Fractal nature of benzene stacking interactions.

CONTEXT: Benzene and other aromatic groups, as planar groups with [Formula: see text] electrons cloud, tend to form stacking interactions which have an important role in various chemical and biological processes. In order to have a better insight in the nature of these interactions, we have performed a fractal analysis on patterns of electron density and electrostatic potential for two benzenes in stacking interaction. The calculated fractal dimension follows the trend of the calculated interaction energy for the interplanar distances of 4.0 to 6.0 Å, which partially coincides with the strongest attractive stacking interactions. The fractal dimension vs. energy dependences were fitted with the logistic curve, and the fitting coefficient was 0.96 up to 1.00. METHODS: For the benzene stacking interaction energy, with a range of conformations and distances between two benzenes, DFT calculations at the B3LYP+D3/aug-cc-pVDZ level were performed with the TURBOMOLE software. The fractal analysis for electron density and electrostatic potential has been done by python scripting.

Water: new aspect of hydrogen bonding in the solid state.

All water-water contacts in the crystal structures from the Cambridge Structural Database with d OO ≤ 4.0 Šhave been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d OH ≤ 3.0 Šand α ≥ 120°) with most being stronger than -3.3 kcal mol-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O-H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (ß1, ß2 ≥ 160°, 80 ≤ α ≤ 140° and T HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry.

Modulating Excited Charge-Transfer States of G-Quartet Self-Assemblies by Earth Alkaline Cations and Hydration.

Guanine self-assemblies are promising supramolecular platforms for optoelectronic applications. The study (Hua et al., J. Phys. Chem. C 2012, 116, 14,682-14,689) reported that alkaline cations cannot modulate the electronic absorption spectrum of G-quadruplexes, although a cation effect is observable during electronic relaxation due to different mobility of Na+ and K+ cations. In this work, we theoretically examined whether divalent Mg2+ and Ca2+ cations and hydration might shift excited charge-transfer states of a cation-templated stacked G-quartet to the absorption red tail. Our results showed that earth alkaline cations blue-shifted nπ* states and stabilized charge-transfer ππ* states relative to those of complexes with alkaline cations, although the number of charge-separation states was not significantly modified. Earth alkaline cations were not able to considerably increase the amount of charge-transfer states below the Lb excitonic states. Hydration shifted charge-transfer states of the Na+-coordinated G-octet to the absorption red tail, although this part of the spectrum was still dominated by monomer-like excitations. We found G-octet electron detachment states at low excitation energies in aqueous solution. These states were distributed over a broad range of excitation energies and could be responsible for oxidative damage observed upon UV irradiation of biological G-quadruplexes.

A linker of the proline-threonine repeating motif sequence is bimodal.

The linker of the endoglucanase from Xanthomonas campestris pv. campestris ((PT)12) has a specific sequence, a repeating proline-threonine motif. In order to understand its role, it has been compared to a regular sequence linker, in this work-the cellobiohydrolase 2 from Trichoderma reesei (CBH2). Elastic properties of the two linkers have been estimated by calculating free energy profile along the linker length from an enhanced sampling molecular dynamics simulation. The (PT)12 exhibits more pronounced elastic behaviour than CBH2. The PT repeating motif results in a two-mode energy profile which could be very useful in the enzyme motions along the substrate during hydrolytic catalysis.

Carbohydrate - Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations.

The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from -1.7 kcal/mol to -6.8 kcal/mol, while in the systems without CH/π interactions are in the range -0.2 to -3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.

Role of aromatic amino acids in amyloid self-assembly.

Amyloids are proteins of a cross-ß structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.

How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface.

Water molecules from crystal structures archived in the CSD show a relatively large range both in the bond angle and bond lengths. High level ab initio calculations at the CCSD(T)/CBS level predicted a possibility for energetically low-cost (±1 kcal mol-1) changes of the bond angle and bond lengths in a wide range, from 96.4° to 112.8° and from 0.930 Å to 0.989 Å, respectively.

Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution.

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O-H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.

Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water-nucleic acid base hydrogen bonds.

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.