High density amorphous ice from cubic ice.
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Journal Article↗
Biomedical subjects
Erwin Mayer
Publications and source records attributed to Erwin Mayer.
Raman spectroscopic study of hydrogen ordered ice XIII and of its reversible phase transition to disordered ice V.
Raman spectra of recovered ordered H(2)O (D(2)O) ice XIII doped with 0.01 M HCl (DCl) recorded in vacuo at 80 K are reported in the range 3600-200 cm(-1). The bands are assigned to the various types of modes on the basis of isotope ratios. On thermal cycling between 80 and 120 K, the reversible phase transition to disordered ice V is observed. The remarkable effect of HCl (DCl) on orientational ordering in ice V and its phase transition to ordered ice XIII, first reported in a powder neutron diffraction study of DCl doped D(2)O ice V (C. G. Salzmann, P. G. Radaelli, A. Hallbrucker, E. Mayer, J. L. Finney, Science, 2006, 311, 1758), is demonstrated by Raman spectroscopy and discussed. The dopants KOH and HF have only a minor effect on hydrogen ordering in ice V, as shown by the Raman spectra.
Hydrogen↗
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↗
The preparation and structures of hydrogen ordered phases of ice.
Two hydrogen ordered phases of ice were prepared by cooling the hydrogen disordered ices V and XII under pressure. Previous attempts to unlock the geometrical frustration in hydrogen-bonded structures have focused on doping with potassium hydroxide and have had success in partially increasing the hydrogen ordering in hexagonal ice I (ice Ih). By doping ices V and XII with hydrochloric acid, we have prepared ice XIII and ice XIV, and we analyzed their structures by powder neutron diffraction. The use of hydrogen chloride to release geometrical frustration opens up the possibility of completing the phase diagram of ice.
Journal Article↗
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↗
Z-DNA's conformer substates revealed by FT-IR difference spectroscopy of nonoriented left-handed double helical poly(dG-dC).
Nonoriented hydrated films of double helical poly(dG-dC) in the Z-form were studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated slow-cooled samples between 290 and 220 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200, 220, and 240 K. IR spectral changes on isothermal relaxation at 200 and 220 K toward equilibrium, caused by interconversion of two conformer substates (CS) called Z1 and Z2, are revealed by IR difference spectra. Pronounced spectral changes on Z1-to-Z2 interconversion occur between approximately 750-1250 cm(-1) and these are attributed to structural changes of the phosphodiester-sugar backbone caused by changes of torsion angles, and to decreasing hydrogen-bonding of the ionic phosphate group with water molecules. These spectral changes on Z1-to-Z2 transition can be related to structural differences between ZI and ZII CS observed in single crystals. ZI/ZII CS occurs only at (dGpdC) base steps, and similar behavior is assumed for Z1/Z2. The Z1/Z2 population ratio was determined via curve resolution of marker bands for Z1 and Z2 centered at 785 and 779 cm(-1). This ratio is 0.64 at 290 K, corresponding to 39% of the phosphates of the (dGpdC) base steps in Z1 and 61% in Z2, and it increases to 1.24 on cooling to 220 K. For the Z2<=>Z1 equilibrium, an enthalpy change of -4.9 +/- 0.2 kJ mol(dGpdC)(-1) is obtained from the temperature dependence of the equilibrium constant. Z1 interconverts into Z2 at isothermal relaxation at 200 and 220 K, whereas on slow cooling from ambient temperature, Z2 interconverts into Z1. This unexpected reversal of CS interconversion is attributed to slow restructuring of hydration shells of the CS on quenching, in the same manner reported by Pichler et al. for the BI and BII CS of B-DNA (J. Phys. Chem. B 106, 3263-3274 (2002)). IR difference curves demonstrate two time scales on isothermal relaxation of Z1-->Z2 interconversion, a fast one for structural relaxation of the sugar-phosphate backbone, and a slow one for relaxation of the hydration shells. This slowing down of restructuring of CS hydration shells at approximately 220-240 K could be the cause for the suppression of biological functions at low temperatures.
DNA, Z-Form↗
Towards an understanding of DNA recognition by the methyl-CpG binding domain 1.
CpG methylation determines a variety of biological functions of DNA. The methylation signal is interpreted by proteins containing a methyl-CpG binding domain (MBDs). Based on the NMR structure of MBD1 complexed with methylated DNA we analysed the recognition mode by means of molecular dynamics simulations. As the protein is monomeric and recognizes a symmetrically methylated CpG step, the recognition mode is an asymmetric one. We find that the two methyl groups do not contribute equally to the binding energy. One methyl group is associated with the major part of the binding energy and the other one nearly does not contribute at all. The contribution of the two cytosine methyl groups to binding energy is calculated to be -3.6 kcal/mol. This implies a contribution of greater than two orders of magnitude to the binding constant. The conserved amino acid Asp32 is known to be essential for DNA binding by MBD1, but so far no direct contact with DNA has been observed. We detected a direct DNA base contact to Asp32. This could be the main reason for the importance of this amino acid. MBD contacts DNA exclusively in the major groove, the minor groove is reserved for histone contacts. We found a deformation of the minor groove shape due to complexation by MBD1, which indicates an information transfer between the major and the minor groove.
5-Methylcytosine↗
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↗
Hydration of hydroxypyrrole influences binding of ImHpPyPy-beta-Dp polyamide to DNA.
Ligands which are able to recognize DNA sequence specifically are of fundamental interest as transcription controlling drugs. Recently a polyamide ligand was developed (ImHpPyPy-beta-Dp) which differentiates in a dimeric arrangement between all four possible base pair steps in the minor groove. This is a landmark for the design of DNA binding drugs because it was believed that such a recognition could only be possible in the major groove of DNA. Although the OH groups of the hydroxypyrrole (Hp) moieties of the ligands are responsible for this sequence discrimination, experiments showed that this OH group also reduces the absolute binding constant. We performed a free energy calculation by means of thermodynamic integration in order to find out the influence of this single hydroxyl on DNA binding. In our simulation, we found that the hydroxyl group reduces binding by about 1.3 kcal/mol, which is in excellent agreement with the experimentally determined value of 1.2 kcal/mol. In further MD simulations, the structural reasons for this reduction was estimated. The results of these simulations qualitatively agree with the X-ray structures, but in contrast, in the simulations both (ImHpPyPy-beta-Dp and ImPyPyPy-beta-Dp) ligand-DNA (d(CCAGTACTGG)(2)) complexes exhibit only slight structural differences. This is consistent with a recently published second pair of similar polyamide DNA crystal structures. Thus, we believe that the explanations resulting from the X-ray structures must be modified. We attribute the large structural differences between the two polyamide DNA complexes to a buffer molecule which binds only in the case of the ImHpPyPy-beta-Dp-DNA complex at the region of interest. We propose that the differential hydration of both ligands in the unbound state is responsible for the reduction of the binding constant. Additionally, we suggest an indirect readout of DNA, because of a lengthening of the Watson-Crick base pairs, which possibly contributes to the differentiation between T.A, A.T from G.C, C.G base pairs.
Computer Simulation↗
Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.
Induced fit effects in the complex of a DNA decamer with two even-skipped transcriptional repressor homeodomain molecules were investigated by means of molecular dynamics simulations. Dynamics of these effects are found to be in the time scale from pico- to nanoseconds. First steps are made by the fast-moving DNA backbone phosphates, which upon binding change their B(I)/B(II) substate distribution. Further rearrangements in the DNA double helix induced upon complexation, like bending of the helix axis, changes of the minor groove width, and of different helical parameters, are slower and occur within a few nanoseconds. The flexibility of the DNA, especially of its backbone, seems thereby to play an important role for specific DNA ligand recognition.
Animals↗
The conformer substates of nonoriented B-type DNA in double helical poly(dG-dC).
A nonoriented hydrated film of poly(dG-dC) with ?20 water molecules per nucleotide (called B* by Loprete and Hartman (Biochem. 32, 4077-4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra. Comparison with difference curves obtained in the same manner from two classical B-DNA forms, namely the d(CGCGAATTCGCG)(2) dodecamer and polymeric NaDNA from salmon testes, revealed that the spectral changes on B(I)-to-B(II) interconversion in the classical B-DNA forms are very similar to those in the B*-form, and that the spectroscopic differences between the B(I) and B(II) features from classical B-DNA and those from the modified B*-form are minor. Nonexponential kinetics of the B(I)-->B(II) transition in the B*-form of poly(dG-dC) at 200 K showed that the structural relaxation time is about three times of that in the classical B-DNA forms (approximately equal to 30 versus approximately equal to 10 min at 200 K). The unexpected reversal of conformer substates interconversion (that is B(II)-->B(I) transition on cooling from 290 K and B(I)-->B(II) transition on isothermal relaxation at 200 K) observed for classical B-DNA occurs also in the modified B*-form. We therefore conclude that restructuring of hydration shells rules the low-temperature dynamics of the B*-form via its two conformer substates in the same manner reported for classical B-DNA by Pichler et al. (J. Phys. Chem. B 106, 3263-3274 (2002)).
Animals↗
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↗
PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA.
We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened. The distance between the scissile phosphate group and the phosphate group of the following thymine base is shortened significantly, indicating a substrate-assisted catalysis. A feasible reason for this vicinity is the catalytically important amino acid residue lysine 70, which bridges the free oxygen atoms of the successive phosphate groups. Due to this geometry, a compact reaction pocket is formed where a water molecule can be held, thus bringing the reaction partners for hydrolysis into contact. The O1-P-O2 angle of the scissile nucleotide is decreased, probably due to a complexation of the negative oxygen atoms through protein and solvent contacts.
Binding Sites↗
Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions.
Although the trp-repressor-operator complex is one of the best studied transcriptional controlling systems, some questions regarding the specific recognition of the operator by the repressor remain. We performed a 2.35 ns long molecular dynamics simulation to clarify the influence of the two B-DNA backbone conformational substates B(I) and B(II) on complexation. The trp-repressor-operator is an ideal biological system for this study because experimental results have already figured out that the interaction between the internucleotide phosphates and the protein is essential for the formation of the high affinity complex. Our simulation supports these results, but more important it shows a strong correlation between the B(I)/B(II) phosphate substate and the number of interactions with this phosphate. In particular the B(I) <==> B(II) transitions occur synchronous to hydrogen bond breaking or formation. To the best of our knowledge, this was observed for the first time. Thus, we conclude that the sequence specific B(I)/B(II) behavior contributes via indirect readout to sequence specific recognition. These results have implication for the design of transcription-controlling drugs in view of the recently published influence of minor groove binders on the B(I)/B(II) pattern. The simulation also agrees with crystallographically observed hydration sites. This is consistent with experimental results and indicates the correctness of the model used.
Bacterial Proteins↗
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↗