The EcoRI restriction endonuclease requires one divalent metal ion in each of two symmetrical and identical catalytic sites to catalyse double-strand DNA cleavage. Recently, we showed that Cu binds outside the catalytic sites to a pair of new sites at H114 in each sub-unit, and inhibits Mg -catalysed DNA cleavage. In order to provide more detailed structural information on this new metal ion binding site, we performed W-band (~94 GHz) and X-band (~9.5 GHz) electron spin resonance spectroscopic measurements on the EcoRI-DNA-(Cu ) complex. Cu binding results in two distinct components with different and values. X-band electron spin echo envelope modulation results indicate that both components arise from a Cu coordinated to histidine. This observation is further confirmed by the hyperfine sub-level correlation results. W-band electron nuclear double resonance spectra provide evidence for equatorial coordination of water molecules to the Cu ions.

Bacteria associate with surfaces and one another by elaborating an extracellular matrix to encapsulate cells, creating communities termed biofilms. Biofilms are beneficial in some ecological niches, but also contribute to the pathogenesis of serious and chronic infectious diseases. New approaches and quantitative measurements are needed to define the composition and architecture of bacterial biofilms to help drive the development of strategies to interfere with biofilm assembly. Solid-state NMR is uniquely suited to the examination of insoluble and complex macromolecular and whole-cell systems. This article highlights three examples that implement solid-state NMR to deliver insights into bacterial biofilm composition and changes in cell-wall composition as cells transition to the biofilm lifestyle. Most recently, solid-state NMR measurements provided a total accounting of the protein and polysaccharide components in the extracellular matrix of an biofilm and transform our qualitative descriptions of matrix composition into chemical parameters that permit quantitative comparisons among samples. We present additional data for whole biofilm samples (cells plus the extracellular matrix) that complement matrix-only analyses. The study of bacterial biofilms by solid-state NMR is an exciting avenue ripe with many opportunities and we close the article by articulating some outstanding questions and future directions in this area.

The electron paramagnetic resonance technique of double electron-electron resonance (DEER) was used to measure nanometre-scale distances between nitroxide spin labels attached to the complement regulatory protein CD55 (also known as decay accelerating factor) and the von Willebrand factor A (vWF-A) domain of factor B. Following a thorough assessment of the quality of the data, distances obtained from good-quality measurements are compared to predicted distances from a previously hypothesised model for the complex and are found to be incompatible. The success of using these distances as restraints in multi-body docking routines is presented critically.

We here report isotope substitution neutron diffraction experiments on two variants of high-density amorphous ice (HDA): its unannealed form prepared pressure-induced amorphization of hexagonal ice at 77 K, and its expanded form prepared decompression of very-high density amorphous ice at 140 K. The latter is about 17 K more stable thermally, so that it can be heated beyond its glass-to-liquid transition to the ultraviscous liquid form at ambient pressure. The structural origin for this large thermal difference and the possibility to reach the deeply supercooled liquid state has not yet been understood. Here we reveal that the origin for this difference is found in the intermediate range structure, beyond about 3.6 Å. The hydration shell markedly differs at about 6 Å. The local order, by contrast, including the first as well as the interstitial space between first and second shell is very similar for both. 'eHDA' that is decompressed to 0.20 GPa instead of 0.07 GPa is here revealed to be rather far away from well-relaxed eHDA. Instead it turns out to be roughly halfway between VHDA and eHDA - stressing the importance for decompressing VHDA to at least 0.10 GPa to make an eHDA sample of good quality.

We report total electron-impact ionisation cross sections (EICSs) of cisplatin, its hydrolysis products and transplatin in the energy range from threshold to 10 keV using the binary-encounter-Bethe (BEB) and its relativistic variant (RBEB), and the Deutsch-Märk (DM) methods. We find reasonable agreement between all three methods, and we also note that the RBEB and the BEB methods yield very similar (almost identical) results in the considered energy range. For cisplatin, the resulting EICSs yield cross section maxima of 22.09 × 10 m at 55.4 eV for the DM method and 18.67 × 10 m at 79.2 eV for the (R)BEB method(s). The EICSs of monoaquated cisplatin yield maxima of 12.54 × 10 m at 82.8 eV for the DM method and of 9.74 × 10 m at 106 eV for the (R)BEB method(s), diaquated cisplatin yields maxima of 7.56 × 10 m at 118.5 eV for the DM method and of 5.77 × 10 m at 136 eV for the (R)BEB method(s). Molecular geometry does not affect the resulting EICS significantly, which is also reflected in very similar EICSs of the - and -isomer. Limitations of the work as well as desirable future directions in the research area are discussed.

A link between the aromatic character of polycyclic aromatic hydrocarbons and gas chromatography elution order in columns with a polysiloxane backbone in the stationary phase is reported for the first time. The aromatic character was calculated using a method that combines the π-Sextet Rule and the Pauling Ring Bond Orders to allow the establishment of the location and migration of aromatic sextets in PAH structures. One GC column with a polysiloxane - like backbone (Rxi-PAH) and three GC columns with a polysiloxane backbone (DB-5, SE-52, and LC-50), were used for the analysis. According to the results of this study, within an isomer group, PAHs that contain a lower number of rings affected by the aromatic sextets tend to elute earlier than PAHs that contain a higher number of rings affected by the aromatic sextets. The PAHs that follow the calculated elution order are 88 % in the Rxi-PAH column, 88 % in the DB-5 column, 93 % in the SE-52 column, and 85% in the LC-50 column. It is expected that future analyses with other aromatic compounds in GC columns with a polysiloxane backbone in the stationary phase will follow a GC elution order that agrees with the aromatic character of the molecules.

The rate of nucleation processes such as the freezing of a supercooled liquid or the condensation of supersaturated vapour is mainly determined by the height of the nucleation barrier and the diffusion coefficient for the motion across it. Here, we use a Bayesian inference algorithm for Markovian dynamics to extract simultaneously the free energy profile and the diffusion coefficient in the nucleation barrier region from short molecular dynamics trajectories. The specific example we study is the nucleation of vapour bubbles in liquid water under strongly negative pressures, for which we use the volume of the largest bubble as a reaction coordinate. Particular attention is paid to the effects of discretisation, the implementation of appropriate boundary conditions and the optimal selection of parameters. We find that the diffusivity is a linear function of the bubble volume over wide ranges of volumes and pressures, and is mainly determined by the viscosity of the liquid, as expected from the Rayleigh-Plesset theory for macroscopic bubble dynamics. The method is generally applicable to nucleation processes and yields important quantities for the estimation of nucleation rates in classical nucleation theory.

Multichannel scattering calculations are presented for the low-energy collisions of the OH cation and He atoms, using an evaluation of the interaction potential, which had been obtained in earlier work, and a time-independent, multichannel treatment of the quantum dynamics carried out in this study using our in-house scattering code ASPIN. Given the presence of spin-rotation coupling effects, within an essentially electrostatic formulation of the interaction forces with He atoms in the trap, the ensuing propensity rules which control the relative size of the state-changing cross sections and of the corresponding inelastic rates, also computed at the most likely temperatures in an ion trap, are presented and analysed in detail.

We investigate the work function (WF) variation of different Au crystallographic surface orientations with carbon atom adsorption. calculations within density-functional theory are performed on carbon deposited (100), (110), and (111) gold surfaces. The WF behaviour with carbon coverage for the different surface orientations is explained by the resultant electron charge density distributions. The dynamics of carbon adsorption at sub-to-one- monolayer (ML) coverage depends on the landscape of the potential energy surfaces. At higher ML coverage, because of adsorption saturation, the WF will have weak surface orientation dependence. This systematic study has consequential bearing on studies of electric-field noise emanating from polycrystalline gold ion-trap electrodes that have been largely employed in microfabricated electrodes.

We report a numerical test of the Adam-Gibbs relation for the TIP4P/2005 model of water. The configurational entropy is here evaluated as the logarithm of the number of different basins in the potential energy landscape sampled in equilibrium conditions. Despite the non-monotonic behaviour which characterise the density dependence of the diffusion coefficient, the Adam-Gibbs relation is satisfied within the numerical precision in a wide range of densities and temperatures. We also show that expressions based on the excess entropy (the logarithm of the number of sampled microstates in phase space) fail in the region of densities where a tetrahedral hydrogen bond network develops.

Vanadium monoxide ( V O) is believed to play an important role in the atmospheres of hot-Jupiters, but high-resolution studies have so far failed to detect it, at least in part because of the inaccuracy of available lists. It is likely that the large hyperfine splittings in the spectra of VO, arising from the large nuclear spin of the V atom, has contributed to the non-detections with the current hyperfine-unresolved VOMYT line list. To aid in the production of a new line list, a fully hyperfine-resolved spectroscopic model has been constructed which includes 15 low-lying electronic states (6 quartets and 9 doublets) of VO with the inclusion of hyperfine couplings based on use of the new, hyperfine-resolved version of the diatomic variational nuclear motion programme Duo. The new spectroscopic model is refined against empirical Marvel energies derived from experimental transitions, and hyperfine couplings are fit for the 3 electronic states for which hyperfine effects have been resolved in lab spectra. This model is used to assign some previously identified perturbations.

Protein allostery is ubiquitous phenomena that are important for cellular signaling processes. Despite extensive methodology development, a quantitative model is still needed to accurately measure protein allosteric response upon external perturbation. Here, we introduced the relative entropy concept from information theory as a quantitative metric to develop a method for measurement of the population shift with regard to protein structure during allosteric transition. This method is referred to as relative entropy-based dynamical allosteric network (REDAN) model. Using this method, protein allostery could be evaluated at three mutually dependent structural levels: allosteric residues, allosteric pathways, and allosteric communities. All three levels are carried out using rigorous searching algorithms based on relative entropy. Application of the REDAN model on the second PDZ domain (PDZ2) in the human PTP1E protein provided metric-based insight into its allostery upon peptide binding.

The structure of a crystalline monolayer of 1,3,5-triazine has been characterised using X-ray diffraction. The monolayer is found to exhibit a hexagonal unit cell with a lattice parameter of 6.161(5) Å, indicating the formation of C-H … N hydrogen bonds. DFT simulations have been performed exhibiting close agreement with the experimental structure. By comparing the strength of the intermolecular interactions both with and in the absence of Van der Waals corrections, it is possible to estimate an interaction strength for the weak C-H … N hydrogen bonds.

We propose a simple procedure for visualizing the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity S2, Claisen rearrangement, Diels-Alder reaction, [3+2] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds. The EDC plots were also shown for copper triflate catalyzed NO fragmentation, where the N-O bond weakening initially occurred on a singlet surface, but continued on a triplet surface after reaching the minimum-energy crossing point (MECP) between the two potential energy surfaces.

Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a "bespoke" fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibility. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations.

Magnetic properties of molecules such as magnetizabilities represent second order derivatives of the energy with respect to external perturbations. To avoid the need for analytic second derivatives and thereby permit evaluation of the performance of methods where they are not available, a new implementation of quantum chemistry calculations in finite applied magnetic fields is reported. This implementation is employed for a collection of small molecules with the aug-cc-pVTZ basis set to assess orbital optimized (OO) MP2 and a recently proposed regularized variant of OOMP2, called -OOMP2. -OOMP2 performs significantly better than conventional second order Møller-Plesset (MP2) theory, by reducing MP2's exaggeration of electron correlation effects. As a chemical application, we revisit an old aromaticity criterion called magnetizability exaltation. In lieu of empirical tables or increment systems to generate references, we instead use straight chain molecules with the same formal bond structure as the target cyclic planar conjugated molecules. This procedure is found to be useful for qualitative analysis, yielding exaltations that are typically negative for aromatic species and positive for antiaromatic molecules. One interesting species, NS, shows a positive exaltation despite having aromatic characteristics.

We investigate the thermodynamic properties of various super-critical model adsorptive systems with different fluid-solid attractive strengths using the confined-density virial expansion, with coefficients calculated using the Mayer-sampling Monte Carlo method up to fifth order. We find that the virial expansion converges for adsorptive systems over a density range corresponding approximately to the film-formation regime. Beyond this regime, higher order effects become increasingly important. The virial expansion of the density profile is also investigated. It is determined that this expansion gives insight into the structure associated with adsorption. We also find that weakly attractive systems have a more negative second virial coefficient than strongly attractive systems. This runs counter to the usual interpretation of bulk fluid virial coefficients. This is due to the infinite-dilution limit being very different for adsorbed fluids compared to bulk fluids.

Using a combination of X-ray diffraction and simulation techniques, we are able to identify a crystalline monolayer of 1,3,5-triiodotrifluorobenzene formed on graphite. The monolayer is found to exhibit an incommensurate hexagonal unit cell with a lattice parameter of 9.28(7) Å, exhibiting a trigonal arrangement of iodine atoms not found in the bulk structure. DFT simulations have been performed exhibiting close agreement with the experimental structure. Importantly these simulations can be used to compare the strength of the intermolecular interactions both with and without Van der Waals corrections. Thus it is possible to estimate that halogen bonding consists of approximately half the total interaction energy. This demonstrates that despite the presence of strong directional non-covalent bonding, dispersion interactions account for a very significant proportion of the total energy.

We present a new software package called M-Chem that is designed from scratch in C++ and parallelized on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research.

We evaluate the performance of approaches that combine coupled-cluster and perturbation theory based on a predefined active space of orbitals. Coupled-cluster theory is used to treat excitations that are internal to the active space and perturbation theory is used for all other excitations, which are at least partially external to the active space. We consider a variety of schemes that differ in how the internal and external excitations are coupled. Such approaches are presented for ground states and excited states within the equation-of-motion formalism. Results are given for the ionization potentials and electron affinities of a test set of small molecules and for the correlation energy and band gap of a few periodic solids.

The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure.