High density amorphous ice from cubic ice.
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Journal Article↗
Biomedical subjects
Thomas Loerting
Publications and source records attributed to Thomas Loerting.
Hydrogen chloride-induced surface disordering on ice.
Characterizing the interaction of hydrogen chloride (HCl) with polar stratospheric cloud ice particles is essential for understanding the processes responsible for ozone depletion. We studied the interaction of gas-phase HCl with ice between 243 and 186 K by using (i) ellipsometry to monitor the ice surface and (ii) coated-wall flow tube experiments, both with chemical ionization mass spectrometry detection of the gas phase. We show that trace amounts of HCl induce formation of a disordered region, or quasi-liquid layer, at the ice surface at stratospheric temperatures. We also show that surface disordering enhances the chlorine activation reaction of HCl with chlorine nitrate (ClONO(2)) and also enhances acetic acid (CH(3)COOH) adsorption. These results impact our understanding of the chemistry and physics of ice particles in the atmosphere.
Journal Article↗
The relation between high-density and very-high-density amorphous ice.
The exact nature of the relationship between high-density (HDA) and very-high-density (VHDA) amorphous ice is unknown at present. Here we review the relation between HDA and VHDA, concentrating on experimental aspects and discuss these with respect to the relation between low-density amorphous ice (LDA) and HDA. On compressing LDA at 125 K up to 1.5 GPa, two distinct density steps are observable in the pressure-density curves which correspond to the LDA --> HDA and HDA --> VHDA conversion. This stepwise formation process LDA --> HDA --> VHDA at 125 K is the first unambiguous observation of a stepwise amorphous-amorphous-amorphous transformation sequence. Density values of amorphous ice obtained in situ between 0.3 and 1.9 GPa on isobaric heating up to the temperatures of crystallization show a pronounced change of slope at ca. 0.8 GPa which could indicate formation of a distinct phase. We infer that the relation between HDA and VHDA is very similar to that between LDA and HDA except for a higher activation barrier between the former. We further discuss the two options of thermodynamic phase transition versus kinetic densification for the HDA --> VHDA conversion.
Chemical Phenomena↗
Amorphous ice: stepwise formation of very-high-density amorphous ice from low-density amorphous ice at 125 K.
On compressing low-density amorphous ice (LDA) at 125 K up to 1.6 GPa, two distinct density steps accompanied by heat evolution are observable in pressure-density curves. Samples recovered to 77 K and 1 bar after the first and second steps show the x-ray diffraction pattern of high-density amorphous ice (HDA) and very HDA (VHDA), respectively. The compression of the once formed HDA takes place linearly in density up to 0.95 GPa, where nonlinear densification and HDA --> VHDA conversion is initiated. This implies a stepwise formation process LDA--> HDA --> VHDA at 125 K, which is to the best of our knowledge the first observation of a stepwise amorphous-amorphous-amorphous transformation sequence. We infer that the relation of HDA and VHDA is very similar to the relation between LDA and HDA except for a higher activation barrier between the former. We discuss the two options of thermodynamic versus kinetic origin of the phenomenon.
Journal Article↗
Isobaric annealing of high-density amorphous ice between 0.3 and 1.9 GPa: in situ density values and structural changes.
We report in situ density values of amorphous ice obtained between 0.3 and 1.9 GPa and 144 to 183 K. Starting from high-density amorphous ice made by pressure-amorphizing hexagonal ice at 77 K, samples were heated at a constant pressure until crystallization to high-pressure ices occurred. Densities of amorphous ice were calculated from those of high-pressure ice mixtures and the volume change on crystallization. In the density versus pressure plot a pronounced change of slope occurs at approximately 0.8 GPa, with a slope of 0.21 g cm(-3) GPa(-1) below 0.8 GPa and a slope of 0.10 g cm(-3) GPa(-1) above 0.8 GPa. Both X-ray diffractograms and Raman spectra of recovered samples show that major structural changes occur up to approximately 0.8 GPa, developing towards those of very high-density amorphous ice reported by (T. Loerting, C. Salzmann, I. Kohl, E. Mayer and A. Hallbrucker, Phys. Chem. Chem. Phys., 2001, 3, 5355) and that further increase of pressure has only a minor effect. In addition, the effect of annealing temperature (T(A)) at a given pressure on the structural changes was studied by Raman spectra of recovered samples in the coupled O-H and decoupled O-D stretching band region: at 0.5 GPa structural changes are observed between approximately 100-116 K, at 1.17 GPa between approximately 121-130 K. Further increase of T(A) or of annealing time has no effect, thus indicating that the samples are fully relaxed. We conclude that mainly irreversible structural changes between 0.3 to approximately 0.8 GPa lead to the pronounced increase in density, whereas above approximately 0.8 GPa the density increase is dominated to a large extent by reversible elastic compression. These results seem consistent with simulation studies by (R. Martonàk, D. Donadio and M. Parrinello, J. Chem. Phys., 2005, 122, 134501) where substantial reconstruction of the topology of the hydrogen bonded network and changes in the ring statistics from e.g. mainly six-membered to mainly nine-membered rings were observed on pressure increase up to 0.9 GPa and further pressure increase had little effect.
Algorithms↗
Liquid-like relaxation in hyperquenched water at < or = 140 K.
Micrometre-sized water droplets were hyperquenched on a solid substrate held at selected temperatures between 150 and 77 K. These samples were characterized by differential scanning calorimetry (DSC) and X-ray diffraction. 140 K is the upper temperature limit to obtain mainly amorphous samples on deposition within 16-37 min. DSC scans of glassy water prepared at 140 K exhibit on heating an endothermic step assignable to glass --> liquid transition, with an onset temperature (T(g)) of 136 +/- 2 K on heating at 30 K min(-1). For T(g) of approximately 136 K, water relaxes during deposition at 140 K for 16 min, moving towards metastable equilibrium. The apparent increase in heat capacity (deltaC(p)) depends, for a given rate of heating, on the rate of prior cooling, and a so-called overshoot develops. 140 K deposits cooled at a rate of 5, 2 or 0.2 K min(-1) show on subsequent reheating at a rate of 30 K min(-1) deltaC(p) values of 0.7, 1.1 and 1.7 J K(-1) mol(-1). This is consistent with liquid-like relaxation at 140 K, and it indicates that different limiting structures are obtained. When these 140 K deposits are in addition annealed at 130 K for 90 min, after slow-cooling at 5, 2 or 0.2 K min(-1), their deltaC(p) values on subsequent reheating are similar to those of hyperquenched glassy water (HGW) deposits made at 77 K and annealed at 130 K. Thus, the previous deltaC(p) value of 1.6 J K(-1) mol(-1) obtained with glassy water samples annealed at 130 K (A. Hallbrucker, E. Mayer and G. P. Johari, Philos. Mag. B, 1989, 60, 179) must be an upper-bound limit because it contains a contribution from an overshoot. The T(g) value of 140 K deposits, which had relaxed during deposition towards metastable equilibrium, is within experimental error the same as that of 140 K deposits annealed in addition at 130 K. This contradicts Yue and Angell's (Y. Yue and C. Angell, Nature, 2004, 427, 717) claim for assigning the endothermic step to a sub-T(g) peak or a "shadow" T(g). Our new data further support the proposed fragile-to-strong transition on cooling liquid water from ambient temperature into the deeply supercooled and glassy state. We also describe in detail experimental aspects to obtain HGW specimens, show the ultrastructure of the deposits using electron microscopy, and discuss the mechanism of our hyperquenching method.
Journal Article↗
Water Behaviour: glass transition in hyperquenched water?
It has been unclear whether amorphous glassy water heated to around 140-150 K remains glassy until it crystallizes or whether instead it turns into a supercooled and very viscous liquid. Yue and Angell compare the behaviour of glassy water under these conditions to that of hyperquenched inorganic glasses, and claim that water stays glassy as it heats up to its crystallization point; they also find a 'hidden' glass-to-liquid transition at about 169 K. Here we use differential scanning calorimetry (DSC) heating to show that hyperquenched water deposited at 140 K behaves as an ultraviscous liquid, the limiting structure of which depends on the cooling rate--as predicted by theoretical analysis of the liquid-to-glass transition. Our findings are consistent with a glass-to-liquid transition-onset temperature (T(g)) in the region of 136 K (refs 3,4), and they indicate that measurements of the liquid's properties may clarify the anomalous properties of supercooled water.
Comment↗
Daunomycin intercalation stabilizes distinct backbone conformations of DNA.
Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG)2 in the B-form with two putative intercalation sites at the 5'-CGA-3' step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5'-CGA-3' steps. Thereby--in contrast to X-ray structures--a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5'-CG-3' bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of BI and BII around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.
Binding Sites↗
Modeling anhydrous and aqua copper(II) amino acid complexes: a new molecular mechanics force field parametrization based on quantum chemical studies and experimental crystal data.
This paper presents the vacuum structures of aquacopper(II) bis(amino acid) complexes with glycine, sarcosine, N,N-dimethylglycine, and N-tert-butyl-N-methylglycine estimated using the B3LYP method. The differences between the B3LYP vacuum structures and experimental crystal structures suggested considerable influence of crystal lattice packing effects on the changes in the complexes' geometries. A previously developed molecular mechanics force field for modeling anhydrous copper(II) amino acidates was reoptimized to simulate these changes and predict the properties of both trans and cis anhydrous and aqua copper(II) amino acid complexes. The modeling included experimental molecular and crystal structures of 13 anhydrous and 10 aqua copper(II) amino acidates with the same atom types (Cu(II), C, H, N, and O) but various copper(II) coordination polyhedron geometries, crystal symmetries, and intermolecular interactions. The empirical parameters of the selected potential energy functions were optimized on the B3LYP vacuum copper(II) coordination geometries of three anhydrous copper(II) amino acidates and on experimental crystalline internal coordinates and unit cell dimensions of six anhydrous and six aqua copper(II) amino acid complexes. The respective equilibrium structures were calculated in vacuo and in simulated crystalline environment. The efficacy of the final force field, FFW, was examined. The total root-mean-square deviations between the experimental and theoretical crystal values were 0.018 A in the bond lengths, 2.2 degrees in the valence angles, 5.5 degrees in the torsion angles, and 0.395 A in the unit cell lengths. FFW reproduced the unit cell volumes in the range from -8.1 to 9.6%. The means of Cu to axial water oxygen distances were 2.4 +/- 0.1 A (experiment) and 2.6 +/- 0.1 A (FFW). This paper describes the ability of the molecular mechanics model and FFW force field to simulate the flexibility of the metal coordination polyhedron. The new force field proved effective in predicting the most stable molecular conformation of copper(II) amino acidato systems in vacuo.
Journal Article↗
Extended method for adiabatic mode reordering.
The task of vibrational mode reordering is very important for reaction valley studies and for the determination of small curvature tunneling effects. An extended algorithm for adiabatic mode reordering is presented. It is based on the method introduced by Konkoli et al. [J Comput Chem 1997, 18, 1282], which is shown to suffer from numerical problems in the region of frequency-crossings and avoided crossings. One improvement is the use of cubic splines for the interpolation of the projected matrix of force constants, which allows larger step sizes between the discrete points along the reaction path, where vibrational analysis is performed. The main improvement is the use of perturbation theory to resolve crossings and avoided crossings. Within this theoretical framework it becomes clear why the method of the maximal overlap between the normal modes cannot work properly, as eigenvectors associated with nearby eigenvalues tend to become "wobbly". Thus a perturbative procedure is designed that is used for all cases where two harmonic frequencies approach each other and the overlap of the associated normal modes is of no practical use. Advantages of the new procedure are the use of larger step sizes along the minimum energy path and the much more reliable resolution of mode-crossings and avoided crossings independent of the systems symmetry. In addition to that it is shown that one should be very cautious in all computational situations when working with eigenvectors associated with nearby eigenvalues.
Journal Article↗
About the stability of sulfurous acid (H2SO3) and its dimer.
The characterization and isolation of sulfurous acid (H2SO3) have never been accomplished and thus still remain one of the greatest open challenges of inorganic chemistry. It is known that H2SO3 is thermodynamically unstable. In this study, however, we show that a Ci-symmetric dimer of sulfurous acid (H2SO3)2 is 3.5 kcal mol-1 more stable than its dissociation products SO2 and H2O at 77 K. Additionally, we have investigated the kinetic stability of the sulfurous acid monomer with respect to dissociation into SO2 and H2O and the kinetic isotope effect (KIE) on this reaction by transition-state theory. At 77 K, the half-life of H2SO3 is 15 x 10(9) years, but for the deuterated molecule (D2SO3) it increases to 7.9 x 10(26) years. At room temperature, the half-life of sulfurous acid is only 24 hours; however, a KIE of 3.2 x 10(4) increases it to a remarkable 90 years. Water is an efficient catalyst for the dissociation reaction since it reduces the reaction barrier tremendously. With the aid of two water molecules, one can observe a change in the reaction mechanism for sulfurous acid decomposition with increasing temperature. The most likely mechanism below 170 K is via an eight-membered transition-state ring; yet, above 170 K, a mechanism with a six-membered transition state ring becomes the predominant one. For deuterated sulfurous acid, this change in reaction mechanism can be observed at 120 K. Consequently, between 120 and 170 K, different predominant reaction mechanisms occur for the decomposition of normal and deuterated sulfurous acid when assisted by two water molecules. However, the much longer half-life of deuterated sulfurous acid and the stability of the sulfurous acid dimer at 77 K are encouraging for future synthesis and characterization under laboratory conditions.
Journal Article↗
Towards the experimental decomposition rate of carbonic acid (H2CO3) in aqueous solution.
Dry carbonic acid has recently been shown to be kinetically stable even at room temperature. Addition of water molecules reduces this stability significantly, and the decomposition (H2CO3 + nH2O --> (n+1)H2O + CO2) is extremely accelerated for n = 1, 2, 3. By including two water molecules, a reaction rate that is a factor of 3000 below the experimental one (10 s(-1)) at room temperature was found. In order to further remove the gap between experiment and theory, we increased the number of water molecules involved to 3 and took into consideration different mechanisms for thorough elucidation of the reaction. A mechanism whereby the reaction proceedes via a six-membered transition state turns out to be the most efficient one over the whole examined temperature range. The determined reaction rates approach experimental values in aqueous solution reasonably well; most especially, a significant increase in the rates in comparison to the decomposition reaction with fewer water molecules is found. Further agreement with experiment is found in the kinetic isotope effects (KIE) for the deuterated species. For water-free carbonic acid, the KIE (i.e., kH2CO3/kD2CO3) for the decomposition reaction is predicted to be 220 at 300 K, whereas it amounts to 2.2-3.0 for the investigated mechanisms including three water molecules. This result is therefore reasonably close to the experimental value of 2 (at 300 K). These KIEs are in much better accordance with the experiment than the KIE for decomposition with fewer water entities.
Carbonic Acid↗