Ab Initio Study of an H24O12 Zwitterion

Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches

Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.

O-H stretch modes of dodecahedral water clusters: a statistical ab initio study

Infrared frequencies calculations were carried out for 20 (H2O)20 water clusters obeying the 5(12) dodecahedral geometry, optimized at the B3LYP/6-311++G** level. Their combined spectra contained 800 O-H stretch modes, ranging from 2181 to 3867 cm(-1) (unscaled), which were treated and studied as a database. Of these, 752 modes (94%) could be assigned to a single dominant O-H stretch. These 752 were classified into five subdatabases depending on the local H-bond type of the dominant stretch. The frequency (nu) was correlated with the O-H distance (b(OH)), with H-bond length (R(OO)) where applicable, and with other variables. The parameter b(OH) alone accounted for 96-99% of the variance in nu for stretches in H-bonds. The correlation with R(OO) is substantially weaker. Normal modes were classified as "high ratio" or "low ratio" depending upon the mode's distribution of kinetic energy among the O-H bonds. High-ratio modes (389 modes, or 49% of our sample) are modeled well as a single oscillator undergoing small perturbations by weak coupling from other oscillators. Low-ratio modes involve strong coupling with at least one other O-H stretch for which b(OH2) is close to b(OH). The IR intensities of modes vary widely but can be explained in terms of a single equation giving dipole moment derivatives as a function of b(OH). For the lowest-energy (H2O)20 clusters, their IR stretch spectra contained eight distinguishable absorption bands. An explanation for eight bands in terms of the theory of polyhedral water clusters is offered.

Can the pH value of water solutions be estimated by quantum chemical calculations of small water clusters?

In the study, various water clusters were explored from the point of view of the proton transfer between H-bonded neighbors. A relatively modest approach--the MP26-31++G(d,p) level--was chosen as acceptable considering the fact that also larger systems have to be included. The tight ion-pair model (with usually three fixed O-O distances) was adopted for the autodissociation process. First, cluster-estimated pH values rapidly decrease as cluster size increases from 2 to 6. For larger clusters in gas phase, the topology of H bonds plays an important role, varying pH from 7 to 13 in hexamers and from 5 to 15 in octamer clusters. The relationship energy/distance was quantified, too. Enhancing our model with the conductorlike screening model (COSMO) approach brought significant improvement in description of the autodissociation reaction with a stable zwitterionic structure. However, when the O-O restrictions were released, the small barrier for backward reaction disappeared, reforming neutral cluster spontaneously. Also Boltzmann weighting procedure was applied, and for the explored clusters in vacuo, the series of pH 25-18-14-13-10 was obtained for cluster sizes n=2, 3, 4, 6, 8. Using the COSMO approach, the analogous series is 15-14-12-10-9. The limit of the series is still about two to three units above the experimentally known pH. In order to reach the size-independent (bulk) value, larger clusters are needed. However, the situation is far from hopeless since (as it was proven in the study) four-coordinated molecules are not involved in the proton transfer process directly; they can only be a part of the surrounding environment.

Zero Point Energy of Polyhedral Water Clusters

Polyhedral water clusters (PWCs) are cage-like (H2O)n clusters where every O participates in exactly three H bonds. For a database of 83 PWCs, 8 < or = n < or = 20, geometry was optimized and zero point energy (ZPE) was calculated at the B3LYP/6-311++G** level. ZPE correlates negatively with electronic energy (E0): each increase of 1 kcal/mol in E0 corresponds to a decrease of about 0.11 kcal/mol in ZPE. For each n, a set of four connectivity parameters accounts for 98% or more of the variance in ZPE. Linear regression of ZPE against n and this set gives an RMS error of 0.13 kcal/mol. The contributions to ZPE from stretch modes only (ZPE(S)) and from torsional modes only (ZPE(T)) also correlate strongly with E0 and with each other.

Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine

Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers' stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu-O(aqua) interactions were estimated to be about 60 kcal mol(-1) and for Cu-N7 bonding in the range of 75-83 kcal mol(-1). The broad range in Cu-N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.