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Liquids for electronic cigarettes and the vapor generated from them were examined by chemical and biological methods in order to reveal potential risk factors and their acceptability for consumers. Although the majority of the liquids on the market appear to be safe, some aroma compositions have been identified as possibly toxic for human vein epithelial cells, similar to tobacco smoke, thus indicating potential health risks and suggesting suitable test procedures before marketing the liquids.

Electronic cigarettes (e-cigarettes) have gained increasing popularity in recent years, mostly because they are supposed to be less harmful than regular cigarettes. Therefore, it is highly imperative to investigate possible noxious effects to protect the consumers. E-liquids consist of propylene glycol, glycerol, aroma compounds and sweeteners. One of these sweeteners is a chlorinated version of sucrose, namely sucralose. The aim of this work was to investigate degradation products of sucralose in the presence of propylene glycol and glycerol at different temperatures of commercially available e-cigarettes. Chemical analysis and biological tests were simultaneously performed on e-liquid aerosol condensates. The results of the chemical analysis, which was executed by employing GC‐MS/GC-FID, demonstrated high amounts of various chloropropanols. The most abundant one is extremely toxic, namely 3-chloropropane-1,2-diol, which can be detected at concentrations ranging up to 10,000 mg/kg. Furthermore, a cytotoxicity investigation of the condensates was performed on HUVEC/Tert2 cells in which metabolic activity was determined by means of resazurin assay. The cellular metabolic activity significantly decreased by treatment with e-liquid aerosol condensate. Due to the results of this study, we advise against the use of sucralose as sweetener in e-liquids.

Immobilized metal ion affinity chromatography (IMAC) is an important chromatographic technique for biomolecules. In order to get a detailed understanding of the hydration of immobilized Fe(III), complexes of Fe(III) with methyl substituted iminodiacetate ([Fe(MSIDA)(H2O)3](+)) as well as with methyl substituted nitrilotriacetate ([Fe(MSNTA)(H2O)2]) were simulated in aqueous solutions with the quantum mechanical charge field molecular dynamics (QMCF MD) approach. The simulations were carried out at the Hartree-Fock (HF) level of theory, since cluster calculations at the HF, MP2, and B3LYP levels of theory showed that this method results in a good compromise between computational effort and accuracy. None of the coordinating water molecules were exchanged during the simulation period of 15 ps. The Fe-OH2O bond distances as well as the Fe-OH2O stretching motions differed among the coordinating water molecules, indicating different bond strengths. For the water molecules in the second hydration layer, mean residence times of 2.7 and 1.9 ps were obtained for [Fe(MSIDA)(H2O)3](+) and [Fe(MSNTA)(H2O)2], respectively. Furthermore, infrared measurements were carried out to characterize the most prominent bond features of aqueous Fe(III)-NTA and to discuss these results in conjunction with the computationally derived frequencies.

We report a highly enantioselective oligomerization of isoleucine stereomers in the salt-induced peptide formation reaction under plausibly prebiotic earth conditions. Up to 6.5-fold superiority in reactivity of L-isoleucine was observed, compared to its D-enantiomer, after 14 evaporation cycles in the presence of Cu(2+) and NaCl. Since isoleucine is among the proteinogenic amino acids that were found enantioenriched in meteorites, this present work may further correlate the extraterrestrial delivery and endogenous production of biological homochirality by virtue of a protein constituent rather than the rarely occurring α-methylated amino acids.

The aqueous solutions of bisulfite (SO(3)H(-)) and sulfonate (HSO(3)(-)) were simulated by the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism. All superimposed trajectories for the atomic coordinates of solutes with three-dimensional alignment here illustrated the reactivities of the ions. Power spectra were evaluated on the basis of the velocity autocorrelation functions (VACFs) with the normal-mode analysis, presenting a higher frequency of the symmetric SO(3) deformation (δ(s)(SO(3))) than the asymmetric SO(3) deformation (δ(as)(SO(3))) modes for the sulfonate ion. The different influence of solvent on the frequency of the O-H and S-H stretching suggests a higher stability of hydrated sulfonate ion. The bisulfite shows a slightly stronger molecular hydration shell than the sulfonate ion with the average number of ion-solvent hydrogen bonds (H-bonds) of 5.3 and 5.0, respectively. Extra water molecules within the molecular hydration shell are found for bisulfite (1.2) and for sulfonate (1.6). The mean residence times for the water ligands classify each ion as a structure maker, while the S-H bond within the sulfonate ion displays a hydrophobic behavior. No tautomerization was observed within the simulation period.

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.

The previously investigated La3+-hydrate has been re-evaluated by means of the quantum mechanical charge field (QMCF) molecular dynamics (MD) approach. Improved description of the hydration characteristics has been realised by including the full second hydration shell into the quantum mechanically treated region and by introducing the influence of the surrounding bulk via an electrostatic embedding technique. Analytical tools such as the ligand angular radial distribution analysis have been employed to gain deeper insight into the structural features of the hydrate. La3+ simultaneously forms nona- and decahydrates with capped trigonal and quadratic prismatic structure, besides small amounts of an octahydrate.

Graphical abstract Highlights ►Concise treatment of highly charged ions with very different properties. ► Performed by ab initio simulations with the recent QMCF-MD methodology. ► Treating hydrates with extreme stability, labile hydrates and instable systems with (sub-)picosecond proton transfer reactions., Based on a series of ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulations, the broad spectrum of structural and dynamical properties of hydrates of trivalent and tetravalent ions is presented, ranging from extreme inertness to immediate hydrolysis. Main group and transition metal ions representative for different parts of the periodic system are treated, as are 2 threefold negatively charged anions. The results show that simple predictions of the properties of the hydrates appear impossible and that an accurate quantum mechanical simulation in cooperation with sophisticated experimental investigations seems the only way to obtain conclusive results.

The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate the bisulfate ion, HSO4-, in aqueous solution. The averaged geometry of bisulfate ion supports the separation of six normal modes of the O*-SO3 unit with C3v symmetry from three modes of the OH group in the evaluation of vibrational spectra obtained from the velocity autocorrelation functions (VACFs) with subsequent normal coordinate analyses. The calculated frequencies are in good agreement with the observations in Raman and IR experiments. The difference of the averaged coordination number obtained for the whole molecule (8.0) and the summation over coordinating sites (10.9) indicates some water molecules to be located in the overlapping volumes of individual hydration spheres. The averaged number of hydrogen bonds (H-bonds) during the simulation period (5.8) indicates that some water molecules are situated in the molecular hydration shell with an unsuitable orientation to form a hydrogen bond with the ion. The mean residence time in the surroundings of the bisulfate ion classify it generally as a weak structure-making ion, but the analysis of the individual sites reveals a more complex behavior of them, in particular a strong interaction with a water molecule at the hydrogen site.

Quantum mechanical/molecular mechanical (QM/MM) and quantum mechanical charge field (QMCF) molecular (MD) simulations have been performed to describe structural and dynamical properties of Na(I) and K(I) in water and to compare the two approaches. The first and second hydration shells were treated by ab initio quantum mechanics at the restricted Hartree-Fock (RHF) level. The structural data are in good agreement with previously published experimental and theoretical results. A considerable number of water exchange reactions were observed within the first shell during the simulation time of 12 ps. The number of exchange events in both shells is higher in the case of K(I) than Na(I) reflecting the weaker ion-ligand bond strength of K(I). Comparison of the "conventional" QM/MM framework with the QMCF method clearly indicates the latter to be advantageous, as ambiguities arising from the coupling of the subregions occurring in the QM/MM MD simulations did not evolve when the QMCF ansatz was applied.

The structural and dynamical properties of the cis-(O-Zn-O angle approximately 90 degrees) and trans-(O-Zn-O angle approximately 180 degrees) isomers of the model diaquotriamminezinc(II) complex in aqueous solution have been evaluated using the hybrid quantum mechanical/molecular mechanical molecular dynamics simulation approach at ab initio Hartree-Fock level. In both complexes, the first hydration shell contains five ligands (two water and three ammonia molecules) arranged in a trigonal bipyramidal geometry. In the metastable cis-isomer two different bond lengths of 2.34 and 2.13 A are observed for the Zn-Oax and Zn-Oeq bonds, respectively. The trans-isomer shows the maximum of the Zn-O distance at 2.26 A. The Zn-N bond distances in both cases are approximately 2.12 A. A geometrical transformation of the cis-isomer into the trans-isomer was observed after 11.5 ps of simulation, and the trans-isomer then remained stable throughout the whole simulation time of 30 ps. A comparative study for both isomers has been performed in terms of radial distribution functions, coordination number distributions, angular distribution functions, tilt and theta angle distributions, ligands' mean residence time, ion-ligand stretching frequencies, and the vibrational and librational motions of water ligands. The results are compared with the data for the previously studied zinc-monoamine and -diamine complexes.

According to recent research on the origin of life it seems more and more likely that amino acids and peptides were among the first biomolecules formed on earth and that a peptide/protein world was thus a key starting point in evolution towards life. Salt-induced Peptide Formation (SIPF) has repeatedly been shown to be the most universal and plausible peptide-forming reaction currently known under prebiotic conditions and forms peptides from amino acids with the help of copper ions and sodium chloride. In this paper we present experimental results for salt-induced peptide formation from methionine. This is the first time that a sulphur-containing amino acid was investigated in this reaction. The possible catalytic effects of glycine and L-histidine in this reaction were also investigated and a possible distinction between the L- and D-forms of methionine was studied as well.

The hydrated sulfate ion has been characterized in aqueous solution in structural and dynamic aspects using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation and large angle X-ray scattering (LAXS) methods. The LAXS data show an average coordination number of the sulfate ion of up to 12 water molecules bound through hydrogen bonding, while the QMCF MD simulation displays a wide range of coordination numbers between 8 and 14 with an average value of approximately 11. The Os...Ow distance cannot be distinguished from the Ow...Ow distance in the LAXS experiment; the weighted mean O...O distance is 2.880(10) A. In the simulation, the Os...Ow and Ow...Ow distances are found to be very similar, namely, 2.86 and 2.84 A, respectively. The S-Os bond and S...Ow distance have been determined by the LAXS experiment as 1.495(6) and 3.61(2) A, respectively, indicating an average nearly tetrahedral S-Os...Ow angle. The approximately 5% deviations of simulation distances (1.47 and 3.82 A) from the experimental ones can probably be ascribed to the neglect of correlation energy in the quantum mechanical method. The mean residence time of water ligands at O atoms, 2.57 ps, is longer than that in pure water, 1.7 ps, characterizing the sulfate ion as a weak structure maker.

Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.

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.

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.

Pattern and dynamics of hydrogen bonds in liquid water were investigated by a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulation at Hartree–Fock (HF) level of theory. A large subregion of the whole system comprising two complete coordination shells was treated quantum mechanically in order to include all polarization and charge transfer effects and to obtain accurate data about structure and dynamics of the intermolecular bonds. The results of this investigation are in agreement with recent experimental findings and suggest that in liquid water every molecule forms in average 2.8, but almost as a rule less than four intermolecular hydrogen bonds.

The progress of computational chemistry in the treatment of liquid systems is outlined, and the combination of the statistical methods (Monte Carlo, MC, and molecular dynamics, MD) with quantum mechanics as the main foundation of this progress is emphasized. The difficulties of experimental studies of liquid systems without having obtained sophisticated theoretical models describing the structural entities and the dynamical behavior of these liquids demonstrate that chemistry research is in a transition phase, where theory and high-performance computing have not only become a valuable supplement, but an essential and almost indispensable component to secure a correct interpretation of measured data.

Structure and dynamics investigations of Ag(+) in 18.6% aqueous ammonia solution have been carried out by means of the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation method. The most important region, the first solvation shell, was treated by ab initio quantum mechanics at the Restricted Hartree-Fock (RHF) level using double-zeta plus polarization basis sets for ammonia and plus ECP for Ag(+). For the remaining region in the system, newly constructed three-body corrected potential functions were used. The average composition of the first solvation shell was found to be [Ag(NH(3))(2)(H(2)O)(2.8)](+). No ammonia exchange process was observed for the first solvation shell, whereas ligand exchange processes occurred with a very short mean residence time of 1.1 ps for the water ligands. No distinct second solvation shell was observed in this simulation.

For more than three decades, classical statistical mechanics simulations have been employed in the study of pure liquids and solutions, often revealing valuable details of the composition and structure of these systems. The question whether the basic assumptions underlying the classical simulations, in particular the neglect of higher n-body effects, are justified and do not have any adverse effect on the results could only be answered after the progress in soft- and hardware enabled the performance of extended quantum-mechanics-based simulations. In the past few years, on the basis of a systematic investigation of ion solvation by means of this new technique, the importance of the ‘quantum effects’ has been identified and their inclusion has been clearly recognised as an often crucial condition to obtain accurate structural data and a reliable description of the solvation dynamics of ions. By now, quantum-mechanics-based simulations have justified their high computational demands by giving access to a large set of otherwise hardly accessible data such as the detailed molecular structure of microspecies formed in solution and ligand exchange processes at the picosecond time scale. From such simulations, and with the help of appropriate evaluation and visualisation tools, new insights have been obtained into the molecular pathways of reactions in solution for a series of main group and transition metal ions as well as for some anions, forming a new theoretical basis for the interpretation of experimental data in terms of reactivity and mechanisms.

Structural and dynamical properties of the hydrated Cs+ ion have been investigated by performing ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at different quantum mechanical levels (HF, B3LYP and BP86). The first shell coordination number was found to be ∼8 in the HF and ∼9 in the B3LYP and BP86 case and several other structural parameters such as angular distribution functions, radial distribution functions, and tilt- and θ-angle distributions allowed to fully characterize the hydration structure of the Cs+ ion. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion−ligand motions, as well as reorientation times. The strong “structure breaking” effect of Cs+ can be interpreted on the basis of different dynamical parameters such as accelerated water reorientation, mean ligand residence time, and the number of ligand exchange processes.

8 pages, 4 figures, 5 tables.-- Available online Oct 9, 2003., Different reaction yields for l- and d-alanine in the salt-induced peptide formation (SIPF) reaction, differences in the circular dichroism spectra and the complex formation constants of the involved chlorocuprate complexes point at a stereoselective differentiation between the two stereoisomers in the SIPF reaction and give a possible explanation towards the origin of homochirality in the process of the origin of life. An explanation of the observed effects can for the time being only be based on assumptions but could possibly be related to the inherent chirality of the CuII ion as a central atom of the [CuCl(gly)(glyH2)(H2O)2]+ complex due to parity violation in weak interactions and to amplification of chirality related to the structural properties of the complex., The question of the origin of homochirality is an essential part of the research concerned with the origin of life. In this paper we report about interesting differences in the complex formation constants and the CD spectra of copper(II)-amino acid complexes with l- and d-alanine due to parity violation and about different yields of peptides in a prebiotically highly relevant reaction based on these complexes., Financial support of this work by the Austrian Federal Government within the Bilateral Spanish–Austrian Cooperation “Acciones Integradas 2000–2001” (project 10/2000) in Science and Technology and by the Austrian Federal Ministry of Education, Science and Culture (bm:bwk, Project GZ 45.445/1-III/B/8a/99).

The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (

A hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to evaluate hydration structure and dynamics of the Cd 2 + ion in aqueous solution. Two hydration shellswere identified at the mean distances of 2.3 and 4.8 A, with coordination numbers of 6 and ∼12, respectively, which is in good agreement with X-ray data. Librational and vibrational spectra of the hydrated Cd 2 + ion have been evaluated, showing a fairly complex spectrum for Cd-O vibrations, whose stretching force constant of 68 N m - 1 is slightly higher than that for Hg-O vibrations. The mean residence time for the 2nd shell ligands was determined as 10 ps, and the calculated hydration energy of -458 kcal/ mol is close to the experimental value of -438 kcal/mol.

A molecular dynamics simulation based on ab initio quantum mechanical forces in combination with molecular mechanics has been performed to describe structural and dynamical properties of Ag+ in water. The first hydration shell, being the chemically most relevant region, was treated by quantum mechanics at Hartree−Fock level using the LANL2DZ ECP for Ag+ and double-ζ plus polarization basis sets for water. The outer region of the system was described using a newly constructed classical three-body corrected potential derived from ab initio energy surfaces. The structure was evaluated in terms of radial and angular distribution functions and coordination number distributions. Water exchange processes between coordination shells have been investigated and evaluated. The results show that the first hydration shell is of rather irregular shape, with an average coordination number of 5.5. Fast water exchange processes between the first and second hydration shell were observed, leading to a preference of 5- and 6...

The hydration shell structure of Fe(II) and Fe(III) ions in their high spin state has been studied by combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, in which the ion and its first hydration sphere were treated at the Hartree−Fock ab initio quantum mechanical level, whereas ab initio generated pair plus three-body potentials were employed for the remaining system. The coordination number in the first hydration shell is 6 for both Fe(II) and Fe(III) ions. The second hydration shell contains 12.4 and 13.4 water molecules for Fe(II) and Fe(III) ions, respectively, in good agreement with the experimental values. The residence time of a water molecule in the second hydration shells of Fe(II) and Fe(III) is 24 and 48 ps, respectively. The complex configuration and ligand orientations observed in this study prove that many-body effects play an important role in the hydration of both Fe(II) and Fe(III) ions. The hydration energies computed from the simulation are...

Molecular dynamics simulations with new reliable quantum chemical potential have been performed for liquid N,N -dimethylformamide (DMFA). Structural properties of DMFA were investigated in comparison with earlier results for liquid formamide (FA) using the atom-atom radial distribution functions, dipole-dipole correlation function, H-bonds network properties and statistical geometry approach. Autocorrelation functions were applied to study the translational/reorientational diffusion and librational/vibrational molecular motion. Liquid FA structure can be described as a continuous rambling H-bond network with great variety of individual H-bond geometry. Stacked and linear dimeric formations arise in the DMFA local structure due to predominance of dipole — dipole interactions. Similar modes of vibrational molecular motions are observed for FA and DMFA. Librational molecular motions have the same time scale for FA and DMFA, but rotational motions are slightly anisotropic for FA.

A combined theoretical and experimental study was performed to elucidate the structural and dynamical properties of the isolated aqueous hexacyanoferrate(II) ion as well as in the presence of potassium counterions. It is shown that in absence of counterions, the highly negatively charged hexacyanoferrate(II) complex is not stable in aqueous solution. However, if the high negative charge is compensated by potassium counterions, a stable complex is observed, which is proven by theoretical simulations as well as by extended X-ray absorption fine structure (EXAFS) experiments. From the simulation it is found that potassium ions surrounding the complex are highly mobile and thus cannot be observed via EXAFS experiments. The structure of aqueous hexacyanoferrate(II) in the presence of potassium ions is identical to that of the solid-state structure, but the mobility of potassium ions is significantly increased in the liquid. These highly mobile potassium ions circulating the complex are the reason for the very short lifetime of hydrogen bonds between solvent water molecules and cyanide ligands being on the femtosecond scale.

Molecular dynamics (MD) simulations based on ab initio evaluated two- and three-body potentials were performed for Ti3+, Cr3+, and Co3+ ions in water. The ions' hydration structure was evaluated in terms of radial distribution functions, coordination numbers, and angular distributions. The first solvation shell shows an exact coordination number of 6 for all ions and average M3+−O distances of 2.08, 2.05, and 2.03 A for Ti3+, Cr3+, and Co3+, respectively. The structural parameters obtained after inclusion of three-body correction terms are in good agreement with experimental values. The energies of hydration obtained from three-body corrected molecular dynamics simulations are also in good agreement with experiment, except for Ti3+ where the classical simulations are failing to reproduce the Jahn−Teller effect.

Two different quantum mechanics/molecular mechanics molecular dynamics simulation techniques (QM/MM-MD) are compared using as an example the hydrated manganous ion. One includes a perturbation field composed of point charges representing the bulk solvent molecules polarizing the QM region in addition to a quantum chemically derived two-body potential. The other includes the two-body potential plus a three-body correction function. In both simulations, the QM region comprises the ion and its first hydration shell and hence includes all many-body terms up to the QM frontier. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and angular distributions. The results show that both QM/MM-MD techniques agree well with experimental findings for the first-shell hydration structure. QM/MM-MD including point charges has been found to be a satisfactory and economic alternative in studying the first hydration shell without the need to undergo the time-consum...

Classical molecular dynamics (MD), classical Monte Carlo (MC), and combined quantum mechanical/molecular mechanical (QM/MM) MD simulations were carried out to investigate the hydration structure of the Ni(II) ion in water using a newly constructed 2-body potential and a function correcting for 3-body effects. A 6-coordinate hydration structure with a maximum probability of the Ni−O distance at 2.25, 2.21, and 2.14 A was observed by the classical MD, classical MC, and QM/MM-MD simulation with 3-body corrections, respectively, while an 8-coordinate structure was observed by the classical MD and MC simulations using only 2-body pair potentials. The average structure parameters obtained by the Hertree-Fock level QM/MM-MD simulation are in agreement with the experimental values. The validity of the 3-body correction function is discussed on the basis of the results for the classical and QM/MM simulations. During the classical MD simulation, a water exchange reaction was observed for the 6-coordinate Ni(II) ion...

The catalytic properties of various forms of alumina were tested for alanine dimerization reaction. The catalytic efficiency of alumina depends on the structure, as well as on acid/base properties of the catalyst. The highest yields of Ala2 were achieved on activated alumina with surface of neutral pH (about 3% conversion after 2 weeks). Thermal analysis of Ala + alumina reaction systems shows that the thermal behavior of amino acid changes substantially in contact with the activated surface of the alumina catalyst. The reaction of Ala is detected as being strongly endothermic by differential thermal analysis of pure amino acid (above 250 degrees C). The alanine endothermic reaction is shifted substantially to lower values (below 200 degrees C) and hardly detectable if activated alumina is present. The reaction mechanism of amino acid activation on alumina surface and its significance for mineral-catalyzed prebiotic peptide bond formation are discussed.

An ab intio two-body analytical potential function was constructed to describe Mn(II)−water interactions. Classical Monte Carlo (MC) and molecular dynamics (MD) simulations have been performed to s...

Molecular dynamics simulations have been performed for 8 methanol-water solutions using rigid and flexible potential models. The heat capacity, the radial distribution functions and potential mean force obtained by MD simulations were compared to previous simulations and experimental results. Special attention has been paid to the anomalous behaviour of the heat capacity of dilute aqueous solutions of methanol. This behaviour can be attributed to a cooperative effect resulting from methanol-methanol associations.

Molecular dynamics computer simulations have been performed for Na+/Cl−-water-formamide mixtures over the whole concentration range of the mixed solvent. It is shown that both Na+ cation and Cl− anion are preferentially solvated by formamide even if only small amounts of formamide are present in the mixture. The Walden products for Na+ and Cl− ions in binary mixture are calculated. It is concluded that the attempts of the direct correlation between the Walden product function shape and the specific ion solvation shell structure might not be successful.

Four 700-ps molecular dynamics simulations were carried out to analyze the structural dynamics of the antigen-binding antibody fragment NC6.8, which is known to exhibit large structural changes upon complexation. The first simulation was started from the x-ray structure of the uncomplexed Fab and produced trajectory averages that closely match the crystallographic results. It allowed assessment of the flexibility of the Fab, revealing an elbow motion of the variable domains with respect to the constant domains. The second simulation was started from the uncomplexed x-ray structure after insertion of the ligand into the binding site. This perturbation resulted in a significantly altered trajectory, with quaternary structural changes corresponding in many aspects to the experimental differences between complexed and uncomplexed state. The observed trend toward a smaller elbow angle and a higher flexion of the H-chain could also be seen in the third simulation, which was started from the x-ray structure of the complex. The changes were revealed to be a clear consequence of the complexation with the ligand because in the fourth simulation (started from the experimental complex structure after removal of the hapten) the Fab remained close to its initial structure. Analyses of the quaternary structure and the binding site of Fab NC6.8 are presented for all four simulations, and possible interpretations are discussed.

An ab initio molecular dynamics simulation based on combined quantum mechanical and molecular mechanical (QM/MM) potential was performed for Na+ in liquid ammonia. With this approach, many-body interactions that are very significant in determining the solvation number are modeled accurately by quantum mechanics. The method appears to resolve the discrepancy between many simulations that have predicted solvation numbers between 5 and 9. Although the solvation number of 5 obtained from our QM/MM simulation has not yet been confirmed by the experimental data, a detailed analysis of the simulation results together with a comparison of previous studies on known systems justifies this prediction.

The Cu2+ hydration shell structure has been studied by a combined ab initio quantum mechanical/molecular mechanical (QM/MM) Monte Carlo simulation, in which the ion and its first hydration sphere are treated at the Born−Oppenheimer ab initio quantum mechanical level, while classical pair and three-body potentials are employed for the remaining system. Whereas traditional simulations based on MM potentials are not able to predict higher-body effects such as the Jahn−Teller (JT) distorted octahedral structure of the first hydration shell of Cu2+, the combined QM/MM approach reproduces correctly this experimentally confirmed property and delivers more accurate hydration energy values as well.

The solvation structure of Cu+ in water and in liquid ammonia has been investigated using the Metropolis Monte Carlo method. The systems consisting of one Cu+ in 215 solvent molecules have been simulated at a temperature of 240 K for ammonia and 298 K for water, respectively. Cu+−ammonia and Cu+−water pair potentials have been newly developed based on ab initio calculations of double-ζ quality. Structural properties were investigated by means of radial distribution functions and their running integration numbers, leading for the first solvation shell to an average coordination number 6 and Cu−N distance of 2.20 A in ammonia, and to number 6 and Cu−O distance of 2.20 A in water. The RDFs, coordination number distributions, and pair interaction energy distribution analyses indicate that ligand exchange reactions take place more easily in water than in liquid ammonia.

The catalytic efficiency in peptide bond formation of various clays was tested by reactions of glycine (gly), diglycine (gly 2 ), glycine+alanine (ala), gly 2 +ala. The main effects of clay structure and composition resulted as following: (1) Clay composition influences the activation of reactant molecules at clay particle edges. (2) Acidity (basicity) of the clay surface can change on the state of the reactant. (3) The clay structure is related to suspension stability and thus accessibility of clay catalytic sites. Mg-rich trioctahedral clays hectorite (smectite) and talc are the most efficient catalysts. Oligomerization of gly and gly 2 proceeds on all clays, whereas oligopeptides including ala units are formed with much lower yields and only on the most efficient catalysts. Besides dipeptides and other linear peptides, also cyclic anhydride (diketopiperazine) is formed with relatively high yields from diglycine. Cyclic anhydrides can directly act in the formation of the linear oligopeptides by ring opening molecular rearrangement and addition of another amino acid (oligopeptide).

The Cu2+−NH3 pair potential and the corresponding three-body correction functions have been newly constructed on the basis of ab initio calculations of double-ζ quality. Monte Carlo simulation resu...

The structures, gas-phase acidities and vibrational spectra of selenoformic O-acid, selenoformic Se-acid and several of their derivatives RCSeOH and RCOSeH (R = H, F, Cl, NH2, CH3) were investigated by DFT calculations. Geometry optimizations and frequency computations were performed at the Becke3LYP level of theory with the 6-311+G(d,p) basis set. For all 10 acids studied, the syn conformers are predicted to have the lowest energy. The syn−anti enthalpy difference varies between 0.3 and 9.9 kcal mol-1, the syn selenol acids being substantially more stable than their syn selenoxo counterparts. The substitution of oxygen by selenium in the selenocarboxylic acids studied leads to increased acidity. The selenol acids are weaker acids than the selenoxo derivatives.

Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3', 5'-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA data and to detect possible outliers in the data set. PLS is applied to correlate the CoMFA data with either calculated AM1 proton affinities or with experimental pKa values. The possibility of making a prediction of pKa values directly from 3D structures of the monomers for polynucleotides is also shown. The influence of the superposition criteria and of conformational changes along the glycosidic bond on the pKa prediction are studied as well.

The description of nonadditive contributions in the first hydration shell of Na+ and K+ has been improved by performing molecular dynamics simulations based on combined ab initio quantum mechanical...

Ab initio molecular orbital calculations at the CBS-Q level of theory have been performed for 72 complexes in order to determine the effects of molecular structure on gas-phase basicity toward H+, Li+, and Mg2+. It is shown that basicities toward metal cations Li+ and Mg2+ differ considerably from the corresponding gas-phase basicities toward H+. Calculated interaction energies vary as H+ ≫ Mg2+ > Li+. The relative basicities of the bases studied depend characteristically on type of cation and coordination site.

The peptide bond formation of alanine (ala), ala + glycine (gly), ala + diglycine (gly2), and ala + gly cyclic anhydride (cyc-gly2) in drying/wetting cycles at 80°C was studied. Silica, alumina, and representative smectites—montmorillonite and hectorite—were used as catalysts, and the dependence of reaction yields on the available amount of water in the reaction systems was evaluated. Silica and alumina catalyze the formation of oligopeptide mainly in temperature fluctuation experiments, whereas higher amounts of water in the reaction system support clay-catalyzed reactions. Silica and alumina are much more efficient for amino acid dimerization than clays. Whereas only 0.1% of ala oligomerized on hectorite and no reaction proceeded on montmorillonite, about 0.9 and 3.8% alanine converted into its dimer and cyclic anhydride on silica and alumina, respectively. Clay minerals, on the other hand, seem to more efficiently catalyze peptide chain elongation than amino acid dimerization. The reaction yields of ala-gly-gly and gly-gly-ala from ala + gly2 and ala + cyc-gly2 reached about 0.3% on montmorillonite and 1.0% on hectorite. The possible mechanisms of these reactions and the relevance of the results for prebiotic chemistry are discussed.

A detailed analysis of reaction-path dynamics of hydrogen abstraction from ethane, fluoroethane, and chloroethane by hydroxyl radical has been performed by the variational transition-state theory augmented with multidimensional semiclassical tunneling approximations. The minimum energy path and its first and second derivatives were calculated at the MP2(full)/6-31G(d,p) level of theory. The calculated barrier heights were further improved by Gaussian-2(MP2) methodology. This dual-level dynamic approach has been used to calculate the reaction rate constants for temperatures from 200 to 1000 K. The contribution from tunneling effect was evaluated using the semiclassical zero-curvature and small-curvature tunneling approximations. The calculated thermal reaction rate constants agree well with the experimental results. The variational effects on the location of central dynamical bottleneck are significant for all three reactions. The competition between potential and vibrational energies in determining the lo...

The concerted proton transfer hypersurface of cyclic water and hydrogen fluoride clusters has been described by high-level molecular quantum mechanical calculations. For the cyclic water clusters the concerted proton transfer transition states have been investigated for the first time with methods including treatment of dynamic electron correlation. The crucial importance of dynamic electron correlation for the barrier heights is demonstrated, A detailed analysis of the minimum energy path has been performed. The reaction swath of the concerted proton transfer was examined indicating a reasonable description by harmonic approximation of the energy hypersurface. Transfer rates have been calculated by means of variational transition state theory with interpolated corrections (VTST-IC) and dual-level direct dynamics (DLDD), both with semiclassical tunneling corrections. Tunneling is very efficient in the concerted proton exchange reaction of the cyclic hydrogen-bonded clusters under investigation. Rate constants for the concerted exchange of hydrogens in important hydrogen fluoride vapor phase species are reported for the first time. In the hydrogen fluoride tetramer and pentamer the concerted proton exchange of four and five protons, respectively, takes place with reaction rates that an comparable with the concerted exchange rates in carboxylic acid dimers and is not hindered by the large number of simultanously moving protons. The concerted proton exchange rates in the studied water clusters are comparably low because of higher exchange barriers. It is shown that hydrogen fluoride clusters can be used to a large extent as ''simplified'' experimental and theoretical models for water clusters.

Structural and dynamical properties of the erbium(III) ion in water have been obtained by means of ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations for the ground state and an excited state. The quality of the simulations has been monitored by recording UV/vis and Raman spectra of dilute solutions of ErCl3 and Er(NO3)3 in water and by comparison with EXAFS data from literature. Slight deviations between these data can be mainly attributed to relativistic effects, which are not sufficiently considered by the methodological framework. In both simulations, a mixture of coordination numbers eight and nine and a ligand exchange on the picosecond range are observed. The strength of the Er-ligand bond is considerably lower than that of trivalent transition metal ions but higher than that for La(III) and Ce(III) in aqueous solution. The main difference between ground state and excited state is the ligand exchange rate of the first shell. The second hydration shell is stable in both cases but with significantly different properties.