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Set Superposition Error (set + superposition_error)
Kinds of Set Superposition Error Selected AbstractsQuantitative assessment of the effect of basis set superposition error on the electron density of molecular complexes by means of quantum molecular similarity measuresINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2009Pedro Salvador Abstract The Chemical Hamiltonian Approach (CHA) method is applied to obtain Basis Set Superposition Error (BSSE)-free molecular orbitals at the Hartree,Fock (HF) and Density Functional Theory (DFT) levels of theory. To assess qualitatively the effect of the BSSE on the first-order electron density, we had previously applied Bader's analysis of the intermolecular critical points located on the electron density, as well as density difference maps for several hydrogen bonded complexes. In this work, Quantum Molecular Similarity Measures are probed as an alternative avenue to properly quantify the electronic relaxation due to the BSSE removal by means of distance indices between the uncorrected and corrected charge densities. It is shown that BSSE contamination is more important at the DFT level of theory, and in some cases, changes on the topology of the electron density are observed upon BSSE correction. Inclusion of diffuse functions have been found to dramatically decrease the BSSE effect in both geometry and electron density. The CHA method represents a good compromise to obtain accurate results with small basis sets. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Nitrogen Trifluoride as a Bifunctional Lewis Base: Implications for the Adsorption of NF3 on Solid SurfacesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2004Paola Antoniotti Abstract The structure, stability, and thermochemistry of isomeric adducts between NF3 and the Lewis acids BH3,nFn (n = 0,3) have been investigated at the coupled-cluster and at the Gaussian-3 (G3) level of theory. At the CCD/cc-pVDZ level both the nitrogen- and the fluorine-coordinated structures of all BH3,nFn,(NF3) (n = 0,3) adducts were characterized as true minima on the potential energy surface, thus providing the first theoretical evidence for the behavior of NF3 as a bifunctional Lewis base when interacting with neutral Lewis acids. At the G3 level, and 298.15 K, including the contribution of the entropy term, the H3B,NF3 adduct is predicted to be more stable than H3B,F,NF2 by 4.3 kcal mol,1; this free energy difference is 3.7 kcal mol,1 at the CCSD(T)/cc-pVTZ//CCD/cc-pVDZ level of theory. Conversely, at the latter computational level, the fluorine-coordinated isomers of the BH2F,(NF3), BHF2,(NF3), and BF3,(NF3) adducts are practically degenerate with the nitrogen-coordinated ones. BH3,nFn,(NF3) (n = 0,3) complexes feature typical bond dissociation energies of ca. 1,2 kcal mol,1, and are predicted to be thermodynamically stable only at low temperatures. However, the appreciable influence of the basis set superposition error (BSSE) prevents a quantitative assessment of these small computed dissociation energies. Finally, we briefly discuss the implications of our calculations for the adsorption of NF3 on solid surfaces. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Quantitative assessment of the effect of basis set superposition error on the electron density of molecular complexes by means of quantum molecular similarity measuresINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2009Pedro Salvador Abstract The Chemical Hamiltonian Approach (CHA) method is applied to obtain Basis Set Superposition Error (BSSE)-free molecular orbitals at the Hartree,Fock (HF) and Density Functional Theory (DFT) levels of theory. To assess qualitatively the effect of the BSSE on the first-order electron density, we had previously applied Bader's analysis of the intermolecular critical points located on the electron density, as well as density difference maps for several hydrogen bonded complexes. In this work, Quantum Molecular Similarity Measures are probed as an alternative avenue to properly quantify the electronic relaxation due to the BSSE removal by means of distance indices between the uncorrected and corrected charge densities. It is shown that BSSE contamination is more important at the DFT level of theory, and in some cases, changes on the topology of the electron density are observed upon BSSE correction. Inclusion of diffuse functions have been found to dramatically decrease the BSSE effect in both geometry and electron density. The CHA method represents a good compromise to obtain accurate results with small basis sets. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Theoretical study of hydrogen-bonded complexes of benzene with hydrides of astrochemical interestINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2008M. Nait Achour Abstract Post Hartree,Fock and DFT calculations have been performed for studying the possibility for a benzene support to be linked to various hydrides through a quasi Bz···HA bond. Interaction energy of compounds, including CH bonds (CH4, CH3F, CH2O, CHN, CHNO), NH bonds (NH3, NH2F, NHC, NHCO, NH3O), and OH bonds (OH2, OHF, NCOH), were evaluated, taking basis set superposition error (BSSE) and zero point vibrational energy (ZPVE) corrections into account. Numerical convergence of results with respect to the ingredients included at different steps of theory (basis set, DFT functionals, correlation treatments, geometry optimization) was tested mainly on the example of the water adduct and, for comparison, the Bz···H3O+ system containing a cation instead of a neutral molecule. A rather large range of adsorption energies is obtained, from about 1 kcal/mol for methane to more than 6 kcal/mol for cyanic acid, according to the acidic character of the adsorbed species in each family of Bz···HA bonds. Some consequences for astrophysical problems involving PAHs in the interstellar medium are pointed out. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Theoretical study of the prion protein based on the fragment molecular orbital methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2009Takeshi Ishikawa Abstract We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called "Parallelized ab initio calculation system based on FMO (PAICS)". © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptideJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2008Haydée Valdés Abstract Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and compare the calculated data with benchmark values (experimental or high-level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT-D) is proposed and shown to provide very good results in both of the above described representative cases. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008 [source] Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis setsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2008Yasuji Inada Abstract Binding energies of selected hydrogen bonded complexes have been calculated within the framework of density functional theory (DFT) method to discuss the efficiency of numerical basis sets implemented in the DFT code DMol3 in comparison with Gaussian basis sets. The corrections of basis set superposition error (BSSE) are evaluated by means of counterpoise method. Two kinds of different numerical basis sets in size are examined; the size of the one is comparable to Gaussian double zeta plus polarization function basis set (DNP), and that of the other is comparable to triple zeta plus double polarization functions basis set (TNDP). We have confirmed that the magnitudes of BSSE in these numerical basis sets are comparative to or smaller than those in Gaussian basis sets whose sizes are much larger than the corresponding numerical basis sets; the BSSE corrections in DNP are less than those in the Gaussian 6-311+G(3df,2pd) basis set, and those in TNDP are comparable to those in the substantially large scale Gaussian basis set aug-cc-pVTZ. The differences in counterpoise corrected binding energies between calculated using DNP and calculated using aug-cc-pVTZ are less than 9 kJ/mol for all of the complexes studied in the present work. The present results have shown that the cost effectiveness in the numerical basis sets in DMol3 is superior to that in Gaussian basis sets in terms of accuracy per computational cost. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Blue-shifting hydrogen bond in the benzene,benzene and benzene,naphthalene complexesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2007Jose M. Hermida-Ramón Abstract Ab initio complete optimizations at MP2/6-31++G** level have been performed in the T-shaped geometry of the benzene,benzene and benzene,naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue-shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 540,546, 2007 [source] Hydrogen bonding strength,measures based on geometric and topological parameters,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2004awomir Janusz Grabowski Abstract Different methods of estimating H-bond strength are presented. The studies are based on the results of MP2/6,311++G** calculations and the binding energies are corrected for the basis set superposition error (BSSE). The wavefunctions were further applied to localize bond critical points and ring critical points. The characteristics based on the Bader theory are also applied as indicators and measures of hydrogen bonding. This study compares samples of different compounds. The H-bond strength measures such as the proton,acceptor distance (H···Y), the length of the proton donating bond, the electron density at H···Y bond critical point, the H-bond energy and others are analysed. The case of the intramolecular hydrogen bonding is also analysed, and its special characteristics are given. Copyright © 2003 John Wiley & Sons, Ltd. [source] On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded SystemsCHINESE JOURNAL OF CHEMISTRY, Issue 12 2003Wei-Zhou Wang Abstract Geometries, harmonic vibrational frequencies and interaction energies of the water-hydrogen sulfide dimer, hydrogen fluoride dimer and glycine zwitterion-water dimer were determined by the counterpoise-corrected (CP-corrected) gradient optimization that explicitly corrects for the basis set superposition error (BSSE) and CP-uncorrected (normal) gradient optimization respectively at the B3LYP and MP2 levels of theory, employing the popular Pople's standard 6,31G(d), 6,31G(d, p) and 6,311 + + G(d, p) basis sets in order to assess the importance of CP-corrected gradient optimization in the study of hydrogen bonded systems. The normal optimization of these three H-bonded systems obtained using these popular basis sets all yielded erratic results, whereas use of CP-corrected gradient optimization led to consistent results with those from larger basis sets. So this CP receipt becomes useful and necessary to correctly describe large systems, where the use of small basis sets may be necessary. [source] Keto-enol tautomerism in linear and cyclic ,-diketones: A DFT study in vacuo and in solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2008Giuliano Alagona Abstract DFT geometry optimizations have been performed at the B3LYP/6-31G* level in the gas phase and at the IEF-PCM/B3LYP/6-31G* level in tetrahydrofuran (THF) and aqueous solutions using scaled radii for the diketo and ketoenol forms of acetylacetone and cyclohexanedione. To evaluate basis set effects, starting from the aforementioned minima, the 6-311++G** optimized structures have been obtained. A number of complexes of both systems including one explicit water molecule have been considered up to the B3LYP/6-311++G** level, for cyclohexanedione taking into account the B3LYP/6-31G* basis set superposition errors as well. The diketo,ketoenol interconversion mechanisms have been investigated at the B3LYP/6-31G* level in vacuo. Interestingly, the geometric constraint due to the presence of the ring facilitates the description of the reaction mechanism in cyclohexanedione. Despite the very different flexibility of the two systems that in the case of acetylacetone prevents a straightforward interconversion of the diketo to the most stable of its ketoenol forms, both reactions occur with a very high barrier (about 62,63 kcal/mol), unaffected by continuum solvents, that decreases by 2.5,3.5 kcal/mol after the inclusion of thermal corrections. The barriers are almost halved, becoming ,31,35 kcal/mol, for the addition of a single water molecule according to various model reaction paths. Thermal corrections are limited (0.8,1.6 kcal/mol) for those adducts. The formation of a 1,1-diol, explored in the case of acetylacetone, might facilitate the obtainment of the most stable diketo conformation, featuring the carbonyl groups in distinct orientations. Inclusion of dispersion and basis set effects via the G2MP2 protocol does not alter the relative stability of both system tautomers. In contrast, the G2MP2 interconversion barriers for the isolated systems in vacuo are close to the B3LYP ones, whereas they turn out to be somewhat higher than the free energy-based B3LYP barriers in the presence of a catalytic water molecule. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Comment on "Aromatic-Backbone Interactions in Model ,-Helical Peptides" [Palermo et al., J Comput Chem 2007, 28, 1208]JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2008Tanja Van Mourik Abstract Palermo et al. have recently published a method to correct for intramolecular basis set superposition errors (J Comput Chem 2007, 28, 1208) in intramolecular interactions occurring in peptides. By considering the intermolecular equivalent of this method, it is shown that the method presented by Palermo et al. underestimates the magnitude of the intramolecular BSSE. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Reply to "Comment on Aromatic-Backbone Interactions in Model ,-Helical Peptides"JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2008József Csontos Abstract In response to Van Mourik's comments on our paper (J Comput Chem 2007, 28, 1208.) we present an extended version of our rotation method. We also prove that intramolecular interaction energies as well the basis set superposition errors calculated with our rotation method are comparable with those obtained by the counterpoise method of Boys and Bernardi (Mol Phys 1970, 19, 533). In intramolecular interaction energy calculations, if the interacting groups are in proximity, our rotation method is recommended to avoid artificial interactions, which can be induced by fragmentation. © 2007 Wiley Periodicals, Inc.J Comput Chem, 2008 [source] | ||||||||||