Coordination of methanol clusters to benzene: a computational study

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.     

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.     

Competing non-covalent interactions in alkali metal ion-acetonitrile-water clusters

Competitive ion-dipole, ion-water, and water-water interactions were investigated at the molecular level in M+ (CH3CN)n(H2O)m cluster ions for M = Na and K. Different [n,m] combinations for two different n + m cluster sizes were characterized with infrared predissociation spectroscopy in the O-H stretch region and MP2 calculations. In all cases, no differences were observed between the two alkali metal ions. The results showed that at the n + m = 4 cluster size, the solvent molecules interact only with the ion, and that the interaction between the ion and the large dipole moment of CH3CN decreases the ion-water electrostatic interactions. At the n + m = 5 cluster size, at least two different hydrogen-bonded structures were identified. In these structures, the ion-dipole interaction weakens the ability of the ion to polarize the hydrogen bonds and thus decreases the strength of the water-water interactions in the immediate vicinity of the alkali metal ion.     

可快速计算水团簇三体作用强度的新方法

将水分子视为由2个O—H键偶极构成, 再将水分子间的三体作用视为长程诱导作用和短程校正之和, 使用Thole模型计算长程诱导作用, 通过同时考虑不同水分子间的置换和同一个水分子中2个键偶极间的置换计算短程校正, 从而提出了一个可快速计算水团簇三体作用强度的新方法. 根据已报道的12347个水三聚体的结构和CCSD(T)三体作用能, 确定了该方法所需参数. 将该方法和所确定的参数应用于67个水团簇体系, 计算这些体系的三体作用能, 并与CCSD(T), MP2, M06-2X方法的计算结果进行比较. 结果表明, 相对于CCSD(T)方法的总三体作用能, 本文方法的均方根偏差(RMSD)仅为3.32 kJ/mol, 平均相对偏差(MRD)仅为2.43%; 对较大水团簇体系, 该方法计算精度稍优于MP2方法, 明显优于M06-2X方法, 并且更快捷高效.     

Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center

The potential energy profiles of five selected bimolecular nucleophilic substitution (S_N2) reactions at nitrogen (N) center have been reinvestigated with the CCSD(T), G3[MP2,CCSD(T)], MP2, and some density functional methods. The basis sets of 6‐31+G(d,p) and 6‐311+G(3d,2p) are used for the MP2 and density functional calculations. Taking the relative energies at the CCSD(T)/CBS level of theory as benchmarks, we recommend the MP2, B97‐K, B2K‐PLYP, BMK, ωB97X‐D, M06‐2X, M05‐2X, CAM‐B3LYP, M08‐SO, and ωB97X methods to generally characterize the potential energy profiles for the S_N2 reactions at N center. Furthermore, these recommended methods with the relatively small 6‐31+G(d,p) basis set may also be used to perform direct classical trajectory simulations to uncover the dynamic behaviors of the S_N2 reactions at N center. © 2012 Wiley Periodicals, Inc.     

Highly Accurate CCSD(T) and DFT–SAPT Stabilization Energies of H‐Bonded and Stacked Structures of the Uracil Dimer

The CCSD(T) interaction energies for the H‐bonded and stacked structures of the uracil dimer are determined at the aug‐cc‐pVDZ and aug‐cc‐pVTZ levels. On the basis of these calculations we can construct the CCSD(T) interaction energies at the complete basis set (CBS) limit. The most accurate energies, based either on direct extrapolation of the CCSD(T) correlation energies obtained with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets or on the sum of extrapolated MP2 interaction energies (from aug‐cc‐pVTZ and aug‐cc‐pVQZ basis sets) and extrapolated ΔCCSD(T) correction terms [difference between CCSD(T) and MP2 interaction energies] differ only slightly, which demonstrates the reliability and robustness of both techniques. The latter values, which represent new standards for the H‐bonding and stacking structures of the uracil dimer, differ from the previously published data for the S22 set by a small amount. This suggests that interaction energies of the S22 set are generated with chemical accuracy. The most accurate CCSD(T)/CBS interaction energies are compared with interaction energies obtained from various computational procedures, namely the SCS–MP2 (SCS: spin‐component‐scaled), SCS(MI)–MP2 (MI: molecular interaction), MP3, dispersion‐augmented DFT (DFT–D), M06–2X, and DFT–SAPT (SAPT: symmetry‐adapted perturbation theory) methods. Among these techniques, the best results are obtained with the SCS(MI)–MP2 method. Remarkably good binding energies are also obtained with the DFT–SAPT method. Both DFT techniques tested yield similarly good interaction energies. The large magnitude of the stacking energy for the uracil dimer, compared to that of the benzene dimer, is explained by attractive electrostatic interactions present in the stacked uracil dimer. These interactions force both subsystems to approach each other and the dispersion energy benefits from a shorter intersystem separation.     

Conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete

The conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory, and density functional theory and employing the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single-point fourth-order perturbation theory, CCSD, and CCSD(T) calculations employing the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectfully, to ascertain the contribution of higher order correlation. Three DFT functionals, B3LYP, wB97XD, and M06-2X, are employed to determine whether they can yield results similar to those obtained at the CCSD(T) level.     

Assessment of the accuracy of density functionals for prediction of relative energies and geometries of low-lying isomers of water hexamers

Water hexamers provide a critical testing ground for validating potential energy surface predictions because they contain structural motifs not present in smaller clusters. We tested the ability of 11 density functionals (four of which are local and seven of which are nonlocal) to accurately predict the relative energies of a series of low-lying water hexamers, relative to the CCSD(T)/aug'-cc-pVTZ level of theory, where CCSD(T) denotes coupled cluster theory with an interative treatment of single and double excitations and a quasi-perturbative treatment of connected triple excitations. Five of the density functionals were tested with two different basis sets, making a total of 16 levels of density functional theory (DFT) tested. When single-point energy calculations are carried out on geometries obtained with second-order M?ller-Plesset perturbation theory (MP2), only three density functionals, M06-L, M05-2X, and M06-2X, are able to correctly predict the relative energy ordering of the hexamers. These three functionals predict that the range of energies spanned by the six isomers is 3.2-5.6 kcal/mol, whereas the other eight functionals predict ranges of 1.0-2.4 kcal/mol; the benchmark value for this range is 3.1 kcal/mol. When the hexamers are optimized at each level of theory, all methods are able to reproduce the MP2 geometries well for all isomers except the boat and bag isomers, and DFT optimization changes the energy ordering for seven of the 16 methods tested. The addition of zero-point energy changes the energy ordering for all of the density functionals studied except for M05-2X and M06-2X. The variation in relative energies predicted by the different methods highlights the necessity for exercising caution in the choice of density functionals used in future studies. Of the 11 density functionals tested, the most accurate results for energies were obtained with the PWB6K, MPWB1K, and M05-2X functionals.     

Accuracy and limitations of second-order many-body perturbation theory for predicting vertical detachment energies of solvated-electron clusters

Vertical electron detachment energies (VDEs) are calculated for a variety of (H(2)O)(n)(-) and (HF)(n)(-) isomers, using different electronic structure methodologies but focusing in particular on a comparison between second-order M?ller-Plesset perturbation theory (MP2) and coupled-cluster theory with noniterative triples, CCSD(T). For the surface-bound electrons that characterize small (H(2)O)(n)(-) clusters (n< or = 7), the correlation energy associated with the unpaired electron grows linearly as a function of the VDE but is unrelated to the number of monomers, n. In every example considered here, including strongly-bound "cavity" isomers of (H(2)O)(24)(-), the correlation energy associated with the unpaired electron is significantly smaller than that associated with typical valence electrons. As a result, the error in the MP2 detachment energy, as a fraction of the CCSD(T) value, approaches a limit of about -7% for (H(2)O)(n)(-) clusters with VDEs larger than about 0.4 eV. CCSD(T) detachment energies are bounded from below by MP2 values and from above by VDEs calculated using second-order many-body perturbation theory with molecular orbitals obtained from density functional theory. For a variety of both strongly- and weakly-bound isomers of (H(2)O)(20)(-) and (H(2)O)(24)(-), including both surface states and cavity states, these bounds afford typical error bars of +/-0.1 eV. We have found only one case where the Hartree-Fock and density functional orbitals differ qualitatively; in this case the aforementioned bounds lie 0.4 eV apart, and second-order perturbation theory may not be reliable.     

Stabilisation energy of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels

Stabilisation energies of stacked structures of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, CN) complexes were determined at the CCSD(T) complete basis set (CBS) limit level. These energies were constructed from MP2/CBS stabilisation energies and a CCSD(T) correction term determined with a medium basis set (6-31G**). The former energies were extrapolated using the two-point formula of Helgaker et al. from aug-cc-pVDZ and aug-cc-pVTZ Hartree-Fock energies and MP2 correlation energies. The CCSD(T) correction term is systematically repulsive. The final CCSD(T)/CBS stabilisation energies are large, considerably larger than previously calculated and increase in the series as follows: hexafluorobenzene (6.3 kcal mol(-1)), hexachlorobenzene (8.8 kcal mol(-1)), hexabromobenzene (8.1 kcal mol(-1)) and hexacyanobenzene (11.0 kcal mol(-1)). MP2/SDD** relativistic calculations performed for all complexes mentioned and also for benzene[dot dot dot]hexaiodobenzene have clearly shown that due to relativistic effects the stabilisation energy of the hexaiodobenzene complex is lower than that of hexabromobenzene complex. The decomposition of the total interaction energy to physically defined energy components was made by using the symmetry adapted perturbation treatment (SAPT). The main stabilisation contribution for all complexes investigated is due to London dispersion energy, with the induction term being smaller. Electrostatic and induction terms which are attractive are compensated by their exchange counterparts. The stacked motif in the complexes studied is very stable and might thus be valuable as a supramolecular synthon.     

Accurate binding energies of hydrogen,halogen, and dihydrogen bonded complexes and cation enhanced binding strengths

Interaction energy (E_int) values of a variety of hydrogen, halogen, and dihydrogen bonded complexes in the weak, medium, and strong regimes have been computed using W1BD, MP2, M06L density functional theory, and hybrid methods MP4//MP2, MP4//M06L, and CCSD(T)//MP2. W1BD level E_int and CCSD(T) results reported in the literature show very good agreement (mean absolute deviation = 0.19 kcal/mol). MP2 underestimates E_int while M06L shows accurate behavior for all except halogen and charge‐assisted hydrogen bonds. MP4//MP2, MP4//M06L, and CCSD(T)//MP2 yield E_int very close to those obtained from W1BD. The high accuracy energy data at MP4/MP2 is used to study the effect of a cation (Li⁺, NH₄⁺) on the E_int. The cation enhances electron donation from the donor to noncovalent bonding region leading to substantial enhancement in E_int (～141–566% for Li⁺ and ～105–539% for NH₄⁺) and promotes a noncovalent bond in the weak regime to medium regime and that in the medium regime to strong regime. © 2014 Wiley Periodicals, Inc.     

Halogen bonds with benzene: An assessment of DFT functionals

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes. © 2013 Wiley Periodicals, Inc.     

Comparison of experimental and computationally predicted sulfoxide bond dissociation enthalpies

The accurate estimation of S-O bond dissociation enthalpies (BDE) of sulfoxides by computational chemistry methods has been a significant challenge. One of the primary causes for this challenge is the well-established requirement of including high-exponent d functions in the sulfur basis set for accurate energies. Unfortunately, even when high-exponent d functions were included in Pople-style basis sets, the relative strength of experimentally determined S-O BDE was incorrectly predicted. The aug-cc-pV(n+d)Z basis sets developed by Dunning include an additional high-exponent d function on sulfur. Thus, it was expected that the aug-cc-pV(n+d)Z basis sets would improve the prediction of sulfoxide S-O BDE. This study presents the S-O BDE predicted by B3LYP, CCSD, CCSD(T), M05-2X, M06-2X, and MP2 combined with aug-cc-pV(n+d)Z, aug-cc-pVnZ, and Pople-style basis sets. The accuracy of these predictions was determined by comparing the computationally predicted values to the experimentally determined S-O BDE. Values within experimental error were obtained for dialkyl sulfoxides when the S-O BDEs were estimated using an isodesmic oxygen transfer reaction at the M06-2X/aug-cc-pV(T+d)Z level of theory. However, the S-O BDE of divinyl sulfoxide was overestimated by this method.     

Performance of spin-component-scaled Møller-Plesset theory (SCS-MP2) for potential energy curves of noncovalent interactions

An examination of the performance of density-fitted, spin-component-scaled, second-order M?ller-Plesset theory (SCS-MP2), SCS-MP2 with parameters optimized for nucleic acids (SCSN-MP2), and their local-correlation variants, SCS-LMP2 and SCSN-LMP2, is presented for the sandwich and T-shaped benzene dimers, the methane-benzene and H(2)S-benzene complexes, and the methane dimer over entire potential energy curves. These are compared to benchmark-quality estimates of the complete-basis-set limit for coupled-cluster theory through perturbative triple excitations, CCSD(T)/CBS. With the exception of the methane dimer, SCSN-LMP2/CBS tends to outperform SCS-LMP2/CBS with maximum relative errors of 6 and 18%, respectively, at the optimal CCSD(T)/CBS intermolecular distances. For the methane dimer, errors for SCS(N)-(L)MP2/CBS remain in the 0.2-0.3 kcal mol(-1) range, corresponding to a larger relative error of 40-50%. Although the local MP2 methods perform very similarly to their conventional counterparts when aug-cc-pVTZ or larger basis sets are used, in the absence of counterpoise correction the local approximation becomes significantly worse for the aug-cc-pVDZ basis set. The changes due to local correlation approximations for the aug-cc-pVDZ basis are reduced when diffuse functions are neglected for hydrogen atoms.     

Coupled cluster,B2PLYP and M06-2X investigation of the thermochemistry of five-membered nitrogen containing heterocycles,furan, and thiophene

Herein, the thermochemical properties of five-membered rings heterocycles were studied employing the CCSD(T) methodology coupled with the correlation consistent basis sets and including corrections for relativistic and core-valence effects as well as anharmonicities of the potentials. For pyrrole, furan, imidazole, pyrazole, 1H-1,2,4-triazole, and 1H-tetrazole, the mean absolute deviation (MAD) of the \Updelta \textH_{\textf, 2 9 8}^\texto \Updelta {\text{H}}_{{{\text{f}}, 2 9 8}}^{\text{o}} , computed at the CCSD(T) level, is 0.5 kcal/mol with respect to the experimental values. In the case of 1H-1,2,3-triazole, 2H-1,2,3-triazole, 4H-1,2,3-triazole, 4H-1,2,4-triazole, 2H-tetrazole, and pentazole, we propose the following \Updelta \textH_{\textf, 2 9 8}^\texto \Updelta {\text{H}}_{{{\text{f}}, 2 9 8}}^{\text{o}} : 62.6, 59.2, 85.0, 54.2, 77.7, and 107.5 kcal/mol, respectively. For thiophene, we revisit our previous result and propose a value of 26.0 kcal/mol. The theoretical estimations were used to study the performance of the M06-2X and B2PLYP functionals. Also, the convergence toward the complete basis set limit (CBS) was analyzed. M06-2X did not show a smooth convergence toward the CBS limit. Particularly, for the cc-pVTZ and cc-pVQZ basis sets, some problems were detected. Yet, along the cc-pVQZ, cc-pV5Z, and cc-pV6Z basis sets, the TAE smoothly decreased. The diminution of the TAE upon increase in basis set was not expected because the opposite behavior is more frequently observed. The MAD of the total atomization energies determined at the M06-2X level was 0.42 kcal/mol, with respect to the CCSD(T) results. In the case of the double hybrid B2PLYP functional, a smooth convergence toward the CBS limit was detected, even though the performance seriously degradated when the basis set was increased. At the CBS limit, the MAD with respect to the CCSD(T) TAEs was 8.26 kcal/mol.     

Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with ab initio theory

We have carried out extensive calculations for neutral, cationic protonated, anionic deprotonated phenol dimers. The structures and energetics of this system are determined by the delicate competition between H-bonding, H-π interaction and π-π interaction. Thus, the structures, binding energies and frequencies of the dimers are studied by using a variety of functionals of density functional theory (DFT) and M?ller-Plesset second order perturbation theory (MP2) with medium and extended basis sets. The binding energies are compared with those of highly reliable coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit. The neutral phenol dimer is unique in the sense that its experimental rotational constants have been measured. The geometry of the neutral phenol dimer is governed by the hydrogen bond formed by two hydroxyl groups and the H-π interaction between two aromatic rings, while the structure of the protonated/deprotonated phenol dimers is additionally governed by the electrostatic and induction effects due to the short strong hydrogen bond (SSHB) and the charges populated in the aromatic rings in the ionic systems. Our salient finding is the substantial differences in structure between neutral, protonated, and deprotonated phenol dimers. This is because the neutral dimer involves in both H(π)···O and H(π)···π interactions, the protonated dimer involves in H(π)···π interactions, and the deprotonated dimer involves in a strong H(π)···O interaction. It is important to compare the reliability of diverse computational approaches employed in quantum chemistry on the basis of the calculational results of this system. MP2 calculations using a small cc-pVDZ basis set give reasonable structures, but those using extended basis sets predict wrong π-stacked structures due to the overestimation of the dispersion energies of the π-π interactions. A few new DFT functionals with the empirical dispersion give reliable results consistent with the CCSD(T)/CBS results. The binding energies of the neutral, cationic protonated, and anionic deprotonated phenol dimers are estimated to be more than 28.5, 118.2, and 118.3 kJ mol(-1), respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.     

Theoretical study of Pt(PR3)(2)(AlCl3) (R = H, Me, Ph, or Cy) including an unsupported bond between transition metal and non-transition metal elements: geometry, bond strength, and prediction

The molecular structure and the binding energy of Pt(PR(3))(2)(AlCl(3)) (R = H, Me, Ph, or Cy) were investigated by DFT, MP2 to MP4(SDTQ), and CCSD(T) methods. The optimized structure of Pt(PCy(3))(2)(AlCl(3)) (Cy = cyclohexyl) by the DFT method with M06-2X and LC-BLYP functionals agrees well with the experimental one. The MP4(SDTQ) and CCSD(T) methods present similar binding energies (BE) of Pt(PH(3))(2)(AlCl(3)), indicating that these methods provide reliable BE value. The DFT(M06-2X)-calculated BE value is close to the MP4(SDTQ) and CCSD(T)-calculated values, while the other functionals present BE values considerably different from the MP4(SDTQ) and CCSD(T)-calculated values. All computational methods employed here indicate that the BE values of Pt(PMe(3))(2)(AlCl(3)) and Pt(PPh(3))(2)(AlCl(3)) are considerably larger than those of the ethylene analogues. The coordinate bond of AlCl(3) with Pt(PR(3))(2) is characterized to be the σ charge transfer (CT) from Pt to AlCl(3). This complex has a T-shaped structure unlike the well-known Y-shaped structure of Pt(PMe(3))(2)(C(2)H(4)), although both are three-coordinate Pt(0) complex. This T-shaped structure results from important participation of the Pt d(σ) orbital in the σ-CT; because the Pt d(σ) orbital energy becomes lower as the P-Pt-P angle decreases, the T-shaped structure is more favorable for the σ-CT than is the Y-shaped structure. [Co(alcn)(2)(AlCl(3))](-) (alcn = acetylacetoneiminate) is theoretically predicted here as a good candidate for the metal complex, which has an unsupported M-Al bond because its binding energy is calculated to be much larger than that of Pt(PCy(3))(2)(AlCl(3)).     

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

Stacking energies in low-energy geometries of pyrimidine, uracil, cytosine, and guanine homodimers were determined by the MP2 and CCSD(T) calculations utilizing a wide range of split-valence, correlation-consistent, and bond-functions basis sets. Complete basis set MP2 (CBS MP2) stacking energies extrapolated using aug-cc-pVXZ (X = D, T, and for pyrimidine dimer Q) basis sets equal to -5.3, -12.3, and -11.2 kcal/mol for the first three dimers, respectively. Higher-order correlation corrections estimated as the difference between MP2 and CCSD(T) stacking energies amount to 2.0, 0.7, and 0.9 kcal/mol and lead to final estimates of the genuine stacking energies for the three dimers of -3.4, -11.6, and -10.4 kcal/mol. The CBS MP2 stacking-energy estimate for guanine dimer (-14.8 kcal/mol) was based on the 6-31G(0.25) and aug-cc-pVDZ calculations. This simplified extrapolation can be routinely used with a meaningful accuracy around 1 kcal/mol for large aromatic stacking clusters. The final estimate of the guanine stacking energy after the CCSD(T) correction amounts to -12.9 kcal/mol. The MP2/6-31G(0.25) method previously used as the standard level to calculate aromatic stacking in hundreds of geometries of nucleobase dimers systematically underestimates the base stacking by ca. 1.0-2.5 kcal/mol per stacked dimer, covering 75-90% of the intermolecular correlation stabilization. We suggest that this correction is to be considered in calibration of force fields and other cheaper computational methods. The quality of the MP2/6-31G(0.25) predictions is nevertheless considerably better than suggested on the basis of monomer polarizability calculations. Fast and very accurate estimates of the MP2 aromatic stacking energies can be achieved using the RI-MP2 method. The CBS MP2 calculations and the CCSD(T) correction, when taken together, bring only marginal changes to the relative stability of H-bonded and stacked base pairs, with a slight shift of ca. 1 kcal/mol in favor of H-bonding. We suggest that the present values are very close to ultimate predictions of the strength of aromatic base stacking of DNA and RNA bases.