Natural polarizability and flexibility via explicit valency: the case of water

A win-win platform: Stabilized black phosphorous nanosheets loading gallium ions for enhancing the healing of bacterial-infected wounds through synergistic antibacterial approaches

Bacterial infection is the most common complication in wound healing, highlighting an urgent need for the development of innovative antibacterial technologies and treatments to address the growing threats posed by bacterial infections. Black phosphorus nanosheets (BPNSs), as a promising two-dimensional nanomaterial, have been utilized in treating infected wounds. However, BP's limited stability restricts its application. In this study, we enhance BP's stability and its antibacterial properties by anchoring gallium ions (Ga3+) onto BP's surface, creating a novel antibacterial platform. This modification reduces BP's electron density and enhances its antibacterial capabilities through a synergistic effect. Under near-infrared (NIR) irradiation, the BP/Ga3+ combination exerts antibacterial effects via photothermal therapy (PTT) and photodynamic therapy (PDT), while also releasing Ga3+. The Ga3+ employ a 'Trojan horse strategy' to disrupt iron metabolism, significantly boosting the antibacterial efficacy of the complex. This innovative material offers a viable alternative to antibiotics and holds significant promise for treating infected wounds and aiding skin reconstruction.

Art, fact and artifact: reflections on the cross-talk between theory and experiment

With the increasing sophistication of each, theory and experiment have become highly specialized endeavors conducted by separate research groups. A result has been a weakening of the coupling between them and occasional hostility. Examples are given and suggestions are offered for strengthening the traditional synergy between theory and experiment.

Adventures in interdisciplinary science: a half century at the nexus between chemistry, physics and biology

A look back over five decades of research.

Emergence of Linnett's "double quartets" from a model of "Lewis dots"

Chemists routinely explicate molecular structures and chemical reactions in terms of the propensities of semiclassical valence electrons (aka "Lewis dots"). Typically, the electrons are viewed as forming spin pairs and recent efforts to translate this concise and intuitive qualitative picture into an efficient and relatable quantitative model have made good progress. But electrons are not always paired and advanced quantum calculations have shown that this is so even in small diamagnetic species such as dicarbon and benzene. Here we show that the latest semiclassical model for paired electrons can clarify the limitations on pairing simply by dissecting the elements of the interparticle potentials. Although not trained to do so, these elements produce a Linnett-like benzene, with three valence electrons in each CC bond, when the electrons are free to move singly. At the same time, sustaining higher order bonds with independently mobile electrons requires adjustments in the details of the model potentials at short distances. This is addressed with new training data and new forms for the contributions from Coulomb integrals. Although trained on hydrogen and carbon species separately, the combination applied to ethyne predicts the pairing of spins in the CH bonds and the dispersion of spins in the CC bond that is found in ab initio calculations. This adjusted force field is named LINNETT, in appreciation of Linnett's insightful double quartet interpretation of the Lewis octet.

On the Choice of Different Water Model in Molecular Dynamics Simulations of Nanopore Transport Phenomena

The water transport through nanoporous multilayered graphene at 300k is investigated using molecular dynamics (MD) simulation with different water models in this study. We used functionalized and non-functionalized membranes along with five different 3-point rigid water models: SPC (simple point charge), SPC/E (extended simple point charge), TIP3P-FB (transferable intermolecular potential with 3 points-Force Balance), TIP3P-EW (transferable intermolecular potential with 3 points with Ewald summation) and OPC3 (3-point optimal point charge) water models. Based on our simulations with two water reservoirs and a porous multilayered graphene membrane in-between them, it is evident that the water transport varies significantly depending on the water model used, which is in good agreement with previous works. This study contributes to the selection of a water model for molecular dynamics simulations of water transport through multilayered porous graphene.

Valence energy correction for electron reactive force field

Reactive force fields (ReaxFF) are a classical method to describe material properties based on a bond-order formalism, that allows bond dissociation and consequently investigations of reactive systems. Semiclassical treatment of electrons was introduced within ReaxFF simulations, better known as electron reactive force fields (eReaxFF), to explicitly treat electrons as spherical Gaussian waves. In the original version of eReaxFF, the electrons and electron-holes can lead to changes in both the bond energy and the Coulomb energy of the system. In the present study, the method was modified to allow an electron to modify the valence energy, therefore, permitting that the electron's presence modifies the three-body interactions, affecting the angle among three atoms. When a reaction path involving electron transfer is more sensitive to the geometric configuration of the molecules, corrections in the angular structure in the presence of electrons become more relevant; in this case, bond dissociation may not be enough to describe a reaction path. Consequently, the application of the extended eReaxFF method developed in this work should provide an improved description of a reaction path. As a first demonstration this semiclassical force field was parametrized for hydrogen and oxygen interactions, including water and water's ions. With the modified methodology both the overall accuracy of the force field but also the description of the angles within the molecules in presence of electrons could be improved.

Modeling Electronic Response Properties with an Explicit-Electron Machine Learning Potential

Explicit-electron force fields introduce electrons or electron pairs as semiclassical particles in force fields or empirical potentials, which are suitable for molecular dynamics simulations. Even though semiclassical electrons are a drastic simplification compared to a quantum-mechanical electronic wave function, they still retain a relatively detailed electronic model compared to conventional polarizable and reactive force fields. The ability of explicit-electron models to describe chemical reactions and electronic response properties has already been demonstrated, yet the description of short-range interactions for a broad range of chemical systems remains challenging. In this work, we present the electron machine learning potential (eMLP), a new explicit electron force field in which the short-range interactions are modeled with machine learning. The electron pair particles will be located at well-defined positions, derived from localized molecular orbitals or Wannier centers, naturally imposing the correct dielectric and piezoelectric behavior of the system. The eMLP is benchmarked on two newly constructed data sets: eQM7, an extension of the QM7 data set for small molecules, and a data set for the crystalline β-glycine. It is shown that the eMLP can predict dipole moments, polarizabilities, and IR-spectra of unseen molecules with high precision. Furthermore, a variety of response properties, for example, stiffness or piezoelectric constants, can be accurately reproduced.

A Review of Recent Developments in Molecular Dynamics Simulations of the Photoelectrochemical Water Splitting Process

In this review, we provide a short overview of the Molecular Dynamics (MD) method and how it can be used to model the water splitting process in photoelectrochemical hydrogen production. We cover classical non-reactive and reactive MD techniques as well as multiscale extensions combining classical MD with quantum chemical and continuum methods. Selected examples of MD investigations of various aqueous semiconductor interfaces with a special focus on TiO2 are discussed. Finally, we identify gaps in the current state-of-the-art where further developments will be needed for better utilization of MD techniques in the field of water splitting.

Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems

Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.

Exchange potentials for semi-classical electrons

Semi-classical electrons offer access to efficient and intuitive simulations of chemical reactions. As for any treatment of fermions, the greatest difficulty is in accounting for anti-symmetry effects. Semi-classical efforts to-date either reference Slater-determinants from ab initio treatments or adopt a heuristic approach inspired by density functional treatments. Here we revisit the problem with a combined approach. We conclude that semi-classical electrons need to reference a non-conventional wave function and find that (1) contrary to earlier suppositions, contributions from the electrostatic terms in the Hamiltonian are of similar magnitude to those from the kinetic terms and (2) the former point to a need to supplement pair potentials with 3-body potentials. The first result explains features of reported heuristic potentials, and the second provides a firm footing for extending the transferability of potentials across a wider range of elements and bonding scenarios.

Chemistry with semi-classical electrons: reaction trajectories auto-generated by sub-atomistic force fields

For a century now, "Lewis dots" have been a mainstay of chemical thinking, teaching and communication. However, chemists have assumed that this semi-classical picture of electrons needs to be abandoned for quantitative work, and the recourse in computational simulations has been to the extremes of first principles treatments of electrons on the one hand and force fields that avoid explicit electrons on the other hand. Given both the successes and limitations of these highly divergent approaches, it seems worth considering whether the Lewis dot picture might be made quantitative after all. Here we review progress to that end, including variations that have been implemented and examples of applications, specifically the acid-base behavior of water, several organic reactions, and electron dynamics in silicon fracture. In each case, the semi-classical approach is highly efficient and generates reasonable and readily interpreted reaction trajectories in turnkey fashion (i.e., without any input about products). Avenues for further progress are also discussed.

Special Pairs Are Decisive in the Autoionization and Recombination of Water

Although water's chemical properties are no less important than its exceptional physical properties, its acid-base behavior is relatively poorly understood. In fact, the Grotthus trajectories for ion recombination predicted by density functional theory do not comport well with the almost 100-fold slower diffusive trajectories observed in time-resolved spectroscopy. And, in the reverse reaction, the barrier to autoionization is not well characterized. Here we develop a self-consistent picture of both processes based on the occurrence and role of ultrashort hydrogen bonds. The predicted populations of these special pairs in bulk water are consistent with the high frequency electrodynamics of water and its pressure dependence. The rate-limiting role of the special pairs manifests in autoionization as a two-stage barrier, first to form a contact ion pair and then to separate it by one water molecule. From this configuration, similar frequencies are observed for further separation vs recombination. The requirement of ultrashort hydrogen bonds for proton transfer in autoionization is consistent with the rise in K_w with increasing pressure and points to a role for density fluctuations in autoionization events. In neutralization, the manifestation of the role of special pairs is the prolonged diffusional process observed in time-resolved spectroscopy experiments. The requirement of special pairs as transition states for proton transfer is less obvious for neutralization in isolated water chains than in the bulk liquid only because an unbroken sequence of ultrashort H-bonds is more easily formed in a 1D H-bonded chain than in a 3D H-bonded network.

Accuracy limit of rigid 3-point water models

Classical 3-point rigid water models are most widely used due to their computational efficiency. Recently, we introduced a new approach to constructing classical rigid water models [S. Izadi et al., J. Phys. Chem. Lett. 5, 3863 (2014)], which permits a virtually exhaustive search for globally optimal model parameters in the sub-space that is most relevant to the electrostatic properties of the water molecule in liquid phase. Here we apply the approach to develop a 3-point Optimal Point Charge (OPC3) water model. OPC3 is significantly more accurate than the commonly used water models of same class (TIP3P and SPCE) in reproducing a comprehensive set of liquid bulk properties, over a wide range of temperatures. Beyond bulk properties, we show that OPC3 predicts the intrinsic charge hydration asymmetry (CHA) of water - a characteristic dependence of hydration free energy on the sign of the solute charge - in very close agreement with experiment. Two other recent 3-point rigid water models, TIP3PFB and H2ODC, each developed by its own, completely different optimization method, approach the global accuracy optimum represented by OPC3 in both the parameter space and accuracy of bulk properties. Thus, we argue that an accuracy limit of practical 3-point rigid non-polarizable models has effectively been reached; remaining accuracy issues are discussed.

Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons

The past decade has seen the first attempts at quantifying a semiclassical description of electrons in molecules. The challenge in this endeavor is to find potentials for electron interactions that adequately capture quantum effects. As has been the case for density functionals, the challenge is particularly great for the effects that follow from the requirement for wave function antisymmetry. Here we extend our empirical inquiry into effective potentials, from prior work on the monatomic atoms and ions of nonmetals, to diatomic molecules and ions formed by these elements. Newly adjusted and trained for the longer distances relevant to diatomics, pairwise potentials are able to fit the bond orders and magnetic properties of homonuclear species. These potentials are then found to do an excellent job of predicting the magnetism of heteronuclear species. In these molecules the predicted distribution of electrons also correctly reflects increasing ionic character with increasing difference in the electronegativities of the participating atoms. The distinctive features of the current potential are discussed, along with issues calling for further improvements.

Surface Propensities of the Self-Ions of Water

The surface charge of water, which is important in a wide range of chemical, biological, material, and environmental contexts, has been a subject of lengthy and heated debate. Recently, it has been shown that the highly efficient LEWIS force field, in which semiclassical, independently mobile valence electron pairs capture the amphiproticity, polarizability and H-bonding of water, provides an excellent description of the solvation and dynamics of hydroxide and hydronium in bulk water. Here we turn our attention to slabs, cylinders, and droplets. In extended simulations with 1000 molecules, we find that hydroxide consistently prefers the surface, hydronium consistently avoids the surface, and the two together form an electrical double layer until neutralization occurs. The behavior of hydroxide can largely be accounted for by the observation that hydroxide moving to the surface loses fewer hydrogen bonds than are gained by the water molecule that it displaces from the surface. At the same time, since the orientation of the hydroxide increases the ratio of dangling hydrogens to dangling lone pairs, the proton activity of the exposed surface may be increased, rather than decreased. Hydroxide also moves more rapidly in the surface than in the bulk, likely because the proton donating propensity of neighboring water molecules is focused on the one hydrogen that is not dangling from the surface.

Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties

The monotonic and non-monotonic variations of atomic properties within and between the rows of the periodic table underlie our understanding of chemistry and accounting for these variations has been a signature strength of quantum mechanics (QM). However, the computational burden of QM motivates the development of more efficient means of describing electrons and reactivity. The recently developed LEWIS • model incorporates lessons learnt from QM into a force field that includes electrons as explicit pseudo-classical particles. Here, we extend LEWIS • across the 2 p and 3 p elements, and show that it is capable of reproducing both monotonic and non-monotonic variations of chemically important atomic properties in a cost-effective manner. An indicator of the strength of the construct is the ability of pairwise potentials trained on ionization energies and the order of spin configurations to predict atomic polarizabilities. In this manner, some insights of QM are uncoupled from its onerous computational burden.

Building Water Models: A Different Approach

Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than the symmetry. Instead, we optimize the distribution of point charges to best describe the "electrostatics" of the water molecule. The resulting "optimal" 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures. The improvements in the proposed model extend beyond bulk properties: compared to common rigid models, predicted hydration free energies of small molecules using OPC are uniformly closer to experiment, with root-mean-square error <1 kcal/mol.

Transferable pseudoclassical electrons for aufbau of atomic ions

Generalizing the LEWIS reactive force field from electron pairs to single electrons, we present LEWIS• in which explicit valence electrons interact with each other and with nuclear cores via pairwise interactions. The valence electrons are independently mobile particles, following classical equations of motion according to potentials modified from Coulombic as required to capture quantum characteristics. As proof of principle, the aufbau of atomic ions is described for diverse main group elements from the first three rows of the periodic table, using a single potential for interactions between electrons of like spin and another for electrons of unlike spin. The electrons of each spin are found to distribute themselves in a fashion akin to the major lobes of the hybrid atomic orbitals, suggesting a pointillist description of the electron density. The broader validity of the LEWIS• force field is illustrated by predicting the vibrational frequencies of diatomic and triatomic hydrogen species.

Point charges optimally placed to represent the multipole expansion of charge distributions

We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior of the approximate potential. A general framework for numerically computing OPCA, for any given number of approximating charges, is described. We then derive a 2-charge practical point charge approximation, PPCA, which approximates the 2-charge OPCA via closed form analytical expressions, and test the PPCA on a set of charge distributions relevant to biomolecular modeling. We measure the accuracy of the new approximations as the RMS error in the electrostatic potential relative to that produced by the original charge distribution, at a distance 2x the extent of the charge distribution--the mid-field. The error for the 2-charge PPCA is found to be on average 23% smaller than that of optimally placed point dipole approximation, and comparable to that of the point quadrupole approximation. The standard deviation in RMS error for the 2-charge PPCA is 53% lower than that of the optimal point dipole approximation, and comparable to that of the point quadrupole approximation. We also calculate the 3-charge OPCA for representing the gas phase quantum mechanical charge distribution of a water molecule. The electrostatic potential calculated by the 3-charge OPCA for water, in the mid-field (2.8 Å from the oxygen atom), is on average 33.3% more accurate than the potential due to the point multipole expansion up to the octupole order. Compared to a 3 point charge approximation in which the charges are placed on the atom centers, the 3-charge OPCA is seven times more accurate, by RMS error. The maximum error at the oxygen-Na distance (2.23 Å) is half that of the point multipole expansion up to the octupole order.

Proton defect solvation and dynamics in aqueous acid and base

Easy come, easy go: LEWIS, a new model of reactive and polarizable water that enables the simulation of a statistically reliable number of proton hopping events in aqueous acid and base at concentrations of practical interest, is used to evaluate proton transfer intermediates in aqueous acid and base (picture, left and right, respectively).