Thermodynamic anomalies, polyamorphism and all that.

The appearance and evolution of thermodynamics anomalies, and related properties, are studied for two classes of system, modelling those dominated by covalent and ionic interactions, respectively. Such anomalies are most familiar in the density but are also present in other thermodynamics variables such as the compressibility and heat capacity. By systematically varying key model parameters the emergence and evolution of these anomalies can be tracked across the phase space. The interaction of the anomalies can often be rationalized by thermodynamics 'rules'. The emergence of these anomalies may also be correlated with the appearance of polyamorphism, the existence of multiple amorphous states which differ in density and entropy. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 1)'.

Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data.

This work describes the development and testing of a method for the identification and classification of conserved water molecules and their networks from molecular dynamics (MD) simulations. The conserved waters in the active sites of proteins influence protein-ligand binding. Recently, several groups have argued that a water network formed from conserved waters can be used to interpret the thermodynamic signature of the binding site. We implemented a novel methodology in which we apply the complex approach to categorize water molecules extracted from the MD simulation trajectories using clustering approaches. The main advantage of our methodology as compared to current state of the art approaches is the inclusion of the information on the orientation of hydrogen atoms to further inform the clustering algorithm and to classify the conserved waters into different subtypes depending on how strongly certain orientations are preferred. This information is vital for assessing the stability of water networks. The newly developed approach is described in detail as well as validated against known results from the scientific literature including comparisons with the experimental data on thermolysin, thrombin, and Haemophilus influenzae virulence protein SiaP as well as with the previous computational results on thermolysin. We observed excellent agreement with the literature and were also able to provide additional insights into the orientations of the conserved water molecules, highlighting the key interactions which stabilize them. The source code of our approach, as well as the utility tools used for visualization, are freely available on GitHub.

Numerical evidence for thermally induced monopoles.

Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell's equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis.

The interactions between thermodynamic anomalies.

The origin of and interactions between key thermodynamic anomalies are derived and analyzed, as are the interactions with the stability (or cavitation) limits. The conditions for interaction are derived from the underlying thermodynamic relations rather than using the more-commonly applied Taylor expansion method. As a result, we derive a general set of equations that govern the interactions between different lines of thermodynamic anomalies using standard manipulation of thermodynamic equations. The validity of the derivations is investigated by comparing them to numerical simulation data and previous Taylor expansion-based results. Simulations are performed using a modified Stillinger-Weber potential in which the balance of the two- and three-body interactions is varied and which serves to highlight the relationships between the various anomalies. The deeply supercooled regime is explored by employing replica exchange methods. The behavior of the anomalies is considered in terms of previously constructed thermodynamic "scenarios." Based on the newly uncovered interaction schemes, we propose a classification strategy for the thermodynamic anomalies (as first- or second-order) which could be extended to additional related anomalies.

Biradical character in the ground state of [Mn@Si12](+): a DFT and CASPT2 study.

Both density functional theory and multi-configurational ab initio (CASPT2) calculations are used to explore the potential energy surface of the hexagonal prismatic cluster [Mn@Si12](+). Unlike isoelectronic Cr@Si12, the ground state is a biradical, with triplet and open-shell singlet states lying very close in energy. The results are discussed in the context of recent experimental studies using infra-red multiple photon dissociation spectroscopy and X-ray MCD spectroscopy.

Thermodynamic anomalies in silicon and the relationship to the phase diagram.

The evolution of thermodynamic anomalies are investigated in the pressure-temperature (pT) plane for silicon using the well-established Stillinger-Weber potential. Anomalies are observed in the density, compressibility and heat capacity. The relationships between them and with the liquid stability limit are investigated and related to the known thermodynamic constraints. The investigations are extended into the deeply supercooled regime using replica exchange techniques. Thermodynamic arguments are presented to justify the extension to low temperature, although a region of phase space is found to remain inaccessible due to unsuppressible crystallisation. The locus corresponding to the temperature of minimum compressibility is shown to display a characteristic 'S'-shape in thepTprojection which appears correlated with the underlying crystalline phase diagram. The progression of the anomalies is compared to the known underlying phase diagrams for both the crystal/liquid and amorphous/liquid states. The locations of the anomalies are also compared to those obtained from previous simulation work and (limited) experimental observations.

The progression of thermodynamic anomalies in MX2 networks with local tetrahedral geometries.

Key thermodynamic anomalies in density and compressibility, as well as the related stability limits, are determined using an ionic model for BeF2 which includes many-body polarization terms. BeF2 is chosen as an example of an archetypal network-forming system whose structure can be rationalised in terms of connected local tetrahedral coordination polyhedra. The anion dipole polarizability (which effectively controls the bond angles linking neighbouring tetrahedra) is used as a single free parameter in order to help rationalise the changes in the anomaly locations in phase space, whilst all other potential parameters remain fixed. The anomalies and stability limits systematically shift to lower temperature and higher pressure as the anion polarizability is increased. At high dipole polarizabilities the temperature of maximum density anomaly locus becomes suppressed into the supercooled regime of the phase space. The movements of the anomaly loci are analysed in terms of the network structure and the correlation with the inter-tetrahedral bond angles is considered. The high sensitivity of the anomalies to the details of the potential models applied is discussed with reference to previous works on related systems. The relationship to analogous studies on Stillinger-Weber liquids is discussed.

Liquid state anomalies and the relationship to the crystalline phase diagram.

A relationship between the observation of a density anomaly and the underlying crystalline phase diagram is demonstrated. The crystal phase diagram and temperature of maximum density (TMD) lines are calculated over a range of parameter space using a Stillinger-Weber potential. Relationships between the loci of density maxima in the PT plane for the liquid state and the underlying crystalline phase diagram are investigated. Two key potential parameters are systematically varied in order to control the balance between the model two- and three-body interaction terms, and the relative effects of varying the potential parameters analyzed. The respective TMD lines diverge at extreme values with one set of lines showing a reentrant behavior. For each parameter set the TMD lines are extrapolated to T=0K. The corresponding pressures are related to the crystalline phase diagram and are found to lie on or near specific crystal-crystal coexistence lines for a wide range of potential parameters. The density anomaly is observed to vanish corresponding to regions in the crystal phase diagram which lack crystal-crystal coexistence lines potentially offering a new interpretation for the emergence of anomalous behavior.