Abstract: β1-Selective thyroid receptor agonists constitute a therapeutic possibility as antiobesity and lipid-lowering agents. Thyroid receptor models were constructed from crystallographic structures and the acceptor/donor nature of 4′-hydroxyl group was investigated by the ONIOM method. All binding energies determined indicated the preference for the protonated form of amino acid residue His 381. Theoretical results confirmed experimental findings that the 4′-position requires a hydrogen bond acceptor/donor group. It also indicates that it should be an acceptor of hydrogen bond as amino acid residue His 381 is preferentially protonated. Also seem to indicate 4′-amino substituted thyromimetics as promising candidates for TR agonists, picturing them as possible alternatives to 4′-phenolic classical thyromimetics. 4′-amino substituted thyromimetics have displayed the closest interaction with protonated residue His 381 and the most stable ligand–LBD model system complex. This provides insight upon the design of novel TR agonists. [Copyright &y& Elsevier]

Abstract: In the present work, semiempirical and hybrid QM/QM′ methods are applied to investigate the structure and properties of a cyclodextrin based molecular reactor, named N,N′-bis(6A-deoxy-β-cyclodextrin-6A-yl)urea (β-CD2ur). In addition to the conformational analysis for the free host, inclusion compounds involving some reactive species participating in the indirubin formation are analyzed and the results discussed on the basis of the templating effect. The outcomes showed two main forms of cyclodextrin dimer in the equilibrium (C1 and C2), differing on the conformation around the urea bridge group. Both conformers presented suitable arrangement to accommodate the reactive species favoring the indirubin isomer formation. The analysis of the complexation processes suggests distinct modes of inclusion for indigo and indirubin isomers, with the latter leading to more favorable processes, therefore establishing some molecular basis for the templating effect. [Copyright &y& Elsevier]

Abstract: A combination of molecular dynamics simulations and the ONIOM2 method was used to simulate a nevirapine molecule dissolved in DMSO, and hence to calculate 1H NMR chemical shifts using the GIAO method. This approach was able to accurately predict the chemical shifts, including that of the acidic proton present, which has its de-shielding greatly influenced by hydrogen bonding effects of the polar solvent. There was less than 0.33ppm difference to experimental data for all shifts. Thus this combined MD–ONIOM2 method can be useful and efficient for systems where solvents significantly influence the electronic environment of a solute. [Copyright &y& Elsevier]

Abstract: The hybrid ONIOM method has been tested for enantioselective deprotonation reaction of N-Boc-pyrrolidine and N-Boc-piperidine using isopropyl-lithium in the presence of sparteine. This study investigates different partitions and level of theories of ONIOM method, while the results are reported with regular DFT and ONIOM calculations. The system requires partitioning into layers that are not ideal for ONIOM, and we assess the effect of the various places where the border region can be placed. [Copyright &y& Elsevier]

Abstract: Second-order Møller–Plesset perturbation (MP2) theory, Hartree–Fock (HF) theory, and 25 density functional theory (DFT) methods have been used to compute the hydrogen bond strengths between water and the polar side chains of four uncharged amino acids (serine, threonine, asparagine, and glutamine) and their corresponding glycine-X-glycine tripeptides (where X is one of the four amino acids just listed). These theoretical methods were also combined in 26 different integrated ONIOM QM:QM schemes in which MP2 was used as the high level method and either HF theory or one of the 25 density functionals was used as the low level method. Three important observations lead to the conclusion that the MP2:HF hybrid method provides the best description of hydrogen bonding in these complexes. (1) With deviations from the MP2 dissociation energies that range from −0.42 to −1.06kcalmol−1 and an average absolute error (AAE) of 0.69kcalmol−1, MPWLYP is the most accurate density functional. Only the MPWLYP, B971, X3LYP, PBE1PBE, and VSXC functionals have AAEs under 1kcalmol−1 while the maximum absolute error exceeds 1kcalmol−1 for all 25 functionals. (2) The integrated ONIOM methods outperform the DFT methods, including the MPWLYP functional. The ONIOM AAEs range from 0.25 to 0.36kcalmol−1, all of which are significantly smaller than the corresponding value for the MPWLYP functional. (3) None of the MP2:DFT approaches is better than the MP2:HF scheme. MP2:HF has the smallest AAE (0.25kcalmol−1), the narrowest range of errors (−0.35 to −0.12kcalmol−1), and the smallest maximum absolute error (0.35kcalmol−1) of all 26 schemes. [Copyright &y& Elsevier]

Abstract: The results of the application of ONIOM (n-layered integrated molecular orbital and molecular mechanic method) approximation to the modelling of the interaction of 1,3,5-trinitrobenzene (TNB) with the siloxane surface of clay minerals are presented. The target cluster having the chemical formula of Al22Si13O81H44 has been subdivided into the high level part which has been calculated at the MP2/6-31G(d) or HF/6-31G(d) level of theory; the medium level part which has been calculated at the HF/6-31G(d) level of the theory, and the low level part which has been calculated at the HF/3-21G or HF/STO-3G level. For the aim of the comparison, we have also considered the interaction of TNB with a pure silicon–oxygen cluster having the formula of Si13O37H22. These calculations have been performed at the HF, MP2, and DFT levels of theory using the standard 6-31G(d) basis set. We have found that the attractive component of adsorption energy consists mainly of two commensurable parts. The first one is electrostatic contribution. This interaction is responsible for the virtually planar orientation of absorbed TNB with respect to the silicon–oxygen plane of clay minerals. Another stabilizing interaction originates from dispersion energy. This contribution amounts to 30–50% of the total adsorption energy. [Copyright &y& Elsevier]

Abstract: The performances of different ONIOM methods in the geometry optimizations of bulky organonickel and organopalladium compounds were systematically assessed for the first time. The whole system was always treated with the HF/LANL2MB method while seven popular density functionals (B3LYP, PBEP86, B3P86, B3PW91, BPBE, PW91PW91, and BP86) and six popular ECP basis sets (CEP-121G, CRENBL, LANL2DZ, LANL2DZ+p, SDD, and sbkjcvdz) were examined for the core layer. It was concluded that the best method for the geometry optimizations was ONIOM(B3P86/LANL2DZ+p//HF/LANL2MB). Its average errors for the calculations of the whole systems were 0.076Å (bond length, Ni), 0.071Å (bond length, Pd), 1.52° (bond angle, Ni), 1.43° (bond angle, Pd), 5.6° (dihedral angle, Ni), and 6.0° (dihedral angle, Pd), respectively. Its root mean squared errors for the whole systems were 0.096Å (bond length, Ni), 0.088Å (bond length, Pd), 2.18° (bond angle, Ni), 2.20° (bond angle, Pd), 11.0° (dihedral angle, Ni), and 11.5° (dihedral angle, Pd), respectively. [Copyright &y& Elsevier]

Abstract: During the last decade, farnesyltransferase enzyme (FTase) has established itself as a very promising target in anticancer research, with more than 100 patents describing farnesyltransferase inhibitors (FTIs) published since 2000. However, several crucial doubts in its catalytic mechanism still remain. Understanding the farnesylation mechanism of the natural substrates of FTase would allow the development of more specific and active inhibitors of this enzyme. One of the fundamental dilemmas which characterize the FTase mechanism is the coordination of the peptide substrate. It is known that peptide coordination results in the formation of a zinc thiolate; however, the exact protonation state of the peptide cysteine that reacts with zinc–thiol or thiolate-remains unknown. In this study, the potential energy surfaces for thiol and thiolate peptides entrance into the active-site zinc coordination sphere were determined. The results show that the Gibbs activation barrier for thiolate entrance is of around 20kcal/mol, whereas for thiol entrance is of only 2.5kcal/mol. Globally, the results demonstrate that the substrate peptide coordinates zinc as a thiol, subsequently losing a proton to give the thiolate bound minimum, and that a direct thiolate attack is not a kinetically competitive alternative. [Copyright &y& Elsevier]

Abstract: Quantum chemical methods were performed to study the structure and electronic properties of a series of C60 derivatives. The integrated, ONIOM molecular orbital method was applied to optimize the structure of all compounds while the DFT/B3LYP 6-31G(d) calculations were performed to examine molecular and electronic properties. It was found that strongest effect of the functional groups on the net charges takes place on the linked atoms between C60 and its side chain. The functional group leads to the changes of atomic net charges on the C60 surface up to 5Å away from the C–C bond where the functional group binds to the surface. Two localized electrostatic potential regions are observed, for the selected compounds, near the hydroxyl oxygen and the hydroxyl hydrogen. The hydroxyl hydrogen atom is the location of the most positive potential. These electrostatic features are likely modulated the hydrophobicity or lipophilicity of the compounds and, hence, indicate how they interact with the receptor. [Copyright &y& Elsevier]

Abstract: Geometries of azophenol–thiourea derivative complexes with acetate, oxalate, malonate, succinate, glutarate, adipate, pimelate, suberate and azelate were carried out using the integrated MO:MO method. The binding and complexation energies of these complexes were derived from the ONIOM(B3LYP/6-31G(d):AM1) calculations. The relative stabilities of the complexes of azophenol–thiourea derivatives with carboxylate guests are reported. The binding interactions of the azophenol–thiourea receptor 1, 2 and carboxylate guests are described as multipoints hydrogen bonding, where the amine and phenolic hydrogen atoms of receptors act as hydrogen bond donors in complex with acetate and all amine-hydrogen and phenolic hydrogen atoms act as hydrogen bond donors in complex with dicarboxylate guests. Thermodynamic properties of binding interactions between receptors 1, 2 and their preorganizations and complexations are also reported. [Copyright &y& Elsevier]

The geometries of various conformations of tetraamino-p-tert-butylthiacalix[4]arene (L) were optimized using the semiempirical AM1, HF/3-21G, density functional theory at B3LYP/6-31G(d) level and various two-layered ONIOM(B3LYP/6-31G(d):MO) methods. In decreasing order, the relative stability of four characteristic conformations obtained from different MO calculations is cone, partial cone, 1,3-alternate and 1,2-alternate conformers. The B3LYP/6-31G(d) and two-layered ONIOM (B3LYP/6-31G(d):AM1) optimized geometries of 1,3-alternate (0101-CCCC) show excellent agreement with the X-ray crystallographic structure. The geometry optimization of various protonated species of L and its zinc complex were carried out at ONIOM (B3LYP/6-31G(d):MNDO), ONIOM (B3LYP/6-31G(d):PM3), ONIOM (B3LYP/6-31G(d):AM1) and ONIOM (B3LYP/6-31G(d):AM1) levels of theory. The energies of protonation, preorganization of L and complexation with zinc were derived from total energies at various ONIOM(B3LYP/6-31G(d):MO) levels. The electrostatic potential surfaces of cone (0000-CCCC) and 1,3-alternate (0101-CCCC) conformers were presented. [Copyright &y& Elsevier]

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. [Copyright &y& Elsevier]

A theoretical quantum study on the distribution of active sites on gold surfaces with (100) orientation is reported. Gold surfaces were modeled by finite clusters, keeping the face centered cubic crystal symmetry and net parameters. We define an electronic unit cell (EUC) as the minimal cluster''s size that allows one to reproduce some electronic properties of the macroscopic surface. These were computed at an ab initio Hartree–Fock LANL1MB pseudopotentials level with an ONIOM-like space partition method. We validated our model comparing the work function (∼5.0 eV), band gap (∼2.45 eV) and density of states calculated in this work, with those values reported in literature. Using the concept of EUC, it was possible to suggest a qualitative macroscopic distribution of active sites on the macroscopic gold surface (100). We found that the electrophilic and nucleophilic active sites for this surface are preferably located on hollow positions and their density number is 1.6×1014 sites/cm2 in both cases. [Copyright &y& Elsevier]

In this paper, the aqueous adiabatic electron affinity (AEA) of Uracil (U) and internal reorganization energy λi of the self-exchange electron transfer (ET) reaction between Uracil and Uracil anion radical (U−⋅) in aqueous solution were studied. The effect of the solvation was studied with the recently developed hybrid quantum molecular chemical method, ONIOM. In all calculations, the geometrical optimization for U and U−⋅ was performed at B3LYP/6-31++G(d) level. As for the solvent surroundings, the seven water molecules as the first hydration shell were adopted and treated with B3LYP, PM3 and AMBER methods, namely, ONIOM (B3LYP:B3LYP), ONIOM (B3LYP:PM3) and ONIOM (B3LYP:Amber) methods, respectively. The values of AEA for Uracil, predicted by the above three methods, are small positive ones. The geometrical differences between neutral and anion radical molecules of U originate mainly from those of dihedral angles. According to the corresponding dipole moment values, the excess electron in U−⋅ should be trapped dominantly by dipole-bound way. The calculated λi values by ONIOM (B3LYP:B3LYP) and ONIOM (B3LYP:PM3) are close to each other within 0.89%. The λi value from ONIOM (B3LYP:Amber) is in agreement with the one from SCRF-CPCM very well. Finally, the calculation results of the detailed geometries and molecular interaction mode effect of U and U−⋅ and related water molecules in the hydration shell were discussed. [Copyright &y& Elsevier]

The applicability of two-layer ONIOM methods to hydrogen bonding has been systematically investigated. The structures of 12 hydrogen bonded dimers composed of water, methanol, ethanol and n-propanol have been optimized using second-order Møller–Plesset perturbation theory (MP2) in conjunction with a double-ζ basis set with polarization and diffuse functions on all atoms, denoted DZP++. The dissociation energies (both counterpoise corrected and uncorrected) of these dimers were computed at the coupled-cluster level that includes all single and double excitations as well as a perturbative estimate of connected triple excitations [CCSD(T)] with the DZP++ basis set. These target values were used to gauge the performance of various ONIOM schemes. The methods, basis sets, and partitioning schemes were all systematically varied to determine which combinations, if any, produces substituent values (S values) for the dissociation energy that mimic those at the target level (i.e. CCSD(T) with the DZP++ basis). All possible combinations of four popular methods [SCF, B3LYP, MP2, CCSD(T)] and seven common basis sets (3-21G, 6-31G, 6-31++G, 6-31+G(d), 6-31++G, 6-31G(d, p), 6-31++G(d, p), DZP++) were investigated. Only the MP2 and DZP++ combination gives satisfactory agreement for all 47 model systems. The proton acceptor is very sensitive to the size of the model system. As such, the minimal model recommended for these primary, aliphatic alcohols should include zero C atoms on the donor and one on the acceptor (Model-0,1). With larger models (Model-1,1 or Model-1,2) less expensive methods and smaller basis sets begin to reproduce the target S values. [Copyright &y& Elsevier]

The performance of the ONIOM method was tested in reproducing the properties of the acid sites of the zeolite ZSM-5. The acid sites in three crystallographic locations (Al3–O19(H)–Si6, Al6–O18(H)–Si9 and Al7–O17(H)–Si4) have been modelled by three combinations of two-layer ONIOM method with varied size (two and eight T atoms) and calculation method (ab initio and DFT) used for the chemically important (active) part. The best correspondence with experimental data was achieved in case of Al6–O18(H)–Si9 site calculated with ONIOM(B3LYP/6-311+G**:MNDO) method using eight T atoms in model system for the following properties: stretching vibrational frequencies, 1H NMR chemical shifts of the bridged hydroxyl groups, vibrational frequency shifts and changes in 1H NMR chemical shifts of the hydroxyl groups upon adsorption of CO. [Copyright &y& Elsevier]