Measuring the free energy of hard-sphere colloidal glasses

Free energy is a key thermodynamic observable that controls the elusive physics of the glass transition. However, measuring the free energy of colloidal glasses from microscopy images is challenging due to the difficulty of measuring the individual particle size in the slightly polydisperse glassy systems. In this paper, we carry out experiments and numerical simulations of colloidal glasses with the aim to find a practical approach to measure the free energy from colloidal particles at mild polydispersity. We propose a novel method which requires only the particle coordinates from a few confocal microscopy snapshots to estimate the average particle diameter and use it as an input for our experimental free energy measurements. We verify our free energy calculations from Cell Theory with the free energy obtained by Thermodynamic Integration. The excellent agreement between the free energies measured using the two methods close to the glass transition packing fraction highlights the dominant role played by \emph{vibrational} entropy in determining a colloidal glass's free energy. Finally, the noticeable free energy difference calculated from uniform and conjectured particle sizes emphasizes the sensitivity on particle free volumes when measuring free energy in the slightly polydisperse colloidal glass.

Computational analysis of the effect of SARS-CoV-2 variant Omicron Spike protein mutations on dynamics, ACE2 binding and propensity for immune escape

The recently reported Omicron (B.1.1.529) SARS-CoV-2 variant has a large number of mutations in the Spike (S) protein compared to previous variants. Here we evaluate the potential effect of Omicron S mutations on S protein dynamics and ACE2 binding as contributing factors to infectivity as well as propensity for immune escape. We define a consensus set of mutations from 77 sequences assigned as Omicron in GISAID as of November 25. We create structural models of the Omicron S protein in the open and closed states, as part of a complex with ACE2 and for each of 77 complexes of S bound to different antibodies with known structures. We have previously utilized Dynamical Signatures (DS) and the Vibrational Entropy Score (VDS) to evaluate the propensity of S variants to favour the open state. Here, we introduce the Binding Influence Score (BIS) to evaluate the influence of mutations on binding affinity based on the net gain or loss of interactions within the protein-protein interface. BIS shows excellent correlation with experimental data (Pearson correlation coefficient of 0.87) on individual mutations in the ACE2 interface for the Alpha, Beta, Gamma, Delta and Omicron variants combined. On the one hand, the DS of Omicron highly favours a more rigid open state and a more flexible closed state with the largest VDS of all variants to date, suggesting a large increase in the chances to interact with ACE2. On the other hand, the BIS shows that apart from N501Y, all other mutations in the interface reduce ACE2 binding affinity. VDS and BIS show opposing effects on the overall effectiveness of Omicron mutations to promote binding to ACE2 and therefore initiate infection. To evaluate the propensity for immune escape we calculated the net change of favourable and unfavourable interactions within each S-antibody interface. The net change of interactions shows a positive score (a net increase of favourable interactions and decrease of unfavourable ones) for 41 out of 77 antibodies, a nil score for 15 and a negative score for 21 antibodies. Therefore, in only 28% of S-antibody complexes (21/77) we predict some level of immune escape due to a weakening of the interactions with Omicron S. Considering that most antibody epitopes and the mutations are within the S-ACE2 interface our results suggest that mutations within the RBD of Omicron may give rise to only partial immune escape, which comes at the expense of reduced ACE2 binding affinity. However, this reduced ACE2 affinity appears to have been offset by increasing the occupancy of the open state of the Spike protein.

Entropy Measurements of Li-Ion Battery Cells with Li- and Mn-Rich Layered Transition Metal Oxides via Linear Temperature Variation

Changes in the partial molar entropy of lithium- and manganese-rich layered transition metal oxides (LMR-NCM) are investigated using a recently established electrochemical measuring protocol, in which the open-circuit voltage (OCV) of a cell is recorded during linear variation of the cell temperature. With this method, the entropy changes of LMR-NCM in half-cells were precisely determined, revealing a path dependence of the entropy during charge and discharge as a function of state of charge, which vanished as a function of OCV. This observation is in line with other hysteresis phenomena observed for LMR-NCM, of which the OCV hysteresis is the most striking one. For a systematic investigation of the entropy changes in LMR-NCM, measurements were conducted during the first activation cycle and in a subsequent cycle. In addition, two LMR-NCM materials with different degrees of overlithiation were contrasted. Contributions from configurational and vibrational entropy are discussed. Our results suggest that the entropy profile during activation exhibits features from the configurational entropy, while during subsequent cycling the vibrational entropy dominates the entropy curve.

Premelting and the Machanisms of Melting in the Alkali Halides

<p>An experimental and theoretical study of premelting behaviour and mechanisms of melting in the alkali-halides is presented. Theories of melting and previous premelting experiments are first reviewed, then an elastic strain theory of melting is developed, which includes dilatation and shear contributions to the elastic energy and to the vibrational entropy, as well as a communal entropy and an entropy due to the isothermal expansion on melting. By fitting experimental melting parameters, dislocation-like local strains are implicated. The bulk and shear moduli are shown to be continuous with respect to dilatation through the melting expansion and one of the shear moduli vanishes at the dilatation of the melt at the melting temperature. A modified Born instability theory of melting is thus valid. Premelting rises in the apparent specific heat and electrical conductivity within 6 K of the melting point are studied and are shown to occur at the surfaces only. The use of guard rings to eliminate surface conduction is essential at all temperatures above the extrinsic/intrinsic conductivity 'knee', and electrical fringing must be taken into account for typical specimen sizes. For various surface orientations, the rises in surface conductivity occur at lower temperatures the lower the surface packing density, and for deformed specimens, the greater the deformation. The results are interpreted in terms of an atomic-scale surface melting below the melting point, and a consequent rapid rise in vaporisation rate. A dislocation theory of surface melting, melting and the solid-liquid interface is developed which gives good agreement with experimental values for the melting temperatures and the interfacial energies.</p>

Premelting and the Machanisms of Melting in the Alkali Halides

<p>An experimental and theoretical study of premelting behaviour and mechanisms of melting in the alkali-halides is presented. Theories of melting and previous premelting experiments are first reviewed, then an elastic strain theory of melting is developed, which includes dilatation and shear contributions to the elastic energy and to the vibrational entropy, as well as a communal entropy and an entropy due to the isothermal expansion on melting. By fitting experimental melting parameters, dislocation-like local strains are implicated. The bulk and shear moduli are shown to be continuous with respect to dilatation through the melting expansion and one of the shear moduli vanishes at the dilatation of the melt at the melting temperature. A modified Born instability theory of melting is thus valid. Premelting rises in the apparent specific heat and electrical conductivity within 6 K of the melting point are studied and are shown to occur at the surfaces only. The use of guard rings to eliminate surface conduction is essential at all temperatures above the extrinsic/intrinsic conductivity 'knee', and electrical fringing must be taken into account for typical specimen sizes. For various surface orientations, the rises in surface conductivity occur at lower temperatures the lower the surface packing density, and for deformed specimens, the greater the deformation. The results are interpreted in terms of an atomic-scale surface melting below the melting point, and a consequent rapid rise in vaporisation rate. A dislocation theory of surface melting, melting and the solid-liquid interface is developed which gives good agreement with experimental values for the melting temperatures and the interfacial energies.</p>

New Insights into the Crystallographic Disorder in the Polymorphic Forms of Aspirin from Low-frequency Vibrational Analysis

Terahertz time-domain spectroscopy (THz-TDS) is applied to two polymorphs of acetylsalicylic acid (aspirin), and the experimental spectra are compared to lattice dynamical calculations using high accuracy density functional theory (DFT). The calculations confirm that forms I and II have very close energetic and thermodynamic properties, and also that they show similar spectral features in the far-infrared region, reflecting the high degree of similarity in their crystal structures. Unique vibrational modes are identified for each polymorph which allow them to be distinguished using THz-TDS measurements. The observation of spectral features attributable to both polymorphic forms in a single sample, however, provides further evidence to support the hypothesis that crystalline aspirin typically comprises intergrown domains of forms I and II. Differences observed in the baseline of the measured THz-TDS spectra indicate a greater degree of structural disorder in samples of form II. Calculated Gibbs free energy curves show a turning point at 75 K, inferring that form II is expected to be more stable than form I above this temperature, as a result of its greater vibrational entropy. The calculations do not account for any differences in configurational entropy that may arise from expected structural defects. Further computational work on these structures, such as ab initio molecular dynamics (AIMD), would be very useful to further explore this perspective.

The Impact of Vibrational Entropy on the Segregation of Cu to Antiphase Boundaries in Fe3Al

We performed a quantum mechanical study of segregation of Cu atoms toward antiphase boundaries (APBs) in Fe3Al. The computed concentration of Cu atoms was 3.125 at %. The APBs have been characterized by a shift of the lattice along the ⟨001⟩ crystallographic direction. The APB energy turns out to be lower for Cu atoms located directly at the APB interfaces and we found that it is equal to 84 mJ/m2. Both Cu atoms (as point defects) and APBs (as extended defects) have their specific impact on local magnetic moments of Fe atoms (mostly reduction of the magnitude). Their combined impact was found to be not just a simple sum of the effects of each of the defect types. The Cu atoms are predicted to segregate toward the studied APBs, but the related energy gain is very small and amounts to only 4 meV per Cu atom. We have also performed phonon calculations and found all studied states with different atomic configurations mechanically stable without any soft phonon modes. The band gap in phonon frequencies of Fe3Al is barely affected by Cu substituents but reduced by APBs. The phonon contributions to segregation-related energy changes are significant, ranging from a decrease by 16% at T = 0 K to an increase by 17% at T = 400 K (changes with respect to the segregation-related energy difference between static lattices). Importantly, we have also examined the differences in the phonon entropy and phonon energy induced by the Cu segregation and showed their strongly nonlinear trends.

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy–entropy (EE) method to calculate the host–guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host–guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol−1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.