In the past several years the MP2 method has been used extensively in studies of noncovalent interactions within biological systems such as proteins, DNA/RNA, and protein-ligand complexes. In this work we assess the performance that can be expected of this method, when paired with several different medium and extended basis sets, for the accurate computation of binding energies of hydrogen bonded and dispersion bound biologically derived complexes. It is found that, overall, the MP2/cc-pVTZ method produces the best, most well balanced, description of noncovalent interactions. Another interesting observation made in this study is that generally the MP2 technique, when paired with any basis set, does not yield reliable results for cyclic hydrogen bonds such as those found in nucleic acid base pairs.

• MeSH
• DNA chemie   MeSH
• financování organizované MeSH
• proteiny chemie   MeSH
• RNA chemie   MeSH
• vodíková vazba MeSH

In this work, we investigate the mode of binding of several steroid hormones, namely aldosterone, deoxycorticosterone, and progesterone to the wild-type and S810L mutated mineralocorticoid (MR) receptor using the newly formulated density functional theory with an empirical dispersion term (DFT-D) molecular electronic structure method. It is found that the MR agonists, aldosterone and deoxycorticosterone, form tight hydrogen bonds with residues Thr945 and Asn770, which leads to the formation of hydrogen bond networks near the steroid D-ring, allowing for activation of this transcription factor. Progesterone, an MR antagonist, fails to form the necessary hydrogen bonds near the steroid D-ring. Progesterone is known to be an agonist of the mutated S810L MR receptor. Our studies indicate that this is possible because of a strong hydrogen bond between progesterone and Thr945 and a relatively strong hydrophobic interaction between progesterone and Asn770.

• MeSH
• financování organizované MeSH
• hormony chemie   metabolismus   MeSH
• leucin genetika   metabolismus   MeSH
• ligandy MeSH
• molekulární modely MeSH
• mutace genetika   MeSH
• receptory mineralokortikoidů genetika   chemie   metabolismus   MeSH
• serin genetika   metabolismus   MeSH
• steroidy chemie   MeSH
• terciární struktura proteinů MeSH
• vodíková vazba MeSH

Dissociation curves calculated using multiple correlated QM methods for 66 noncovalent complexes (Řezáč et al., J Chem Theory Comput 2011, 7, 2427) have allowed us to interpolate equilibrium intermolecular distances for each studied method. Comparison of these data with CCSD(T)/complete basis set reference geometries provides information on how these methods perform in geometry optimizations. The large set of systems considered here is necessary for reliable statistical evaluation of the results and assessment of the robustness of the studied methods. Our results show that advanced methods such as MP3 and CCSD provide significant improvement over MP2 only when empirical scaling is used. The best results can be achieved with spin component scaled CCSD optimized for noncovalent interactions, with a root mean square error of 0.4% of the equilibrium distance. Scaled MP3, the MP2.5 method, yields comparably good results (error 0.5%) while being substantially cheaper.

• MeSH
• chemické modely MeSH
• komplexní sloučeniny MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.

• MeSH
• financování organizované MeSH
• konformace nukleové kyseliny MeSH
• molekulární modely MeSH
• nukleové kyseliny chemie   MeSH

In this work we investigate the performance of the DFT method, augmented with an empirical dispersion function (DFT-D), paired with the PCM implicit solvation model, for the computation of noncovalent interaction energies of biologically-relevant, solvated model complexes. It is found that this method describes intermolecular interactions within water and ether (protein-like) environments with roughly the same accuracy as in the gas phase. Another important finding is that, when environmental effects are taken into account, the empirical dispersion term associated with the DFT-D method need be modified very little (or not at all), in order to obtain the optimum, most well balanced, performance.

• MeSH
• algoritmy MeSH
• biologické modely MeSH
• chemické modely MeSH
• DNA chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• kvantová teorie MeSH
• makromolekulární látky chemie   MeSH
• povrchové vlastnosti MeSH
• přenos energie MeSH
• proteiny chemie   MeSH
• RNA chemie   MeSH
• rozpustnost MeSH
• roztoky MeSH
• termodynamika MeSH
• vodíková vazba MeSH

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 DeltaCCSD(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.

• MeSH
• algoritmy MeSH
• benzen chemie   MeSH
• chemické modely MeSH
• dimerizace MeSH
• financování organizované MeSH
• přenos energie MeSH
• uracil chemie   MeSH
• vodíková vazba MeSH

Proline-tryptophan complexes derived from experimental structures are investigated by quantum chemical procedures known to properly describe the London dispersion energy. We study two geometrical arrangements: the "L-shaped", stabilized by an H-bond, and the "stacked-like", where the two residues are in parallel orientation without any H-bond. Interestingly, the interaction energies in both cases are comparable and very large ( approximately 7 kcal mol(-1)). The strength of stabilization in the stacked arrangement is rather surprising considering the fact that only one partner has an aromatic character. The interaction energy decomposition using the SAPT method further demonstrates the very important role of dispersion energy in such arrangement. To elucidate the structural features responsible for this unexpectedly large stabilization we examined the role of the nitrogen heteroatom and the importance of the cyclicity of the proline residue. We show that the electrostatic interaction due to the presence of the dipole, caused by the nitrogen heteroatom, contributes largely to the strength of the interaction. Nevertheless, the cyclic arrangement of proline, which allows for the largest amount of dispersive contact with the aromatic partner, also has a notable-effect. Geometry optimizations carried out for the "stacked-like" complexes show that the arrangements derived from protein structure are close to their gas phase optimum geometry, suggesting that the environment has only a minor effect on the geometry of the interaction. We conclude that the strength of proline non-covalent interactions, combined with this residue's rigidity, might be the explanation for its prominent role in protein stabilization and recognition processes.

• MeSH
• chemické modely MeSH
• chemie fyzikální metody   MeSH
• financování organizované MeSH
• konformace proteinů MeSH
• ligandy MeSH
• mapování interakce mezi proteiny MeSH
• molekulární konformace MeSH
• prolin chemie   MeSH
• proteiny chemie   MeSH
• statická elektřina MeSH
• terciární struktura proteinů MeSH
• tryptofan chemie   MeSH
• vazba proteinů MeSH
• vodíková vazba MeSH

• MeSH
• autofagie * fyziologie   MeSH
• biotest metody   normy   MeSH
• lidé MeSH
• počítačová simulace MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Research Support, N.I.H., Extramural MeSH
• směrnice MeSH