Molecular dynamics study of tryptophylglycine: A dipeptide nanotube with confined water

To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG-H2O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel MD program ddgmq (software package) and a consistent force field. Simulations were performed on both the water-containing system and a model system without water molecules. The details of the structural behavior with temperature are investigated for the entire simulated temperature range. Phase transitions were obtained at 115, 245, 270, 3 10, and 3 85 K, due to the contributions of both the peptide and the confined water subsystems. The crystalline, amorphous, liquidlike, liquid, and superheated phases of water were observed in the temperature ranges 40-115, 115-245, 245-310, 310385, and >385 K, respectively. At 300 K, the diffusion constant of the confined water is 0.46 x 10(-5) cm(2) s(-1), a value comparable to that of other peptide nanotubes. The empty peptide system melts at 440 K. Mechanisms of the negative thermal expansion (NTE) along the tube axis were investigated for different temperature ranges. The contraction of the crystalline water (or amorphous water) draws also the tube walls in and leads to NTE below 245 K. The other NTEs appear to be connected to the collapse of the ice network or the solid peptide network between 245 K and room temperature or from 310 to 440 K, respectively.

Molecular Dynamics Study of the Incommensurate Phase in Hexamethylenetetramine Suberate

David Brown, Gervais Chapuis

Incommensurate structure of Hexamethylenetetramine suberate (C6H12N4)(HOOC-(CH2)6-COOH) has been solved from single crystal x-ray diffraction data. A molecular dynamics simulation of this system was carried out from 15 K to 580K. A second-generation consistent forcefield (CFF) and a compensating pressure tensor field were used to describe the interactions between atoms and to account for deficiencies in the forcefield. Starting from the experimental 298K structure, the phase transitions were investigated over an extended temperature range. A high symmetry commensurate structure exists at temperatures between 410K and 290K. For temperatures lower than 290K, a new periodicity appears in the structure. The system reaches a low symmetry lock-in phase at about 150K. An incommensurate structure appears between the high and low symmetry phases between 290K and 150K. The new periodicity associated with the incommensurate modulation is due to the appearance of additional long range ordering of the carbon chains. The present simulation not only reproduces well the experimental x-ray diffraction results but also gives new insight into the origin of the incommensurate behavior.

2002

Thermal induced structural properties of silver(I) sulphate (Ag2SO4)

Philip Pattison

The crystal structures of silver(I) sulphate, Ag2SO4, have been investigated as a function of temperature. A main feature is the phase transition from the low-temperature ordered phase, F ddd, to the high-temperature disordered phase, P63/mmc. In particular, the high-temperature structure is solved from single crystal synchrotron X-ray measurements. In this phase the title compound undergoes a colossal (anisotropic) thermal expansion of 136(4)x10-6K-1. This is presumably owing to a high anisotropic vibration state of one of the two crystallographically independent Ag-atoms. Simultaneously occurring high ionic conductivity may be associated with silver ions moving along the c-axis using a paddle-wheel assisted percolative mechanism. Onset of metallic silver in the single crystals is documented, seemingly dependent on thermal pre-history, mosaic structure and chemical synthesis. Possible mechanisms explaining this effect, comprising disproportionation or photo-decomposition, are suggested.

Wiley-Blackwell2016

Local excitations in amorphous solids

Wencheng Ji

Amorphous solids are structurally disordered. They are very common and include glasses, colloids, and granular materials, but are far less understood than crystalline solids. Key aspects of these materials are controlled by the presence of excitations in which a group of particles rearranges. This motion can be triggered by (a) quantum fluctuations associated with two-level systems (TLS), which dominate the low temperature properties of conventional glasses and have practical importance on superconducting qubits; by (b) thermal fluctuations associated with activations, which are related to the famous and challenging

glass transition'' problem; or by (c) exerting an external stress or strain associated with shear transformations, which control the plasticity. Hence, it is important to understand how temperature and system preparation determines the density and geometry of these excitations. The possible unification of these excitations into a common description is also a fundamental problem.  These local excitations are thought to have a close relationship with

Quasi-localised modes (QLMs)'' which are present in the low-frequency vibrational spectrum in amorphous solids. Understanding the properties of QLMs and clarifying the relation between QLMs and these local excitations are important to the study of the latter. In this thesis: (1) we provide a theory for the QLMs, D_L(omega) ~ omega^alpha, that establishes the link between QLMs and shear transformations for systems under quasi-static loading. It predicts two regimes depending on the density of shear transformations P(x)~ x^theta (with x the additional stress needed to trigger a shear transformation). If theta>1/4, alpha=4 and a finite fraction of quasi-localised modes form shear transformations, whose amplitudes vanish at low frequencies. If theta

EPFL2021