Hannes H. Loeffler

Molecular dynamics simulations of Ca2+ in water: Comparison of a classical simulation including three-body corrections and Born–Oppenheimer ab initio and density functional theory quantum mechanical/molecular mechanics simulations

A classical molecular dynamics simulation including three-body corrections was compared with combined ab initio quantum mechanics/molecular mechanics molecular dynamics simulations (QM/MM–MD), which were carried out at Hartree–Fock (HF) and density functional theory (DFT) level for Ca2+ in water. In the QM approach the region of primary interest—the first hydration sphere of the calcium ion—was treated by Born–Oppenheimer quantum mechanics, while the rest of the system was described by classical pair potentials. Coordination numbers of 7.1, 7.6, and 8.1 were found in the classical, the HF, and the DFT simulation, respectively, using the same double-ζ basis set in both QM methods. The CPU time for one DFT step was about 50% above the time for a HF step, but due to a smaller number of steps needed for equilibration in the DFT case, there was no significant difference in the overall simulation time.

The hydration structure of the lithium ion

The hydration structure of Li+ has been studied by means of hybrid quantum-mechanical molecular mechanical molecular dynamics simulations at Hartree–Fock and density-functional level of theory. The size of the quantum-mechanical region and the form of the potential function are shown to be of crucial importance for reliable results. Radial distribution functions, coordination number distributions, and various angular distributions have been used to discuss details of the hydration structure, together with bond lengths and bond angles of the water molecules in the first hydration shell. The lithium ion is found to be mainly fourfold coordinated with some smaller amounts of fivefold coordination. The lithium–water cluster exhibits a nearly perfect tetrahedral but still very flexible structure, in which coordinated water molecules are considerably tilted away from planarity. Water molecules in the first hydration shell are shown to be considerably polarized compared to gas-phase structures.

Librational, vibrational, and exchange motions of water molecules in aqueous Ni(II) solution: classical and QM/MM molecular dynamics simulations

Abstract The librational and vibrational motions of water molecules in the first and second hydration spheres of the Ni 2+ ion were evaluated by means of velocity autocorrelation functions obtained by classical and combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. The rotational frequencies around three principal axes and the intramolecular vibrational frequencies of the water molecule were calculated using normal-coordinate analyses. The rate constant of the water exchange in the second hydration sphere of the Ni 2+ ion was estimated to be ca. 5×10 10 s −1 . A water-exchange mechanism with an associative character appears to be predominant, but less associative exchanges are also observed.

Dynamics of the solvation process of Ca2+ in water

Abstract Combined quantum mechanics/molecular mechanics–molecular dynamics simulations (QM/MM–MD) were carried out at Hartree–Fock (HF) and density functional theory (DFT) level for Ca 2+ in water to investigate the exchange process of water molecules between first and second hydration shell. In both cases one exchange reaction took place during a simulation time of about 10 ps. The time needed for this water exchange is 1.2 ps in the DFT/MM and 2.0 ps in the QM/MM–HF simulation. From the data obtained so far, the exchange rate can be estimated to be larger than 10 −11 s.

QM/MM-MD simulation of hydrated vanadium(II) ion

Abstract A molecular dynamics (MD) simulation utilizing a combined quantum mechanical molecular mechanical (QM/MM) potential was carried out to study the hydration structure of V(II). Structural data in form of radial distribution functions, coordination numbers, angular distributions and bond length distributions were obtained. The results show an almost perfect octahedral coordination of the first hydration shell with a rigid structure, and a flexible second shell containing 13–20 (average: 16.4) ligands. The cation affects the hydration structure to distances up to 8 A.

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 B12 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.

Many-body effects on structure and dynamics of aqueous ionic solutions

We performed several molecular dynamic studies of metal cations in aqueous solution. The alkali metal ion Li+ and the first‐row transition metal ion Mn2+ have been chosen as model systems. Two different three‐body corrections are proposed to mimic the crucial many‐body effects of electrolyte solutions. The correction function, which includes attractive features of the three‐body potential, performs considerably better than the purely repulsive interaction function. Structural and dynamic results show that this simple enhancement is able to satisfactorily reproduce experimental and higher‐level results for the first hydration shell.

MD and MC simulations of hydrated manganous ion including three-body effects

An ab initio three-body analytical potential function was constructed for the Mn(II) – water system. Classical molecular dynamics (MD) and Monte Carlo (MC) simulations including the three-body correction terms were carried out to study the hydration structure of Mn(II). Structural data in form of radial distribution functions, coordination numbers, angular distributions and bond length distributions were obtained. The inclusion of the three-body correction was found to be crucial for the description of the system, and results thus obtained are in good agreement with experimental values. q 2002 Elsevier Science B.V. All rights reserved.

Calculation of sequence‐dependent free energies of hydration of dipeptides formed by alanine and glycine

The relative free energies of hydration of the dipeptides glycylalanine and alanyl‐glycine in their naturally occurring form have been calculated both for the zwitterionic and protonated species. Emphasis was laid on comparisons between the conventional cutoff method and the Particle Mesh Ewald method to account for possible differences in electrostatic contributions to the free energy. Furthermore, the convergence behavior of the total free energy and its individual contributions were examined. The results, obtained by means of the thermodynamic integration technique as implemented in the free energy module of the AMBER program suite, suggest that in aqueous solution glycylalanine is more stable than alanylglycine by 2.7 kcal/mol in the zwitterionic form and by 3.5 kcal/mol in the protonated form.