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.     

The use of the hybrid density functional theory (DFT) approach for calculation of vibrational spectra: nitromethane

The molecular geometry of nitromethane was optimized and its force field and vibrational spectrum were calculated by the BECKE3LYP method. The accuracy of optimization of the geometry of MeNO₂ obtained by this method using the 6–311G(d,p) and 6–311++G(d,p) basis sets is not poorer than that obtained at the second-order Møller-Plesset level of perturbation theory (MP2). The vibrational frequencies of nitromethane and its d₁, d₂, and d₃ isotopomers obtained by the BECKE3LYP method are in much better agreement with the experimental data than those calculated at the MP2 level using the same basis set. The average absolute error of calculations performed without the use of any scaling factors is ～2% for frequencies; the maximum deviation is ～4%.     

N-methylformamide-benzene complex as a prototypical peptide N-H...pi hydrogen-bonded system: density functional theory and MP2 studies

Although the existence of peptide N-H...pi hydrogen bonds recently has been reported in protein structures, little is known about their strength and binding nature and, therefore, the relative importance of the interaction. To shed light on this binding, the N-methylformamide-benzene complex, as a model of the peptide N-H...pi hydrogen bonding, was studied by using density functional theory and M?ller-Plesset second-order perturbation (MP2) methods. The geometry of the complex was fully optimized at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels. The optimized interaction distances are about 3.6 and 3.2 A, respectively, at the two levels. The binding energy corrected by basis set superposition error with the MP2/cc-pVTZ method based on the MP2/6-31G geometry is -4.37 kcal/mol, which is as strong as the conventional hydrogen bonding. The calculated results suggest that the peptide N-H...pi hydrogen bonding is of sufficient strength to play an important role in the stabilization of protein structures. These results are helpful to better understand the characteristics and nature of the peptide N-H...pi interaction as well as to modify current force fields to better represent this special interaction.     

Intermolecular potential for thermal H2O-He collisions

Theoretical potentials for rotational excitation of H2O by He were constructed via several methods, all of which start with a large basis set SCF interaction. The semiempirical Hartree-Fock with damped dispersion (HFD) model adds a damped long-range attraction with parameters adjusted to fit experimental total differential cross sections. Purely ab initio potentials add correlation energies obtained via perturbation theory (MP2 and MP4) or a variational method (ICF1). Scattering calculations were performed on all surfaces to compare with available beam scattering and pressure broadening data and to assess sensitivity of state-to-state rates to uncertainties in the potential. From comparison with the limited experimental data, the ICF1 surface appears to be marginally better than the MP4 surface. Thermal rates calculated from this surface should be accurate to better than 50%, at least for the larger, more important rates.     

Accurate calculation of the heats of formation for large main group compounds with spin-component scaled MP2 methods

Three MP2-type electron correlation treatments and standard density functional theory (DFT) approaches are used to predict the heats of formation for a wide variety of different molecules. The SCF and MP2 calculations are performed efficiently using the resolution-of-the-identity (RI) approximation such that large basis set (i.e., polarized valence quadruple-zeta quality) treatments become routinely possible for systems with 50-100 atoms. An atom equivalent scheme that corrects the calculated atomic energies is applied to extract the "real" accuracy of the methods for chemically relevant problems. It is found that the spin-component-scaled MP2 method (SCS-MP2, J. Chem. Phys, 2003, 118, 9095) performs best and provides chemical accuracy (MAD of 1.18 kcal/mol) for a G2/97 test set of molecules. The computationally more economical SOS-MP2 variant, which retains only the opposite-spin part of the correlation energy, is slightly less accurate (MAD of 1.36 kcal/mol) than SCS-MP2. Both spin-component-scaled MP2 treatments perform significantly better than standard MP2 (MAD of 1.77 kcal/mol) and DFT-B3LYP (MAD of 2.12 kcal/mol). These conclusions are supported by results obtained for a second test set of complex systems containing 70 molecules, including charged, strained, polyhalogenated, hypervalent, and large unsaturated species (e.g. C60). For this set, DFT-B3LYP performs badly (MAD of 8.6 kcal/mol) with many errors >10-20 kcal/mol while the spin-component-scaled MP2 methods are still very accurate (MAD of 2.8 and 3.7 kcal/mol, respectively). DFT-B3LYP shows an obvious tendency to underestimate molecular stability as the system size increases. Out of six density functionals tested, the hybrid functional PBE0 performs best. All in all, the SCS-MP2 method, together with large AO basis sets, clearly outperforms current DFT approaches and seems to be the most accurate quantum chemical model that routinely can predict the thermodynamic properties of large main group compounds.     

Comparison between 6-31 + bond functions and 6-31 G* basis sets in UMP calculations of dissociation energies of the first row element compounds. I

A basis set with bond functions (6-31G + BF) has been tested for its applicability to calculation of dissociation energies of single and multiple bonds by Moeller-Plesset perturbation theory at the second and third orders. Results have been compared with those calculated in the 6-31G* basis set. The 6-31G + BF basis at the MP 2 and MP 3 levels yields better results than 6-31G* basis and the time consumption is less as well. Consideration of the bond functions on the bonds neighboring the bond being broken has no significant influence on the dissociation energies either at the SCF or at the MP 2 levels. If both reactants and products can be characterized by two-center bonds, the 6-31G + BF basis and UMP2 variant of perturbation theory can be recommended for practical calculation of D_e values, especially for the systems where the use of more exact bases is rather difficult.     

Binding energies of hydrogen-bonded complexes from extrapolation with localized basis sets

By incorporating effective basis sets containing diffuse functions only in the interaction region of hydrogen-bonded complexes into the simple extrapolation scheme suitable for such basis sets, an accurate estimation of the MP2 basis set limit hydrogen-bonding energies of formic acid tetramer, formamide tetramer, alanine-water, phenol-water, and guanine-cytosine base pair is made with all estimates falling within 0.1-0.3 kcalmol of the reference basis set limits. The basis sets for extrapolation are composed of the cc-pVDZ and cc-pVDZ plus highest polarization functions from the cc-pVTZ set, or cc-pVDZ and cc-pVTZ set, all of which are augmented by the diffuse functions of the atoms in the interaction region of hydrogen bond. In contrast to the extrapolated estimates by this method, density functional theory binding energies with B3LYP, B971, and TPSS methods yield the differences from the reference values as large as 3.9 kcalmol with much higher computational cost in most cases, signifying the efficacy of the employed extrapolation scheme for study of large hydrogen-bonded complexes.     

What are the most efficient basis set strategies for correlated wave function calculations of reaction energies and barrier heights?

As electronic structure methods are being used to obtain quantitatively accurate reaction energies and barrier heights for increasingly larger systems, the choice of an efficient basis set is becoming more critical. The optimum strategy for achieving basis set convergence can depend on the way that electron correlation is treated and can take advantage of flexibility in the order in which basis functions are added. Here we study several approaches for estimating accurate reaction energies and barrier heights from post-Hartree-Fock electronic structure calculations. First and second, we evaluate methods of estimating the basis set limit of second order Mo?ller-Plesset perturbation theory and of coupled cluster theory with single and double excitations and a quasiperturbative treatment of connected triple excitations by using explicitly correlated basis functions (in the F12a implementation) along with valence, polarization, and diffuse one-electron basis functions. Third, we test the scheme of adding a higher-order correction to MP2 results (sometimes called MP2∕CBS + ΔCCSD(T)). Finally, we evaluate the basis set requirements of these methods in light of comparisons to Weizmann-3.2, Weizmann-4, and CCSDT(2)(Q)∕CBS+CV+R results.     

Trends in R-X bond dissociation energies (R = Me, Et, i-Pr, t-Bu; X = H, CH3, OCH3, OH, F): a surprising shortcoming of density functional theory

The performance of a variety of high-level composite procedures, as well as lower-cost density functional theory (DFT)- and second-order perturbation theory (MP2)-based methods, for the prediction of absolute and relative R-X bond dissociation energies (BDEs) was examined for R = Me, Et, i-Pr and t-Bu, and X = H, CH(3), OCH(3), OH and F. The methods considered include the high-level G3(MP2)-RAD and G3-RAD procedures, a variety of pure and hybrid DFT methods (B-LYP, B3-LYP, B3-P86, KMLYP, B1B95, MPW1PW91, MPW1B95, BB1K, MPW1K, MPWB1K and BMK), standard restricted (open-shell) MP2 (RMP2), and two recently introduced variants of MP2, namely spin-component-scaled MP2 (SCS-MP2) and scaled-opposite-spin MP2 (SOS-MP2). The high-level composite procedures show very good agreement with experiment and are used to evaluate the performance of the lower-level DFT- and MP2-based procedures. The best DFT methods (KMLYP and particularly BMK) provide very reasonable predictions for the absolute heats of formation and R-X BDEs for the systems studied. However, all of the DFT methods overestimate the stabilizing effect on BDEs in going from R = Me to R = t-Bu, leading in some cases to incorrect qualitative behavior. In contrast, the MP2-based methods generally show larger errors (than the best DFT methods) in the absolute heats of formation and BDEs, but better behavior for the relative BDEs, although they do tend to underestimate the stabilizing effect on BDEs in going from R = Me to R = t-Bu. The potentially less computationally expensive SOS-MP2 method offers particular promise as a reliable method that might be applicable to larger systems.     

Experimental versus Calculated Proton Affinities for Aromatic Carboxylic Acid Anions and Related Phenide Ions

Herein, we present the comparison of a large set of experimentally measured proton affinity (PA) values for 65 aromatic carboxylate anions with the values calculated by using selected popular DFT (B3LYP, PBE0, and M05‐2X) and composite [G3(MP2), G4(MP2)] quantum chemistry methods. The root‐mean‐square error (RMSE) values for the chosen methods are RMSE_PBE0=1.7, RMSE_B3LYP=4.6, RMSE_M05‐2X=6.6, RMSE_G3MP2=6.3, RMSE_G4MP2=4.5 kJ mol^?1. In the second part of the study, 82 PA values for substituted phenide ions and a few heteroaromatic anions were calculated. Again, very good agreement between the calculated and experimental values has been observed: RMSE_PBE0=1.9, RMSE_B3LYP=4.5, RMSE_M05‐2X=6.3, RMSE_G3MP2=4.9, RMSE_G4MP2=5.5 kJ mol^?1. Our results show that, for medium‐sized carboxylate anions, all tested methods give reliable results and, surprisingly, much more computationally demanding composite methods do not perform significantly better than the time‐efficient DFT methods.     

Optimized accurate auxiliary basis sets for RI-MP2 and RI-CC2 calculations for the atoms Rb to Rn

The introduction of the resolution-of-the-identity (RI) approximation for electron repulsion integrals in quantum chemical calculations requires in addition to the orbital basis so-called auxiliary or fitting basis sets. We report here such auxiliary basis sets optimized for second-order Møller–Plesset perturbation theory for the recently published (Weigend and Ahlrichs Phys Chem Chem Phys, 2005, 7, 3297–3305) segmented contracted Gaussian basis sets of split, triple-ζ and quadruple-ζ valence quality for the atoms Rb–Rn (except lanthanides). These basis sets are designed for use in connection with small-core effective core potentials including scalar relativistic corrections. Hereby accurate resolution-of-the-identity calculations with second-order Møller–Plesset perturbation theory (MP2) and related methods can now be performed for molecules containing elements from H to Rn. The error of the RI approximation has been evaluated for a test set of 385 small and medium sized molecules, which represent the common oxidation states of each element, and is compared with the one-electron basis set error, estimated based on highly accurate explicitly correlated MP2–R12 calculations. With the reported auxiliary basis sets the RI error for MP2 correlation energies is typically two orders of magnitude smaller than the one-electron basis set error, independent on the position of the atoms in the periodic table.     

A new scheme for determining the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of glycine and alanine peptides

In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.     

Bond dissociation energies and radical stabilization energies: an assessment of contemporary theoretical procedures

Various contemporary theoretical procedures have been tested for their accuracy in predicting the bond dissociation energies (BDEs) and the radical stabilization energies (RSEs) for a test set of 22 monosubstituted methyl radicals. The procedures considered include the high-level W1, W1', CBS-QB3, ROCBS-QB3, G3(MP2)-RAD, and G3X(MP2)-RAD methods, unrestricted and restricted versions of the double-hybrid density functional theory (DFT) procedures B2-PLYP and MPW2-PLYP, and unrestricted and restricted versions of the hybrid DFT procedures BMK and MPWB1K, as well as the unrestricted DFT procedures UM05 and UM05-2X. The high-level composite procedures show very good agreement with experiment and are used to evaluate the performance of the comparatively less expensive DFT procedures. RMPWB1K and both RBMK and UBMK give very promising results for absolute BDEs, while additionally restricted and unrestricted X2-PLYP methods and UM05-2X give excellent RSE values. UM05, UB2-PLYP, UMPW2-PLYP, UM05-2X, and UMPWB1K are among the less well performing methods for BDEs, while UMPWB1K and UM05 perform less well for RSEs. The high-level theoretical results are used to recommend alternative experimental BDEs for propyne, acetaldehyde, and acetic acid.     

High level of ab initio and density functional theory computational study of structural and energetic properties of tetrafluorhydrazine rotamers

The HF, MP2, MP3, MP4, and QCISD ab initio methods were compared with local, hybrid, and gradient-corrected density functional theory (DFT) methods for computing structures and energies of N2F4 rotamers. In all DFT calculations 6-311 + G(2d) basis set was used. The generated structures energies of trans- and gauche-N₂F₄ rotamers, and their dissociation energies to nitrogen difluoride were compared with experimental data. Suitable hybrid and gradient-corrected DFT methods for determining structures and energies for these and similar molecular systems were discussed.     

Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: effect of dispersion and BSSE

We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded "closed-book" conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n=D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M05-2X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds.     

General orbital invariant MP2-F12 theory

A general form of orbital invariant explicitly correlated second-order closed-shell Moller-Plesset perturbation theory (MP2-F12) is derived, and compact working equations are presented. Many-electron integrals are avoided by resolution of the identity (RI) approximations using the complementary auxiliary basis set approach. A hierarchy of well defined levels of approximation is introduced, differing from the exact theory by the neglect of terms involving matrix elements over the Fock operator. The most accurate method is denoted as MP2-F12/3B. This assumes only that Fock matrix elements between occupied orbitals and orbitals outside the auxiliary basis set are negligible. For the chosen ansatz for the first-order wave function this is exact if the auxiliary basis is complete. In the next lower approximation it is assumed that the occupied orbital space is closed under action of the Fock operator [generalized Brillouin condition (GBC)]; this is equivalent to approximation 2B of Klopper and Samson [J. Chem. Phys. 116, 6397 (2002)]. Further approximations can be introduced by assuming the extended Brillouin condition (EBC) or by neglecting certain terms involving the exchange operator. A new approximation MP2-F12/3C, which is closely related to the MP2-R12/C method recently proposed by Kedzuch et al. [Int. J. Quantum Chem. 105, 929 (2005)] is described. In the limit of a complete RI basis this method is equivalent to MP2-F12/3B. The effect of the various approximations (GBC, EBC, and exchange) is tested by studying the convergence of the correlation energies with respect to the atomic orbital and auxiliary basis sets for 21 molecules. The accuracy of relative energies is demonstrated for 16 chemical reactions. Approximation 3C is found to perform equally well as the computationally more demanding approximation 3B. The reaction energies obtained with smaller basis sets are found to be most accurate if the orbital-variant diagonal Ansatz combined with localized orbitals is used for the first-order wave function. This unexpected result is attributed to geminal basis set superposition errors present in the formally more rigorous orbital invariant methods.     

Density functional theory and post-Hartree-Fock studies on molecular structure and harmonic vibrational spectrum of formaldehyde

Density functional theory (DFT) with the Becke's three-parameter exchange correlation functional and the functional of Lee, Yang and Parr, gradient-corrected functionals of Perdew, and Perdew and Wang [the DFT(B3LYP), DFT(B3P86) and DFT(B3PW91) methods, respectively], and several levels of conventional ab initio post-Hartree-Fock theory (second- and fourth-order perturbation theory M?ller-Plesset MP2 and MP4(SDTQ), coupled cluster with the single and double excitations (CCSD), and CCSD with perturbative triple excitation [CCSD(T)], configuration interaction with the single and double excitations [CISD], and quadratic configuration interaction method [QCISD(T)], using several basis sets [ranging from a simple 6-31G(d,p) basis set to a 6-311+ +G(3df, 2pd) one], were applied to study of the molecular structure (geometrical parameters, rotational constants, dipole moment) and harmonized infrared (IR) spectrum of formaldehyde (CH₂O). High-level ab initio methods CCSD(T) and QCISD(T) with the 6-311+ +G(3df, 2pd) predict correctly molecular parameters, vibrational harmonic wavenumbers and the shifts of the harmonic IR spectrum of ¹²CH₂ ¹⁶O upon isotopic substitution. Received: 30 January 1997 / Accepted: 7 May 1997     

Analytic derivatives for perturbatively corrected "double hybrid" density functionals: theory, implementation, and applications

A recently proposed new family of density functionals [S. Grimme, J. Chem. Phys. 124, 34108 (2006)] adds a fraction of nonlocal correlation as a new ingredient to density functional theory (DFT). This fractional correlation energy is calculated at the level of second-order many-body perturbation theory (PT2) and replaces some of the semilocal DFT correlation of standard hybrid DFT methods. The new "double hybrid" functionals (termed, e.g., B2-PLYP) contain only two empirical parameters that have been adjusted in thermochemical calculations on parts of the G2/3 benchmark set. The methods have provided the lowest errors ever obtained by any DFT method for the full G3 set of molecules. In this work, the applicability of the new functionals is extended to the exploration of potential energy surfaces with analytic gradients. The theory of the analytic gradient largely follows the standard theory of PT2 gradients with some additional subtleties due to the presence of the exchange-correlation terms in the self-consistent field operator. An implementation is reported for closed-shell as well as spin-unrestricted reference determinants. Furthermore, the implementation includes external point charge fields and also accommodates continuum solvation models at the level of the conductor like screening model. The density fitting resolution of the identity (RI) approximation can be applied to the evaluation of the PT2 part with large gains in computational efficiency. For systems with approximately 500-600 basis functions the evaluation of the double hybrid gradient is approximately four times more expensive than the calculation of the standard hybrid DFT gradient. Extensive test calculations are provided for main group elements and transition metal containing species. The results reveal that the B2-PLYP functional provides excellent molecular geometries that are superior compared to those from standard DFT and MP2.