Ab initio quantum mechanical charge field molecular dynamics simulation (QMCF-MD) of Bi(3+) in water.

The hydration of the Bi(III) ion was determined via an ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation. Ten picosecond sampling was carried out to determine structural and dynamical properties of the Bi(III) ion in aqueous solution. In the first hydration shell, the ion is 9-fold coordinated with a maximum probability of the Bi-O distance at 2.51 Å. In total, 11 exchanges were observed in the first-shell showing associative, dissociative, and interexchange character. As with the dominant existence of 9-fold coordination, the geometry of the Bi(III) ion is in between the tricapped trigonal prism and the capped square antiprism.

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of L-histidine and zwitterionic L-histidine.

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-histidine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water on structures of His·M(H2O)m, m=0.1 complexes have been determined theoretically employing density functional theories using extended basis sets. Of the five stable complexes investigated the relative stability of the gas-phase complexes computed with DFT methods (with one exception of K+ systems) suggest metallic complexes of the neutral L-histidine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of L-histidine in the presence of the metal cations Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+ were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to L-histidine is exhibited by the Cu2+ cation. The computed Gibbs energies ΔG are negative, span a rather broad energy interval (from -130 to -1,300 kJ/mol), and upon hydration are appreciably lowered.

QM/MM MD simulations of iodide ion (I(-)) in aqueous solution: a delicate balance between ion-water and water-water H-bond interactions.

The characteristics of an iodide ion (I(-)) in aqueous solution were investigated by means of HF/MM and B3LYP/MM molecular dynamics simulations, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels using the LANL2DZdp and D95 V+ basis sets for I(-) and water, respectively. According to both the HF/MM and B3LYP/MM results, the ion-water interactions are relatively weak, compared to the water-water hydrogen bonds, thus causing an unstructured nature of the hydration shell. Comparing the HF and B3LYP treatments for the description of this hydrated ion, the overestimation of the ion-water hydrogen-bond strength by the B3LYP method is recognizable, yielding a remarkably more compact and too rigid ion-water complex.

QM/MM dynamics of CH3COO(-)-water hydrogen bonds in aqueous solution.

Two combined QM/MM molecular dynamics (MD) simulations, namely, HF/MM and B3LYP/MM, in which the central CH(3)COO(-) and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set, have been performed to investigate the characteristics of CH(3)COO(-)-water hydrogen bonds in dilute aqueous solution. Both HF/MM and B3LYP/MM simulations clearly indicate relatively strong hydrogen bonds between CH(3)COO(-) oxygens and their nearest-neighbor waters compared with those of water-water hydrogen bonds in the bulk. In addition, it is observed that first-shell waters are either "loosely" or "tightly" bound to their respective CH(3)COO(-) oxygen atoms, leading to large fluctuations in the coordination number, ranging from 2 to 5, with the prevalent value of 3. Among the HF and B3LYP methods for the description of the QM-treated region, the latter predicts slightly higher hydrogen-bond strength in the CH(3)COO(-)-water complex.

Combined QM/MM MD study of HCOO(-)-water hydrogen bonds in aqueous solution.

Characteristics of HCOO(-)-water hydrogen bonds in dilute aqueous solution have been investigated by means of combined HF/MM and B3LYP/MM molecular dynamics simulations, in which the central HCOO(-) and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using DZV+ basis set. Both HF/MM and B3LYP/MM simulations supply information that the hydrogen bonds between HCOO(-) oxygens and first-shell waters are relatively strong, that is, compared to the water-water hydrogen bonds. Regarding to the HF/MM and B3LYP/MM trajectories, it is observed that first-shell waters are either "loosely" or "tightly" bound to their respective HCOO(-) oxygen atoms, showing large fluctuations in the hydration number, varying from 2 to 6 (HF/MM) and 1 to 5 (B3LYP/MM), with the prevalent value of 3. Comparing the HF and B3LYP methods for the description of QM treated region, the first one leads to slightly too weak and thus longer hydrogen bonds, while the latter predicts them stronger but with the wrong dynamical data.

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of L-arginine and zwitterionic L-arginine.

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-arginine is examined. The effects of metal ions (Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+)) and water on structures of Arg x M(H2O)m , m = 0, 1 complexes have been determined theoretically by employing the density functional theories (DFT) and using extended basis sets. Of the three stable complexes investigated, the relative stability of the gas-phase complexes computed with DFT methods (with the exception of K(+) systems) suggests metallic complexes of the neutral L-arginine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of arginine in the presence of the metal cations Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+) were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to arginine is exhibited by the Cu(2+) cation. The computed Gibbs energies DeltaG(o) are negative, span a rather broad energy interval (from -150 to -1500 kJ/mol), and are appreciably lowered upon hydration.

The possible influence of L-histidine on the origin of the first peptides on the primordial Earth.

One of the most unsettled problems of prebiotic evolution and the origin of life is the explanation why one enantiomeric form of biomolecules prevailed. In the experiments presented in this paper, the influence of L-histidine on the peptide formation in the Salt-Induced Peptide Formation (SIPF) reaction of the enantiomeric forms of valine, proline, serine, lysine, and tryptophan, and the catalytic effects in this first step toward the first building blocks of proteins on the primordial earth were investigated. In the majority of the produced dipeptides, a remarkable increase of yields was shown, and the preference of the L-amino acids in the peptide formation in most cases cannot be denied. In summary, our data provide further experimental evidence for the plausibility of the SIPF reaction and point at a possible important role of L-histidine in the chemical evolution on the primordial Earth.

Effect of metal Ions (Ni²âº, Cu²âº and Zn²âº) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms.

Methods of quantum chemistry have been applied to double-charged complexes involving the transition metals Ni(2+), Cu(2+) and Zn(2+) with the aromatic amino acids (AAA) phenylalanine, tyrosine and tryptophan. The effect of hydration on the relative stability and geometry of the individual species studied has been evaluated within the supermolecule approach. The interaction enthalpies, entropies and Gibbs energies of nine complexes Phe•M, Tyr•M, Trp•M, (M = Ni(2+), Cu(2+) and Zn(2+)) were determined at the Becke3LYP density functional level of theory. Of the transition metals studied the bivalent copper cation forms the strongest complexes with AAAs. For Ni(2+)and Cu(2+) the most stable species are the NO coordinated cations in the AAA metal complexes, Zn(2+)cation prefers a binding to the aromatic part of the AAA (complex II). Some complexes energetically unfavored in the gas-phase are stabilized upon microsolvation.

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure of glycine and zwitterionic glycine.

Interactions between metal ions and amino acids are common both in solution and in the gas phase. Here, the effect of metal ions and water on the structure of glycine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water on structures of Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (m = 0, 2, 5) complexes have been determined theoretically by employing the hybrid B3LYP exchange-correlation functional and using extended basis sets. Selected calculations were carried out also by means of CBS-QB3 model chemistry. The interaction enthalpies, entropies, and Gibbs energies of eight complexes Gly.Mn+ (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) were determined at the B3LYP density functional level of theory. The computed Gibbs energies DeltaG degrees are negative and span a rather broad energy interval (from -90 to -1100 kJ mol(-1)), meaning that the ions studied form strong complexes. The largest interaction Gibbs energy (-1076 kJ mol(-1)) was computed for the NiGly2+ complex. Calculations of the molecular structure and relative stability of the Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+; m = 0, 2, and 5) systems indicate that in the complexes with monovalent metal cations the most stable species are the NO coordinated metal cations in non-zwitterionic glycine. Divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ prefer coordination via the OO bifurcated bonds of the zwitterionic glycine. Stepwise addition of two and five water molecules leads to considerable changes in the relative stability of the hydrated species. Addition of two water molecules at the metal ion in both Gly.Mn+ and GlyZwitt.Mn+ complexes reduces the relative stability of metallic complexes of glycine. For Mn+ = Li+ or Na+, the addition of five water molecules does not change the relative order of stability. In the Gly.K+ complex, the solvation shell of water molecules around K+ ion has, because of the larger size of the potassium cation, a different structure with a reduced number of hydrogen-bonded contacts. This results in a net preference (by 10.3 kJ mol(-1)) of the GlyZwitt.K+H2O5 system. Addition of five water molecules to the glycine complexes containing divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ results in a net preference for non-zwitterionic glycine species. The computed relative Gibbs energies are quite high (-10 to -38 kJ mol(-1)), and the NO coordination is preferred in the Gly.Mn+(H2O)5 (Mn+ = Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) complexes over the OO coordination.

A combined QM/MM molecular dynamics simulations study of nitrate anion (NO3-) in aqueous solution.

The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.

On the mechanisms of oligopeptide reactions in solution and clay dispersion.

Mechanisms of the reactions of representative dipeptides (Gly2, Gly-Ala), oligopeptides (Gly3, Gly4) and the polypeptide (poly-Gly)n) in solution and clay suspensions at 85 degrees C were investigated. The reaction products and their yields were analysed and determined by means of HPLC. Interestingly, hydrolysis, where water molecules act as the reactant, was not the main reaction, even for oligopeptides. Formation of cyclic dipeptides prevailed in the reactions of dimers as well as oligopeptides. The breakdown of oligopeptide molecules proceeded via an intramolecular cyclization reaction. For example, the reaction of Gly3 led to the formation of equal amounts of cyclic dipeptide, c(Gly)2 and Gly. The presence of clay (montmorillonite) significantly increased yields in the reactions of dipeptides but it did not have much effect on the reactions of oligopeptides. However, an opposite effect of clay, protection of poly(Gly)n against decomposition, was proven.