Estimates of the ab initio limit for pi-pi interactions: the benzene dimer

State-of-the-art electronic structure methods have been applied to the simplest prototype of aromatic pi-pi interactions, the benzene dimer. By comparison to results with a large aug-cc-pVTZ basis set, we demonstrate that more modest basis sets such as aug-cc-pVDZ are sufficient for geometry optimizations of intermolecular parameters at the second-order M?ller-Plesset perturbation theory (MP2) level. However, basis sets even larger than aug-cc-pVTZ are important for accurate binding energies. The complete basis set MP2 binding energies, estimated by explicitly correlated MP2-R12/A techniques, are significantly larger in magnitude than previous estimates. When corrected for higher-order correlation effects via coupled cluster with singles, doubles, and perturbative triples [CCSD(T)], the binding energies D(e) (D(0)) for the sandwich, T-shaped, and parallel-displaced configurations are found to be 1.8 (2.0), 2.7 (2.4), and 2.8 (2.7) kcal mol(-1), respectively.     

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together. Extrapolation to the CBS limit is done by using two-point extrapolation methods and different basis sets (aug-cc-pVDZ - aug-cc-pVTZ, aug-cc-pVTZ - aug-cc-pVQZ, cc-pVTZ - cc-pVQZ) are utilized. The CCSD(T) correction term, determined as a difference between CCSD(T) and MP2 interaction energies, is evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of complex geometries were used, optimized or experimental ones. The JSCH-2005 benchmark set, which is now available to the chemical community, can be used for testing lower-level computational methods. For the first screening the smaller training set (S22) containing 22 model complexes can be recommended. In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted.     

Aliphatic C-H/pi interactions: Methane-benzene, methane-phenol, and methane-indole complexes

Noncovalent C-H/pi interactions are prevalent in biochemistry and are important in molecular recognition. In this work, we present potential energy curves for methane-benzene, methane-phenol, and methane-indole complexes as prototypes for interactions between C-H bonds and the aromatic components of phenylalanine, tyrosine, and tryptophan. Second-order perturbation theory (MP2) is used in conjunction with the aug-cc-pVDZ and aug-cc-pVTZ basis sets to determine the counterpoise-corrected interaction energy for selected complex configurations. Using corrections for higher-order electron correlation determined with coupled-cluster theory through perturbative triples [CCSD(T)] in the aug-cc-pVDZ basis set, we estimate, through an additive approximation, results at the very accurate CCSD(T)/aug-cc-pVTZ level of theory. Symmetry-adapted perturbation theory (SAPT) is employed to determine the physically significant components of the total interaction energy for each complex.     

Influence of Hartree-Fock exchange on the calculated Mössbauer isomer shifts and quadrupole splittings in ferrocene derivatives using density functional theory

Influence of molecular geometry, type of exchange-correlation functional, and contraction scheme of basis set applied at the iron nuclei have been tested in the calculation of 57Fe M?ssbauer isomer shifts and quadrupole splittings for a wide range of ligand types, as well as oxidation and spin states, in inorganic and organometallic systems. It has been found that uncontraction of the s-part of Wachter's full-electron basis set at the iron nuclei does not appreciably improve the calculated isomer shifts. The observed correlations for all tested sets of geometries are close to each other and predominantly depend on the employed exchange-correlation functional with B3LYP functional being slightly better as compared to BPW91. Both hybrid (B3LYP) and pure (BPW91) exchange-correlation functionals are suitable for the calculation of isomer shifts in organometallic compounds. Surprisingly, it has been found that the hybrid B3LYP exchange-correlation functional completely fails in accurate prediction of quadrupole splittings in ferrocenes, while performance of the pure BPW91 functional for the same systems was excellent. This observation has been explained on the basis of relationship between the amount of Hartree-Fock exchange involved in the applied exchange-correlation functional and the calculated HOMO-LUMO energy gap in ferrocenes. On the basis of this explanation, use of only pure exchange-correlation functionals has been suggested for accurate prediction of M?ssbauer spectra parameters in ferrocenes.     

Hydrogen peroxide clusters: the role of open book motif in cage and helical structures

Hartree-Fock (HF) calculations using 6-31G*, 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets show that hydrogen peroxide molecular clusters tend to form hydrogen-bonded cyclic and cage structures along the lines expected of a molecule which can act as a proton donor as well as an acceptor. These results are reiterated by density functional theoretic (DFT) calculations with B3LYP parametrization and also by second-order M?ller-Plesset perturbation (MP2) theory using 6-31G* and 6-311++G(d,p) basis sets. Trends in stabilization energies and geometrical parameters obtained at the HF level using 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are similar to those obtained from HF/6-31G* calculation. In addition, the HF calculations suggest the formation of stable helical structures for larger clusters, provided the neighbors form an open book structure.     

Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids

Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds.     

Dimers of boroglycine and methylamine boronic acid: a computational comparison of the relative importance of dative versus hydrogen bonding

Boronic acids are widely used in materials science, pharmacology, and the synthesis of biologically active compounds. In this Article, geometrical structures and relative energies of dimers of boroglycine, H2N-CH2-B(OH)2, and its constitutional isomer H3C-NH-B(OH)2, were computed using second-order M?ller-Plesset perturbation theory and density functional theory; Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the MP2 calculations, and the Pople 6-311++G(d,p) basis set was employed for a majority of the DFT calculations. Effects of an aqueous environment were incorporated into the results using PCM and COSMO-RS methodology. The lowest-energy conformer of the H2N-CH2-B(OH)2 dimer was a six-membered ring structure (chair conformation; Ci symmetry) with two intermolecular B:N dative-bonds; it was 14.0 kcal/mol lower in energy at the MP2/aug-cc-pVDZ computational level than a conformer with the classic eight-centered ring structure (Ci symmetry) in which the boroglycine monomers are linked by a pair of H-O...H bonds. Compared to the results of MP2 calculations with correlation-consistent basis sets, DFT calculations using the PBE1PBE and TPSS functionals with the 6-311++G(d,p) basis set were significantly better at predicting relative conformational energies of the H2N-CH2-B(OH)2 and H3C-NH-B(OH)2 dimers than corresponding calculations using the BLYP, B3LYP, OLYP, and O3LYP functionals, particularly with respect to dative-bonded structures.     

Assessment of multicoefficient correlation methods, second-order Møller-Plesset perturbation theory, and density functional theory for H3O(+)(H2O)n (n = 1-5) and OH(-)(H2O)n (n = 1-4)

We have assessed the ability of 52 methods including 15 multicoefficient correlation methods (MCCMs), two complete basis set (CBS) methods, second-order M?ller-Plesset perturbation theory (MP2) with 5 basis sets, the popular B3LYP hybrid functional with 6 basis sets, and 24 combinations of local density functional and basis set to accurately reproduce reaction energies obtained at the Weizmann-1 level of theory for hydronium, hydroxide, and pure water clusters. The three best methods overall are BMC-CCSD, G3SX(MP3), and M06-L/aug-cc-pVTZ. If only microsolvated ion data is included, M06-L/aug-cc-pVTZ is the best method; it has errors only half as large as the other density functionals. The deviations between the three best performing methods are larger for the larger hydronium- and hydroxide-containing clusters, despite a decrease in the average reaction energy, making it impossible to determine which of the three methods is overall the best, so they might be ranked in order of increasing cost, with BMC-CCSD least expensive, followed by M06-L/aug-cc-pVTZ. However, the cost for M06-L will increase more slowly as cluster size increases. This study shows that the M06-L functional is very promising for condensed-phase simulations of the transport of hydronium and hydroxide ions in aqueous solution.     

Basis set convergence of the coupled-cluster correction, δ(MP2)(CCSD(T)): best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases

In benchmark-quality studies of non-covalent interactions, it is common to estimate interaction energies at the complete basis set (CBS) coupled-cluster through perturbative triples [CCSD(T)] level of theory by adding to CBS second-order perturbation theory (MP2) a "coupled-cluster correction," δ(MP2)(CCSD(T)), evaluated in a modest basis set. This work illustrates that commonly used basis sets such as 6-31G*(0.25) can yield large, even wrongly signed, errors for δ(MP2)(CCSD(T)) that vary significantly by binding motif. Double-ζ basis sets show more reliable results when used with explicitly correlated methods to form a δ(MP2-F12)(CCSD(T(*))-F12) correction, yielding a mean absolute deviation of 0.11 kcal mol(-1) for the S22 test set. Examining the coupled-cluster correction for basis sets up to sextuple-ζ in quality reveals that δ(MP2)(CCSD(T)) converges monotonically only beyond a turning point at triple-ζ or quadruple-ζ quality. In consequence, CBS extrapolation of δ(MP2)(CCSD(T)) corrections before the turning point, generally CBS (aug-cc-pVDZ,aug-cc-pVTZ), are found to be unreliable and often inferior to aug-cc-pVTZ alone, especially for hydrogen-bonding systems. Using the findings of this paper, we revise some recent benchmarks for non-covalent interactions, namely the S22, NBC10, HBC6, and HSG test sets. The maximum differences in the revised benchmarks are 0.080, 0.060, 0.257, and 0.102 kcal mol(-1), respectively.     

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.     

Computational studies of electron paramagnetic resonance parameters for paramagnetic molybdenum complexes. 1. Method validation on small and medium-sized systems

A variety of density functional methods have been evaluated in the computation of electronic g-tensors and molybdenum hyperfine couplings for systems ranging from the Mo atom through MoIIIN, [MoVOCl4]-, and [MoVOF5]2- to two larger MoV complexes MoXLCl2 (X=O, S; L=tris(3,5-dimethylpyrazolyl)hydroborate anion). In particular, the influence of the molybdenum basis set and of various exchange-correlation functionals with variable admixtures of Hartree-Fock exchange on the computed EPR parameters have been evaluated in detail. Careful basis-set studies have provided a moderate-sized 12s6p5d all-electron basis on molybdenum that gives hyperfine tensors in excellent agreement with much larger basis sets and that will be useful for calculations on larger systems. The best agreement with experimental data for both hyperfine and g-tensors is obtained with hybrid functionals containing approximately 30-40% Hartree-Fock exchange. Only for MoSLCl2 does increasing spin contamination with increasing exact-exchange admixture restrict the achievable computational accuracy. In all cases, spin-orbit corrections to the hyperfine tensors are sizable and have to be included in accurate calculations. Scalar relativistic effects enhance the isotropic Mo hyperfine coupling by approximately 15-20%. Two-component g-tensor calculations with variational inclusion of spin-orbit coupling show that the Deltag parallel components in [MoVOCl4]- and [MoVOF5]2- depend on higher-order spin-orbit contributions and are thus described insufficiently by the usual second-order perturbation approaches. Computed orientations of g- and hyperfine tensors relative to each other and to the molecular framework for the MoXLCl2 complexes provide good agreement between theory and single-crystal electron paramagnetic resonance experiments. In these cases, the hyperfine tensor orientations are influenced only slightly by spin-orbit effects.     

Quantum-chemical calculations of carbon-isotope fractionation in CO2(g), aqueous carbonate species, and carbonate minerals

Quantum chemical calculations on large supermolecular carbonate-water and carbonate mineral clusters are used to predict equilibrium constants for 13,12C-isotope-exchange reactions between CO2(g), aqueous carbonate species, and the common carbonate minerals. For the aqueous species, we evaluate the influence of the size and conformational variability of the solvation shell, the exchange-correlation functional, and the basis set. The choice of exchange-correlation functional (PBE vs B3LYP), the basis set (6-31G* vs aug-cc-pVDZ), and solvation shell size (first shell only vs first shell and a partial second shell) each produce changes of approximately 5-10 per mil in the reduced partition function ratio. Conformational variability gives rise to a standard error of approximately 0.5 per mil using approximately 10 solute-solvent conformations. The best results are obtained with the B3LYP/aug-cc-pVDZ combination, but because the improvements in the basis set and exchange correlation functional drive the reduced partition function ratios in opposite directions, reasonably good results are also obtained with the PBE/6-31G* combination. To construct molecular clusters representative of mineral environments, a new method is introduced on the basis of conservation of Pauling bond strength. Using these clusters as models for minerals, calculations of mineral-gas and mineral-aqueous carbon-isotope fractionation factors, are in good agreement with experimental measurements. Carbon-isotope fractionation factors for gas, aqueous, and mineral phases are thus integrated into a single theoretical/computational framework.     

Basis set and electron correlation effects on the polarizability and second hyperpolarizability of model open-shell pi-conjugated systems

The basis set and electron correlation effects on the static polarizability (alpha) and second hyperpolarizability (gamma) are investigated ab initio for two model open-shell pi-conjugated systems, the C(5)H(7) radical and the C(6)H(8) radical cation in their doublet state. Basis set investigations evidence that the linear and nonlinear responses of the radical cation necessitate the use of a less extended basis set than its neutral analog. Indeed, double-zeta-type basis sets supplemented by a set of d polarization functions but no diffuse functions already provide accurate (hyper)polarizabilities for C(6)H(8) whereas diffuse functions are compulsory for C(5)H(7), in particular, p diffuse functions. In addition to the 6-31G(*)+pd basis set, basis sets resulting from removing not necessary diffuse functions from the augmented correlation consistent polarized valence double zeta basis set have been shown to provide (hyper)polarizability values of similar quality as more extended basis sets such as augmented correlation consistent polarized valence triple zeta and doubly augmented correlation consistent polarized valence double zeta. Using the selected atomic basis sets, the (hyper)polarizabilities of these two model compounds are calculated at different levels of approximation in order to assess the impact of including electron correlation. As a function of the method of calculation antiparallel and parallel variations have been demonstrated for alpha and gamma of the two model compounds, respectively. For the polarizability, the unrestricted Hartree-Fock and unrestricted second-order M?ller-Plesset methods bracket the reference value obtained at the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples level whereas the projected unrestricted second-order M?ller-Plesset results are in much closer agreement with the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples values than the projected unrestricted Hartree-Fock results. Moreover, the differences between the restricted open-shell Hartree-Fock and restricted open-shell second-order M?ller-Plesset methods are small. In what concerns the second hyperpolarizability, the unrestricted Hartree-Fock and unrestricted second-order M?ller-Plesset values remain of similar quality while using spin-projected schemes fails for the charged system but performs nicely for the neutral one. The restricted open-shell schemes, and especially the restricted open-shell second-order M?ller-Plesset method, provide for both compounds gamma values close to the results obtained at the unrestricted coupled cluster level including singles and doubles with a perturbative inclusion of the triples. Thus, to obtain well-converged alpha and gamma values at low-order electron correlation levels, the removal of spin contamination is a necessary but not a sufficient condition. Density-functional theory calculations of alpha and gamma have also been carried out using several exchange-correlation functionals. Those employing hybrid exchange-correlation functionals have been shown to reproduce fairly well the reference coupled cluster polarizability and second hyperpolarizability values. In addition, inclusion of Hartree-Fock exchange is of major importance for determining accurate polarizability whereas for the second hyperpolarizability the gradient corrections are large.     

Scaling factors for vibrational frequencies and zero-point vibrational energies of some recently developed exchange-correlation functionals

The scaling factors for the vibrational frequencies and zero-point vibrational energies evaluated at various combinations of recently developed exchange-correlation functionals and various basis sets are reported. The exchange-correlation functionals considered are B972, B98, HCTH, OLYP, O3LYP, G96LYP, PBE0 and VSXC functionals; the basis sets employed are 3-21G, 6-31G*, 6-31G**, 6-31+G, 6-311G*, 6-311G**, 6-311G(df,p), 6-311+G(df,p), cc-pVDZ and aug-cc-pVDZ. The experimental harmonic frequencies of 122 small molecules and the zero-point vibrational energies of 39 small molecules are used to determine the scaling factors through the least-square fitting procedure. It was found that the scaling factors do not depend significantly on the basis sets considered. The vibrational frequency scaling factors evaluated by using the B98 and PBE0 functionals are recommended on the basis of smallest root mean square error. The zero-point vibrational energy scaling factors evaluated from the B972 functional with Pople's double-zeta basis set and the HCTH functional with Pople's triple-zeta basis set are recommended on the basis of smallest root mean square error.     

Computational studies on ethylene addition to nickel bis(dithiolene)

The density functionals B3LYP, B3PW91, BMK, HSE06, LC-ωPBE, M05, M06, O3LYP, TPSS, ω-B97X, and ω-B97XD are used to optimize key transition states and intermediates for ethylene addition to Ni(edt)(2) (edt = S(2)C(2)H(2)). The efficacy of the basis sets 6-31G**, 6-31++G**, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ is also examined. The geometric parameters optimized with different basis sets and density functionals are similar and agree well with experimental values. The ω-B97XD functional gives relative energies closest to those from CCSD, while M06 and HSE06 yield results close to those from CCSD(T). CASSCF and CASSCF-PT2 calculation results are also given. Variation of the relative energies from different density functionals appears to arise, in part, from the multireference character of this system, as confirmed by the T1 diagnostic and CASSCF calculations.     

A new database and benchmark of the bond energies of noble-gas-containing molecules

We have developed a new database of structures and bond energies of 59 noble-gas-containing molecules. The structures were calculated by CCSD(T)/aug-cc-pVTZ methods and the bond energies were obtained using the CCSD(T)/complete basis set method. Many wavefunction-based and density functional theory methods have been benchmarked against the 59 accurate bond energies. Our results show that the MPW1B95, B2GP-PLYP, and DSD-BLYP functionals with the aug-cc-pVTZ basis set excel in predicting the bond energies of noble-gas molecules with mean unsigned errors (MUEs) of 2.0 to 2.1 kcal/mol. When combinations of Dunning's basis sets are used, the MPW1B95, B2GP-PLYP, DSD-BLYP, and BMK functionals give significantly lower MUEs of 1.6 to 1.9 kcal/mol. Doubly hybrid methods using B2GP-PLYP and DSD-BLYP functionals and MP2 calculation also provide satisfactory accuracy with MUEs of 1.4 to 1.5 kcal/mol. If the Ng bond energies and the total atomization energies of a group of 109 main-group molecules are considered at the same time, the MPW1B95/aug-cc-pVTZ single-level method (MUE = 2.7 kcal/mol) and the B2GP-PLYP and DSD-PLYP functionals with combinations of basis sets or using the doubly hybrid method (MUEs = 1.9-2.2 kcal/mol) give the overall best result.     

Theoretical study of the pyrolysis of methyltrichlorosilane in the gas phase. 2. Reaction paths and transition states

The kinetics for the previously proposed 114-reaction mechanism for the chemical vapor deposition (CVD) process that leads from methyltrichlorosilane (MTS) to silicon carbide (SiC) are examined. Among the 114 reactions, 41 are predicted to proceed with no intervening barrier. For the remaining 73 reactions, transition states and their corresponding barrier heights have been explored using second-order perturbation theory (MP2) with the aug-cc-pVDZ basis set. Final energies for the reaction barriers were obtained using both MP2 with the aug-cc-pVTZ basis set and coupled cluster theory (CCSD(T)) with the aug-cc-pVDZ basis set. CCSD(T)/aug-cc-pVTZ energies were estimated by assuming additivity of basis set and correlation effects. Partition functions for the computation of thermodynamic properties of the transition states were calculated with MP2/aug-cc-pVDZ. Forward and reverse Gibbs free energy barriers were obtained at 11 temperatures ranging from 0 to 2000 K. Important reaction pathways are illustrated at 0 and 1400 K.     

An analytical derivative procedure for the calculation of vibrational Raman optical activity spectra

We present an analytical time-dependent Hartree-Fock algorithm for the calculation of the derivatives of the electric dipole-magnetic dipole polarizability with respect to atomic Cartesian coordinates. Combined with analogous procedures to determine the derivatives of the electric dipole-electric dipole and electric dipole-electric quadrupole polarizabilities, it enables a fully analytical evaluation of the three frequency-dependent vibrational Raman optical activity (VROA) invariants within the harmonic approximation. The procedure employs traditional non-London atomic orbitals, and the gauge-origin dependence of the VROA intensities has, therefore, been assessed for the commonly used aug-cc-pVDZ and rDPS:3-21G basis sets.