Bernd M. Rode

Peptides and the origin of life1

Abstract Considering the state-of-the-art views of the geochemical conditions of the primitive earth, it seems most likely that peptides were produced ahead of all other oligomer precursors of biomolecules. Among all the reactions proposed so far for the formation of peptides under primordial earth conditions, the salt-induced peptide formation reaction in connection with adsorption processes on clay minerals would appear to be the simplest and most universal mechanism known to date. The properties of this reaction greatly favor the formation of biologically relevant peptides within a wide variation of environmental conditions such as temperature, pH, and the presence of inorganic compounds. The reaction-inherent preferences of certain peptide linkages make the argument of ‘statistical impossibility’ of the evolutionary formation of the ‘right’ peptides and proteins rather insignificant. Indeed, the fact that these sequences are reflected in the preferential sequences of membrane proteins of archaebacteria and prokaryonta distinctly indicates the relevance of this reaction for chemical peptide evolution. On the basis of these results and the recent findings of self-replicating peptides, some ideas have been developed as to the first steps leading to life on earth.

Characterization of dynamics and reactivities of solvated ions by ab initio simulations.

Based on a systematic investigation of trajectories of ab initio quantum mechanical/molecular mechanical simulations of numerous cations in water a standardized procedure for the evaluation of mean ligand residence times is proposed. For the characterization of reactivity and structure‐breaking/structure‐forming properties of the ions a measure is derived from the mean residence times calculated with different time limits. It is shown that ab initio simulations can provide much insight into ultrafast dynamics that are presently not easily accessible by experiment.

A QM/MM simulation method applied to the solution of Li+ in liquid ammonia

Abstract A molecular dynamics simulation method based on combined quantum mechanical and classical potentials is proposed. This method computes the interactions between particles in a focus region, we call it “Hot Spot”, at quantum chemical level within an affordable computational effort. Application to solution chemistry was examined by simulating Li + solvation in liquid ammonia. The new method yields a coordination number of 4 in contrast to 6 obtained from pair-potential simulation. Dynamical properties were found in agreement with the structural change of the solvation shell. The semi-empirical MNDO method was also tested within this approach, but proved inappropriate for the treatment of electrolyte solutions.

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.

Structure and ultrafast dynamics of liquid water: A quantum mechanics/ molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Beckes three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.

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.

Extended ab initio quantum mechanical/molecular mechanical molecular dynamics simulations of hydrated Cu2+

Copper(II) was used as a model system to investigate the relevance of including the full second hydration shell in ab initio treatment while describing hydrated ions in hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations. Three different simulation techniques were applied (Hartree–Fock, B3LYP, and resolution of the identity density functional theory) to find a good compromise between accuracy and simulation speed. To discuss details of the hydration structure radial distribution functions, coordination number distributions and various angular distributions have been used. Dynamical properties such as vibrational motions of water molecules and ion–oxygen stretching motions were investigated using approximative normal coordinate analyses. QM/MM MD simulations offer a detailed time picture of the dynamic Jahn–Teller effect of Cu2+ showing short-term as well as long-term distortions to occur within <200 fs and 2–3 ps. The results prove that for transition metal ions such a...

The hydration shell structure of Li+ investigated by Born–Oppenheimer ab initio QM/MM dynamics

Abstract A combined ab initio quantum mechanical (QM) and molecular mechanical (MM) molecular dynamics simulation has been applied to study the non-additive contributions to the surroundings of Li + in water. The first hydration sphere of Li + is treated by Born–Oppenheimer ab initio quantum mechanics, while the rest is described by classical pair potentials. A tetrahedral structure of four water molecules in the first solvation shell of Li + is found by this combined QM/MM method with a valence double-zeta basis set, in contrast to the octahedral structure obtained by the traditional simulation using pair potentials.

Silica, Alumina and Clay Catalyzed Peptide Bond Formation: Enhanced Efficiency of Alumina Catalyst

Catalytic efficiencies of clay (hectorite), silica and alumina were tested in peptide bond formation reactions of glycine (Gly), alanine (Ala), proline (Pro), valine (Val) and leucine (Leu). The reactions were performed as drying/wetting (hectorite) and temperature fluctuation (silica and alumina) experiments at 85 °C. The reactivity of amino acids decreased in order Gly > Ala > Pro ≈ Val ≈ Leu. The highest catalytic efficiency was observed for alumina, the only catalyst producing oligopeptides in all investigated reaction systems. The peptide bond formation on alumina is probably catalyzed by the same sites and via similar reaction mechanisms as some alumina-catalyzed dehydration reactions used in industrial chemistry.

The Combination of Salt Induced Peptide Formation Reaction and Clay Catalysis: A Way to Higher Peptides under Primitive Earth Conditions

Two reactions with suggested prebiotic relevance for peptide evolution, the saltinduced peptide formation reaction and the peptide chain elongation/stabilization on clay minerals have been combined in experimental series starting from dipeptides and dipeptide/amino acid mixtures. The results show that both reactions can take place simultaneously in the same reaction environment and that the presence of mineral catalysts favours the formation of higher oligopeptides. These findings lend further support to the relevance of these reactions for peptide evolution on the primitive earth. The detailed effects of the specific clay mineral depend both on the nature of the mineral and the reactants in solution.