Analyzing the performance of conformational search programs on compound databases.

We have studied the sampling performance of conformational search programs using geometric and energetic criteria. Ideally, a conformational search algorithm should identify the largest possible number of low-energy structures (energy criterion) covering the widest possible range of molecular shapes (geometric criterion). Geometric analysis consisted in comparing the distribution of conformations within the generated ensembles by multidimensional scaling and by analysing the eigenvalue structure of the pairwise coordinate covariance matrices. The energetic comparison was carried out by assessing the energy distribution of conformers after minimizing them all using the same semi-empirical quantum mechanics optimization protocol. The present investigation focused on five conformational search programs: DGEOM, QXP, ROTATE, LMOD and OMEGA. We have applied these methodologies to a maximally diverse 604-compound subset of the LeadQuest library. The program LMOD performs best according to the energetic criterion, whereas a wider range of geometrically diverse conformations is sampled by the other programs, at the cost of higher median conformer energies. In terms of speed, OMEGA is fastest. We recommend the use of LMOD or OMEGA for high-quality conformational search applications.

Double hydrogen tunneling revisited: the breakdown of experimental tunneling criteria.

Formic acid dimer was chosen as a model system to investigate synchronous double proton transfer by means of variational transition state theory (VTST) for various isotopically modified hydrogen species. The electronic barrier for the double proton transfer was evaluated to be 7.9 kcal/mol, thus being significantly lower than it was determined in previous studies. The tunneling probabilities were evaluated at temperatures from 100 up to 400 K and typical Arrhenius behavior with enhancement by tunneling is observed. When comparing the transmission factors kappa in dependence of the mass of the tunneling hydrogen, it was found that there are two maxima, one at very low masses (e.g., 0.114 amu, corresponding to the muonium entity) and one maximum at around 2 amu (corresponding to deuterium). With the knowledge of the VTST-hydrogen transfer rates and the corresponding tunneling corrections, various tunneling criteria were tested (e.g., Swain-Schaad exponents) and were shown to fail in this reaction in predicting the extent of tunneling. This finding adds another aspect in the ongoing "Tunneling-Enhancement by Enzymes" discussion, as the used tunneling criteria based on experimental reaction rates may fail to predict tunneling behavior correctly.

Influence of backbone conformations of human carbonic anhydrase II on carbon dioxide hydration: hydration pathways and binding of bicarbonate.

In this study, the hydration of carbon dioxide and the formation of bicarbonate in human carbonic anhydrase II have been examined. From semiempirical QM/MM molecular dynamics studies, dominant conformations of the protein backbone, possibly contributing to the catalytic activity, have been isolated and further examined by means of density functional QM/MM methods. In agreement with experimental observations, a binding site for cyanate, which acts as an inhibitor, has been located, whereas for carbon dioxide, depending on the conformation of the protein environment, either a different binding site or no binding site has been found. In the latter case, carbon dioxide diffuses barrierless to the zinc-bound oxygen, and then a weakly bound bicarbonate complex is formed. The formed complex is characterized by a long C-O bond to the zinc-bound hydroxide. The nature of the calculated stationary points was verified by determination of vibrational frequencies. Finally, the dissociation of the formed bicarbonate from zinc has been considered. Therefore, a water molecule was included in the QM zone of the QM/MM hybrid potential, and minimization yielded a pentacoordinated intermediate. From a potential energy scan, an activation energy of 6.2 kcal/mol for dissociation of bicarbonate from Zn has been found.

A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems.

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.

Energetic and stereochemical effects of the protein environment on substrate: a theoretical study of methylmalonyl-CoA mutase.

QM/MM methods were used to study the isomerization step from (2R)-methylmalonyl-CoA to succinyl-CoA. A pathway via a "fragmentation-recombination" mechanism is ruled out on energetic grounds. For the other radicalic pathway, involving an addition recombination step, geometries and vibrational contributions have been determined, and a barrier height of 11.70 kcal/mol was found. The effect of adjacent hydrogen-donating groups was found to reduce the energy barrier by 1-2 kcal/mol each and thus to provide a significant catalytic effect for this reaction. By means of molecular dynamics studies, the stereochemistry of the methylmalonyl-CoA mutase catalyzed reaction was examined. It is shown that TYR89 is essential for maintaining stereoselectivity of the abstraction of a hydrogen in the backreaction. The subsequent selective formation of one isomer of methylmalonyl-CoA is probably due to the presence of a bulky side chain.

Hydration of hydroxypyrrole influences binding of ImHpPyPy-beta-Dp polyamide to DNA.

Ligands which are able to recognize DNA sequence specifically are of fundamental interest as transcription controlling drugs. Recently a polyamide ligand was developed (ImHpPyPy-beta-Dp) which differentiates in a dimeric arrangement between all four possible base pair steps in the minor groove. This is a landmark for the design of DNA binding drugs because it was believed that such a recognition could only be possible in the major groove of DNA. Although the OH groups of the hydroxypyrrole (Hp) moieties of the ligands are responsible for this sequence discrimination, experiments showed that this OH group also reduces the absolute binding constant. We performed a free energy calculation by means of thermodynamic integration in order to find out the influence of this single hydroxyl on DNA binding. In our simulation, we found that the hydroxyl group reduces binding by about 1.3 kcal/mol, which is in excellent agreement with the experimentally determined value of 1.2 kcal/mol. In further MD simulations, the structural reasons for this reduction was estimated. The results of these simulations qualitatively agree with the X-ray structures, but in contrast, in the simulations both (ImHpPyPy-beta-Dp and ImPyPyPy-beta-Dp) ligand-DNA (d(CCAGTACTGG)(2)) complexes exhibit only slight structural differences. This is consistent with a recently published second pair of similar polyamide DNA crystal structures. Thus, we believe that the explanations resulting from the X-ray structures must be modified. We attribute the large structural differences between the two polyamide DNA complexes to a buffer molecule which binds only in the case of the ImHpPyPy-beta-Dp-DNA complex at the region of interest. We propose that the differential hydration of both ligands in the unbound state is responsible for the reduction of the binding constant. Additionally, we suggest an indirect readout of DNA, because of a lengthening of the Watson-Crick base pairs, which possibly contributes to the differentiation between T.A, A.T from G.C, C.G base pairs.