Nowdays, quantum chemical computations are able to rival with cutting-edge experimental techniques in accuracy. High-accuracy model chemistries like the HEAT and Wn family of protocols are especially useful for open-shell species of which the experimental investigation can be fairly cumbersome. Since most of the atmospheric processes involve free radicals in non-conventional conditions the field of atmospheric chemistry is well-suited for studies utilizing the arsenal of highly accurate theoretical approaches. Recently, a couple of families of organic compounds with atmospheric importance have been investigated by our group including fluorinated and chlorinated methane derivatives (doi:10.1021/jp105268m), formaldehyde derivatives (doi:10.1021/jp1085203), nitrogen-oxide derivatives (doi:10.1021/jp112116x), and sulfur-containing molecules (doi:10.1021/jp203406d).
Ubiquitous weakly polar interactions are an important subset of non-covalent interactions in proteins where they play a crucial role in structure stabilization. They involve at least one aromatic residue (Ar) and include aromatic-aromatic (Ar-Ar), Ar-backbone (Ar-Bb), aromatic-sulfur (Ar‑S) and CH-π interactions (doi:10.1021/jp077674h). The individual Ar-Bb interaction energies can be substantial in being notably close to the strength of an average H-bond which is ca. 20 kJ·mol-1 in biological systems (ISBN-13: 978-0198509707).
We showed that the tertiary fold of avian pancreatic polypeptide is solely stabilized by weakly polar interactions (-114 kJ·mol-1) involving residues Phe20 and Tyr27 (doi:10.1002/qua.21521). It is remarkable that there are no H-bonds, salt- or disulphide bridges between the α- and the polyproline-II helix. (Move the cursor over the thumbnail pictures to get more detailed information.)
We also showed that about half of the total stabilization energy (-218 kJ·mol-1) of the so-called Trp-cage motif of the TC5b protein is from weakly polar interactions (doi:10.1021/jp077674h). (The other half is from H-bonds. The average energies were calculated using all of the available 38 NMR structures.)
Previously, ECD and NMR measurements indicated the proximity of the tyrosyl side chain to the backbone of N-Ac-AAAAYA-NHMe and when the conformational preferences of the peptide were investigated using quantum chemical computations, it was shown that the aromatic side chain interacts with the backbone of the peptide in the most stable conformers (doi:10.1002/jcc.20578).
Weakly polar interactions can also affect the conformational preferences of small molecules. The global minimum of melatonin, calculated at the MP2/6-31G* level, is stabilized by an Ar-side chain intramolecular interaction (doi:10.1002/jcc.20907). The interaction energy between the N-acetyl side chain and the indolyl ring, obtained from LMP2/aug-cc-pVTZ calculations, was -15.1 kJ·mol.-1 The MP2/6-31G* conformational PES was considerable different from that calculated at the HF/6-31G* level of theory (doi:10.1016/j.theochem.2003.08.005). Neither higher level correlation terms nor ZPVE corrections has substantial effect on the PES.
We developed the rotation method to correct the intramolecular BSSE (doi:10.1002/jcc.20868). It can be considered as the intramolecular equivalent of the CP procedure of Boys and Bernardi. We proved that the interaction energies obtained by the rotation method are comparable with those can be derived from the CP procedure, furthermore, both series approach the same limit with increasing basis set size.
To adequately describe intra- or/and intermolecular interactions post-HF methods with large basis set are usually needed. However, the most accurate electron correlation methods are extremely time consuming. Therefore, due to their favorable speed, DFT and the local variants of the MP2 method are frequently used to study large systems. We found that the BHandHLYP functional outperforms the LMP2 method in describing weakly polar interactions in proteins (doi:10.1002/jcc.20898).
Since appropriate structural mimicking to preserve the effects of neighboring residues is particularly important in protein modeling we have tested several types of capping groups in the computations of interaction energies of short peptide fragments. Most accurate results were obtained with N-Ac and NHMe protecting groups, respectively, at the N- and C-terminal ends (doi:10.1002/qua.21553).
We used a scaled effective one electron method as well as HF and MP2 methods to identify the conformers of normal alkanes (up to undecane). Based on the conformational PESs of the butane, pentane, hexane and heptane molecules 4 rules were deducted, which allowed to predict whether or not a particular sequence of torsional angles describes a conformer (doi:10.1021/jp981866i). In a follow-up study, with the help of graph theory, recurrence relations were defined to enumerate the number of possible conformational isomers of an arbitrary long normal alkane (doi:10.1023/A:1026472102742).