Manoj K. Kesharwani

Benchmark ab Initio Conformational Energies for the Proteinogenic Amino Acids through Explicitly Correlated Methods. Assessment of Density Functional Methods

The relative energies of the YMPJ conformer database of the 20 proteinogenic amino acids, with N- and C-termination, have been re-evaluated using explicitly correlated coupled cluster methods. Lower-cost ab initio methods such as MP2-F12 and CCSD-F12b actually are outperformed by double-hybrid DFT functionals; in particular, the DSD-PBEP86-NL double hybrid performs well enough to serve as a secondary standard. Among range-separated hybrids, ωB97X-V performs well, while B3LYP-D3BJ does surprisingly well among traditional DFT functionals. Treatment of dispersion is important for the DFT functionals; for the YMPJ set, D3BJ generally works as well as the NL nonlocal dispersion functional. Basis set sensitivity for DFT calculations on these conformers is weak enough that def2-TZVP is generally adequate. For conformer corrections to heats of formation, B3LYP-D3BJ and especially DSD-PBEP86-D3BJ or DSD-PBEP86-NL are adequate for all but the most exacting applications. The revised geometries and energetics for the YMPJ database have been made available as Supporting Information and should be useful in the parametrization and validation of molecular mechanics force fields and other low-cost methods. The very recent dRPA75 method yields good performance, without resorting to an empirical dispersion correction, but is still outperformed by DSD-PBEP86-D3BJ and particularly DSD-PBEP86-NL. Core-valence corrections are comparable in importance to improvements beyond CCSD(T*)/cc-pVDZ-F12 in the valence treatment.

The cc-pV5Z-F12 basis set: reaching the basis set limit in explicitly correlated calculations

We have developed and benchmarked a new extended basis set for explicitly correlated calculations, namely cc-pV5Z-F12. It is offered in two variants, cc-pV5Z-F12 and cc-pV5Z-F12(rev2), the latter of which has additional basis functions on hydrogen not present in the cc-pVnZ-F12 (n = D,T,Q) sequence. A large uncontracted ‘reference’ basis set is used for benchmarking. cc-pVnZ-F12 (n = D–5) is shown to be a convergent hierarchy. Especially the cc-pV5Z-F12(rev2) basis set can yield the valence CCSD (coupled cluster with all single and double substitutions) component of total atomisation energies, without any extrapolation, to an accuracy normally associated with aug-cc-pV{5,6}Z extrapolations. Hartree-Fock self-consistent field (SCF) components are functionally at the basis set limit, while the MP2 limit can be approached to as little as 0.01 kcal/mol without extrapolation. The determination of (T) appears to be the most difficult of the three components and cannot presently be accomplished without extrapolation or scaling. (T) extrapolation from cc-pV{T,Q}Z-F12 basis sets, combined with CCSD-F12b/cc-pV5Z-F12 calculations, appears to be an accurate combination for explicitly correlated thermochemistry. For accurate work on noncovalent interactions, the basis set superposition error with the cc-pV5Z-F12 basis set is shown to be so small that counterpoise corrections can be neglected for all but the most exacting purposes.

Explicitly correlated coupled cluster benchmarks with realistic-sized ligands for some late-transition metal reactions: basis sets convergence and performance of more approximate methods

CCSD(T)-F12b benchmark calculations have been performed for the energetics and barrier heights of three late-transition metal systems, in increasing order of size: oxidative additions at bare Pd, a model for the Grubbs catalyst, and competitive CC/CH activation by a Rh(PCP) pincer complex. The results depend weakly on the basis set on the main-group atoms but are rather more sensitive to the basis set on the metal. An aug-cc-pwCVTZ-PP set on the metal combined with cc-pVTZ-F12 on the main-group elements yields barriers that are effectively converged in the basis set, but even the combination with aug-cc-pwCVTZ-PP on the metal and cc-pVDZ-F12 on the main group, or of def2-TZVPP on the metal and def2-TZVP on the main group, works well enough for most benchmark purposes. Inner-shell correlation cannot be neglected for even semi-accurate work. Simple nonempirical (meta-)GGAs with D3BJ dispersion work quite well for the Grubbs and pincer cases but break down for the Pd example, which requires exact exchange. Hybrids of these same functionals, such as PBE0, TPSS0, and B3PW91, are among the best performers through rung four on Perdew’s ladder. For the Grubbs case, dispersion is very important and D3BJ clearly is superior over D2. Only the DSD double hybrids consistently perform well in the absence of dispersion corrections.

Assessment of CCSD(T)-F12 Approximations and Basis Sets for Harmonic Vibrational Frequencies.

We consider basis set convergence and the effect of various approximations to CCSD(T)-F12 for a representative sample of harmonic frequencies (the HFREQ2014 set). CCSD(T*)(F12*)/cc-pVDZ-F12 offers a particularly favorable compromise between accuracy and computational cost: its RMSD <3 cm(-1) from the valence CCSD(T) limit is actually less than the remaining discrepancy with the experimental value at the valence CCSD(T) limit (about 5 cm(-1) RMSD). CCSD(T)-F12a and CCSD(T)-F12b appear to benefit from error compensation between CCSD and (T).

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions.

Significance Chiral molecules are the building blocks of life. Although artificially, it is difficult to separate two different enantiomers of the same molecules; in nature, this process is efficient. This work proposes a mechanism for understanding this efficiency. In many bioprocesses, the interactions between molecules result from electron reorganization in the molecules, like that which occurs when an external electric field is applied. We show that the charge reorganization in chiral molecules is accompanied by a polarization of the spins associated with the displaced charge. The symmetry constraints imposed by the spin polarization may help account for the enantioselectivity. Calculations indicate that this contribution to the interaction energy for two molecules of the same handedness can be comparable with the available thermal energy. Noncovalent interactions between molecules are key for many biological processes. Necessarily, when molecules interact, the electronic charge in each of them is redistributed. Here, we show experimentally that, in chiral molecules, charge redistribution is accompanied by spin polarization. We describe how this spin polarization adds an enantioselective term to the forces, so that homochiral interaction energies differ from heterochiral ones. The spin polarization was measured by using a modified Hall effect device. An electric field that is applied along the molecules causes charge redistribution, and for chiral molecules, a Hall voltage is measured that indicates the spin polarization. Based on this observation, we conjecture that the spin polarization enforces symmetry constraints on the biorecognition process between two chiral molecules, and we describe how these constraints can lead to selectivity in the interaction between enantiomers based on their handedness. Model quantum chemistry calculations that rigorously enforce these constraints show that the interaction energy for methyl groups on homochiral molecules differs significantly from that found for heterochiral molecules at van der Waals contact and shorter (i.e., ∼0.5 kcal/mol at 0.26 nm).

The aug-cc-pVnZ-F12 basis set family: Correlation consistent basis sets for explicitly correlated benchmark calculations on anions and noncovalent complexes

We have developed a new basis set family, denoted as aug-cc-pVnZ-F12 (or aVnZ-F12 for short), for explicitly correlated calculations. The sets included in this family were constructed by supplementing the corresponding cc-pVnZ-F12 sets with additional diffuse functions on the higher angular momenta (i.e., additional d-h functions on non-hydrogen atoms and p-g on hydrogen atoms), optimized for the MP2-F12 energy of the relevant atomic anions. The new basis sets have been benchmarked against electron affinities of the first- and second-row atoms, the W4-17 dataset of total atomization energies, the S66 dataset of noncovalent interactions, the Benchmark Energy and Geometry Data Base water cluster subset, and the WATER23 subset of the GMTKN24 and GMTKN30 benchmark suites. The aVnZ-F12 basis sets displayed excellent performance, not just for electron affinities but also for noncovalent interaction energies of neutral and anionic species. Appropriate CABSs (complementary auxiliary basis sets) were explored for the S66 noncovalent interaction benchmark: between similar-sized basis sets, CABSs were found to be more transferable than generally assumed.

The S66 Non-Covalent Interactions Benchmark Reconsidered Using Explicitly Correlated Methods Near the Basis Set Limit*

The S66 benchmark for non-covalent interactions has been re-evaluated using explicitly correlated methods with basis sets near the one-particle basis set limit. It is found that post-MP2 ‘high-level corrections’ are treated adequately well using a combination of CCSD(F12*) with (aug-)cc-pVTZ-F12 basis sets on the one hand, and (T) extrapolated from conventional CCSD(T)/heavy-aug-cc-pV{D,T}Z on the other hand. Implications for earlier benchmarks on the larger S66×8 problem set in particular, and for accurate calculations on non-covalent interactions in general, are discussed. At a slight cost in accuracy, (T) can be considerably accelerated by using sano-V{D,T}Z+ basis sets, whereas half-counterpoise CCSD(F12*)(T)/cc-pVDZ-F12 offers the best compromise between accuracy and computational cost.