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 morecommonly 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.

Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 10 7 and 5 × 10 7 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. Chem. Phys. 139, 014504 (2013) and 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.

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.soft matter | molecular simulation | colloids | monopoles | nonequilibrium thermodynamics T he existence of quasi-monopoles in a system of heated or cooled colloidal particles in a polar or paramagnetic fluid follows directly from nonequilibrium thermodynamics, combined with the equations of electro/magneto-statics (1). Although suggested theoretically, they have thus far not been studied experimentally. This paper provides numerical evidence indicating that the predicted effects are real and robust. In what follows, we consider the case of thermally induced quasi-monopoles in a dipolar liquid, but all our results also apply to paramagnetic liquids. It has been shown that a thermal gradient will create an electric field in a liquid of dipolar molecules with sufficiently low symmetry (2, 3). In the absence of any external electric field, a heated or cooled colloidal particle placed in such a liquid will generate an electric field according to the phenomenological relation (2, 4, 5)where T (r) is the temperature and S TP the thermo-polarization coefficient, with a magnitude that is not known a priori. For water near room temperature, S TP has been estimated to be S TP ≈ 0.1 mV/K (4, 6). Let us next consider the electric polarization around a heated (or cooled) colloidal particle, for brevity also referred to simply as a colloid. We note that the sole function of the colloid is to generate a temperature gradient field in the solvent, which in turn couples to the electric field via Eq. 1. Other heat sources (sinks) would lead to the same effect. In steady state the temperature profile at a distance r from the center of an isolated, spherical colloid of radius R satisfiesand hencewhere T∞ is the temperature in the bulk liquid andr the radially outward-pointing unit vector. Note that E TP decays as 1/r 2 . Using Gauss's theorem, we can then writewhere 0 is the dielectric permittivity of a vacuum. In words, the flux through a closed surface around a neutral colloi...

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.

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 P T 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 analysed. The respective TMD lines diverge at extreme values with one set of lines showing a re-entrant behaviour. 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 behaviour.

A new procedure for full conformational analyses comprising the statistical analysis of molecular dynamics trajectories was developed and applied. This method included a coordinate space for sampling using molecular dynamics simulations, reduction of dimensionality using tensor decomposition tools, determination of probability distributions in a reduced space, and finally the search for all of the strict extrema points of probability distributions. These extracted extrema points formed an initial guess for geometry optimization and clustering of conformers. A complete conformational space of 1-oxaspiro[2,5]octane and its cis- and trans-4-, 5- and 6-methyl substituted derivatives was also determined. In each case, eight conformers were found with two chair-like conformers predominant at room temperature. It was found that chair-like conformers with an epoxide ring oxygen atom in the pseudo-axial position had less strain, as well as all of their conformers with the methyl substituent in an equatorial position on a cyclohexane moiety.

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.

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.