Petr Jurečka

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.

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high‐level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated—B‐LYP, B3‐LYP, PBE, TPSS, TPSSh, and BH‐LYP—and even surpass the MP2/cc‐pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, sR, scaling globally the vdW radii. For good results, a basis set of at least triple‐ζ quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen‐bonded and stacked complexes considered, respectively.

Refinement of the Cornell et al. Nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with several previous glycosidic torsion parametrizations.

Adsorption of Small Organic Molecules on Graphene

We present a combined experimental and theoretical quantification of the adsorption enthalpies of seven organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate, hexane, and toluene) on graphene. Adsorption enthalpies were measured by inverse gas chromatography and ranged from -5.9 kcal/mol for dichloromethane to -13.5 kcal/mol for toluene. The strength of interaction between graphene and the organic molecules was estimated by density functional theory (PBE, B97D, M06-2X, and optB88-vdW), wave function theory (MP2, SCS(MI)-MP2, MP2.5, MP2.X, and CCSD(T)), and empirical calculations (OPLS-AA) using two graphene models: coronene and infinite graphene. Symmetry-adapted perturbation theory calculations indicated that the interactions were governed by London dispersive forces (amounting to ∼60% of attractive interactions), even for the polar molecules. The results also showed that the adsorption enthalpies were largely controlled by the interaction energy. Adsorption enthalpies obtained from ab initio molecular dynamics employing non-local optB88-vdW functional were in excellent agreement with the experimental data, indicating that the functional can cover physical phenomena behind adsorption of organic molecules on graphene sufficiently well.

Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations.

High-level OVOS (optimized virtual orbital space) CCSD(T) interaction energy calculations (up to the aug-cc-pVQZ basis set) and various extrapolations toward the complete basis set (CBS) limit are presented for the most important structures on the benzene dimer potential energy surface. The geometries of these structures were obtained via an all-coordinate gradient geometry optimization using the DFT-D/BLYP method, covering the empirical dispersion correction fitted exclusively for this system. The fit was carried out against two estimated CCSD(T)/CBS potential energy curves corresponding to the distance variation between two benzene rings for the parallel-displaced (PD) and T-shaped (T) structures. The effect of the connected quadruple excitations on the interaction energy was estimated using the CCSD(TQf) method in a 6-31G*(0.25) basis set, destabilizing the T and T-shaped tilted (TT) structures by ≈0.02 kcal/mol and the PD structure by ≈0.04 kcal/mol. Our best CCSD(T)/CBS results show, within the error bars of the applied methodology, that the energetically lowest-lying structure is the TT structure, which is nearly 0.1 kcal/mol more stable than the almost isoenergetic PD and T structures. The specifically parametrized DFT-D/BLYP method leads to a correct energy ordering of the structures, with the errors being smaller by 0.2 kcal/mol with respect to the most accurate CCSD(T) values.

On the convergence of the (ΔECCSD(T) - ΔEMP2) term for complexes with multiple H-bonds

Abstract The MP2 and CCSD(T) interaction energies of the following cyclic complexes were studied: formic acid dimer (FO–FO), formamide dimer (FA–FA), formamidine dimer (FI–FI), formamide⋯formamidine complex (FA–FI) and the formamidinoaldehyde⋯amidinoformamide (FL–AF) complex. Various AO basis sets up to the cc-pVTZ were investigated. It was shown that the ( ΔE CCSD(T) − ΔE MP2 ) correction term evaluated with the 6-31G* basis set is overestimated while rather accurate values were obtained with 6-31G*(0.25) and cc-pVDZ (0.25, 0.15) basis sets. Because the latter one performs well also for stacked complexes it can be recommended for evaluation of the correction term of extended complexes possessing both H-bonded and stacked structures.

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.

RI-MP2 calculations with extended basis sets—a promising tool for study of H-bonded and stacked DNA base pairs

The interaction energies of 9-methyladenine···1-methylthymine H-bonded and 9-methyladenine···9-methylguanine stacked pairs were evaluated at the MP2 and resolution of the identity MP2 (RI-MP2) levels. The interaction energies are almost identical for both methods. The RI-MP2 method is about one order of magnitude faster than the exact MP2 method and, therefore, this method is well suited for the study of large models of biological importance. The basis set dependence of both base pairs was studied and reasonable relative energy characteristics were obtained only if at least the valence double-ζ-polarisation SVP basis set with modified (diffuse) polarisation functions on non-hydrogen and hydrogen atoms was used. However, reliable absolute stabilisation energies of both base pairs were only obtained if at least the aug-SVP basis set is applied. Stack interaction energies and three- and four-body energy terms for selected base-pair steps of B-DNA were calculated for the first time using the RI-MP2 method and the aug-SVP basis set.