Charge Assignment Research Articles

Exploring the structural feature of water, alcohols, and their binary mixtures with concrete atomic charge assignments in Dreiding forcefield

The water, alcohols, and their binary mixtures are widely used in molecular simulations. However, the Dreiding force field lacks a generally accepted method for assigning atomic charges to these solvents during simulations. In this study, we propose a universal charge assignment for water and eight water-miscible alcohols in Dreiding. Through extensive molecular simulations, we demonstrate the good accuracy of our charge assignments in displaying characteristic of these solvents and their mixtures, including liquid density and structure. Moreover, we investigate equilibrium snapshot, radial distribution function, coordination number and hydrogen bonding, all of which confirm the miscibility of alcohols with water or ethanol. Notably, we reveal that the structure diversity among different mixtures can be attributed to distinctive characteristic of alcohols, including molecular volume, as well as the number and position of hydroxyls.

Digital Ion Trap Isolation and Mass Analysis of Macromolecular Analytes with Multiply Charged Ion Attachment.

Multiply charged ions produced by electrospray ionization (ESI) of heterogeneous mixtures of macromolecular analytes under native conditions are typically confined to relatively narrow ranges of mass-to-charge (m/z) ratio, often with extensive overlap. This scenario makes charge and mass assignments extremely challenging, particularly when individual charge states are unresolved. An ion/ion reaction strategy involving multiply charged ion attachment (MIA) to the mixture components in a narrow range of m/z can facilitate charge and mass assignment. In MIA operation, multiply charged reagent ions are attached to the analyte ions of opposite polarity to provide large m/z displacements resulting from both large changes in mass and charge. However, charge reduction of the high m/z ions initially generated under native ESI conditions requires the ability to isolate high m/z ions and to analyze even higher m/z product ions. Digital ion trap (DIT) operation offers means for both high m/z ion isolation and high m/z mass analysis, in addition to providing conditions for the reaction of oppositely charged ions. The feasibility of conducting MIA experiments in a DIT that takes advantage of high m/z ion operation is demonstrated here using a tandem 2D-3D DIT instrument. Proof-of-concept MIA experiments with cations derived from β-galactosidase using the 20- charge state of human serum immunoglobulin G (IgG, ∼149 kDa) as the reagent anion are described. MIA experiments involving mixtures of ions derived from the E. coli. ribosome are also described. For example, three components in a mixture of 70S particles (>2.2 MDa) were resolved and assigned with masses and charges following an MIA experiment involving the 20- charge state of human serum IgG.

LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations.

Generating simulation-ready molecular models for the LAMMPS molecular dynamics (MD) simulation software package is a difficult task and impedes the more widespread and efficient use of MD in materials design and development. Fixed-bond force fields generally require manual assignment of atom types, bonded interactions, charges, and simulation domain sizes. A new LAMMPS pre- and postprocessing toolkit (LUNAR) is presented that efficiently builds molecular systems for LAMMPS. LUNAR automatically assigns atom types, generates bonded interactions, assigns charges, and provides initial configuration methods to generate large molecular systems. LUNAR can also incorporate chemical reactivity into simulations by facilitating the use of the REACTER protocol. Additionally, LUNAR provides postprocessing for free volume calculations, cure characterization calculations, and property predictions from LAMMPS thermodynamic outputs. LUNAR has been validated via building and simulation of pure epoxy and cyanate ester polymer systems with a comparison of the corresponding predicted structures and properties to benchmark values, including experimental results from the literature. LUNAR provides the tools for the computationally driven development of next-generation composite materials in the Integrated Computational Materials Engineering (ICME) and Materials Genome Initiative (MGI) frameworks. LUNAR is written in Python with the usage of NumPy and can be used via a graphical user interface, a command line interface, or an integrated design environment. LUNAR is freely available via GitHub.

The SU(3)C × SU(3)L × U(1)X (331) Model: Addressing the Fermion Families Problem within Horizontal Anomalies Cancellation.

One of the most important and unanswered problems in particle physics is the origin of the three generations of quarks and leptons. The Standard Model does not provide any hint regarding its sequential charge assignments, which remain a fundamental mystery of Nature. One possible solution of the puzzle is to look for charge assignments, in a given gauge theory, that are inter-generational, by employing the cancellation of the gravitational and gauge anomalies horizontally. The 331 model, based on an SU(3)C×SU(3)L×U(1)X does this in an economical way and defines a possible extension of the Standard Model, where the number of families has necessarily to be three. We review the model in Pisano, Pleitez, and Frampton's formulation, which predicts the existence of bileptons. Another characteristics of the model is to unify the SU(3)C×SU(2)L×U(1)X into the 331 symmetry at a scale that is in the TeV range. Expressions of the scalar mass eigenstates and of the renormalization group equations of the model are also presented.

EspalomaCharge: Machine Learning-Enabled Ultrafast Partial Charge Assignment.

Atomic partial charges are crucial parameters in molecular dynamics simulation, dictating the electrostatic contributions to intermolecular energies and thereby the potential energy landscape. Traditionally, the assignment of partial charges has relied on surrogates of ab initio semiempirical quantum chemical methods such as AM1-BCC and is expensive for large systems or large numbers of molecules. We propose a hybrid physical/graph neural network-based approximation to the widely popular AM1-BCC charge model that is orders of magnitude faster while maintaining accuracy comparable to differences in AM1-BCC implementations. Our hybrid approach couples a graph neural network to a streamlined charge equilibration approach in order to predict molecule-specific atomic electronegativity and hardness parameters, followed by analytical determination of optimal charge-equilibrated parameters that preserve total molecular charge. This hybrid approach scales linearly with the number of atoms, enabling for the first time the use of fully consistent charge models for small molecules and biopolymers for the construction of next-generation self-consistent biomolecular force fields. Implemented in the free and open source package EspalomaCharge, this approach provides drop-in replacements for both AmberTools antechamber and the Open Force Field Toolkit charging workflows, in addition to stand-alone charge generation interfaces. Source code is available at https://github.com/choderalab/espaloma-charge.

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations.

Protein carbonylation by reactive aldehydes derived from lipid peroxidation leads to cross-linking, oligomerization, and aggregation of proteins, causing intracellular damage, impaired cell functions, and, ultimately, cell death. It has been described in aging and several age-related chronic conditions. However, the basis of structural changes related to the loss of function in protein targets is still not well understood. Hence, a route to the in silico construction of new parameters for amino acids carbonylated with reactive carbonyl species derived from fatty acid oxidation is described. The Michael adducts for Cys, His, and Lys with 4-hydroxy-2-nonenal (HNE), 4-hydroxy-2-hexenal (HHE), and a furan ring form for 4-Oxo-2-nonenal (ONE), were built, while malondialdehyde (MDA) was directly attached to each residue. The protocol describes details for the construction, geometry optimization, assignment of charges, missing bonds, angles, dihedral angles parameters, and its validation for each modified residue structure. As a result, structural effects induced by the carbonylation with these lipid derivatives have been measured by molecular dynamics simulations on different protein systems such as the thioredoxin enzyme, bovine serum albumin and the membrane Zu-5-ankyrin domain employing root-mean-square deviation (RMSD), root mean square fluctuation (RMSF), structural secondary prediction (DSSP) and the solvent-accessible surface area analysis (SASA), among others.

Predicting Quantum-Mechanical Partial Charges in Arbitrarily Long Boron Nitride Nanotubes to Accurately Simulate Nanoscale Water Transport.

Single-walled boron nitride nanotubes (BNNTs) have been explored for various applications, ranging from water desalination to osmotic power harvesting. However, no simulation work so far has modeled the changes in the partial charge distribution when a flat sheet is rolled into a tube, hindering the ability to perform accurate molecular dynamics (MD) simulations of water flow through BNNTs. To address this knowledge gap, we employ electronic density functional theory (DFT) calculations to precisely estimate quantum-mechanically derived partial charges on boron (B) and nitrogen (N) atoms in BNNTs of varying lengths and diameters. We observe a spatially varying charge distribution inside both armchair and zigzag nanotubes of finite lengths. Performing DFT calculations for longer BNNTs is computationally intractable, even with state-of-the-art computing resources. To solve this issue, we devise a charge assignment scheme to predict partial charges for longer BNNTs using DFT data for shorter nanotubes, thus overcoming the need to perform more expensive DFT calculations. We show that these charges reproduce the electrostatic potential predicted from first-principles simulations. Subsequently, we carried out MD simulations to predict the effect of the charge distribution inside BNNTs on water flow enhancement via them. We find that using uniform charges leads to an underprediction in flow enhancement, as compared to using quantum-mechanical charges for both armchair and zigzag BNNTs. We also incorporate atomic vibrations into our simulations and show that these vibrations lead to a reduction in the water flow through aperiodic BNNTs. Our work demonstrates the requirement of a quantum-mechanical charge assignment scheme for BNNTs and evolves a framework to assign charges to nanotubes of arbitrary length, thus allowing realistic MD simulations of long BNNTs using accurate partial charges.

Hadrophobic axion from a GUT

We propose a new kind of axion model derived from the grand unified theory (GUT) based on SU(5)×U(1)PQ. We demonstrate that, given a certain charge assignment and potential flavor models, the axion is naturally hadrophobic and provides a novel explanation for the required condition using isospin symmetry. This axion can be the QCD axion that solves the strong CP problem. Furthermore, to satisfy the limit on the axion-electron coupling from the tip of the red giant branch, we impose the condition of electrophobia to determine a possible Peccei-Quinn charge assignment consistent with GUT. We then discuss the possibility that the hadrophobic and electrophobic axion serves as an inflaton and dark matter, as in the axionlike particle miracle scenario. Interestingly, in the viable parameter region, the strong CP phase must be suppressed, providing another solution to the strong CP problem. This scenario is intimately linked to flavor physics, dark matter searches, and stellar cooling. Detecting such an axion with peculiar couplings in various experiments would serve as a probe for GUT and the origin of flavor. Published by the American Physical Society 2024

Anomaly-free dark matter models with one-loop neutrino masses and a gauged U(1) symmetry

We systematically study and classify scotogenic models with a local U(1) gauge symmetry. These models give rise to radiative neutrino masses and a stable dark matter candidate, but avoid the theoretical problems of global and discrete symmetries. We restrict the dark sector particle content to up to four scalar or fermionic SU(2) singlets, doublets or triplets and use theoretical arguments based on anomaly freedom, Lorentz and gauge symmetry to find all possible charge assignments of these particles. The U(1) symmetry can be broken by a new Higgs boson to a residual discrete symmetry, that still stabilizes the dark matter candidate. We list the particle content and charge assignments of all non-equivalent models. Specific examples in our class of models that have been studied previously in the literature are the U(1)D scotogenic and singlet-triplet scalar models breaking to Z2. We also briefly discuss the new phenomenological aspects of our model arising from the presence of a new massless dark photon or massive Z′ boson as well as the additional Higgs boson.

A simple approach to simulate corona-charged electret filters

This paper presents a novel computational model devised to simulate how different ways of corona-charging a fibrous filter can impact its aerosol collection efficiency. The model assigns different bipolar charges to the fibers in the media based on how the corona-generated negative ions impact these fibers they travel from the corona needles towards the grounded surface underneath the media. The charge assignment process is based on observations made from simulating the electrohydrodynamic field around the corona needles. With the fibers virtually charged, the trajectory of positively and negatively charged aerosol particles, ranging in size from 30 to 500 nm, were simulated across the filter thickness to quantify the effect of fiber charge distribution on the filter efficiency. The performance of our virtual filter was found to be better when it was exposed to the corona ions on both the face and back sides. More interestingly, it was found that the filtration efficiency of the filter was dependent on the order by which its face and back sides were charged. The filter was observed to capture smaller particles (less than 150 nm) more efficiently when it was first charged on the face side and then charged on the back side. The opposite effect was observed when the charging order was reversed. This difference in filtration performance was found to arise from the differences in the solid volume fraction of the filter across its thickness.

DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment.

We present a robust and computationally efficient approach for assigning partial charges of atoms in molecules. The method is based on a hierarchical tree constructed from attention values extracted from a graph neural network (GNN), which was trained to predict atomic partial charges from accurate quantum-mechanical (QM) calculations. The resulting dynamic attention-based substructure hierarchy (DASH) approach provides fast assignment of partial charges with the same accuracy as the GNN itself, is software-independent, and can easily be integrated in existing parametrization pipelines, as shown for the Open force field (OpenFF). The implementation of the DASH workflow, the final DASH tree, and the training set are available as open source/open data from public repositories.

Pharmacophore Oriented MP2 Characterization of Charge Distribution for Anti-SARS-CoV-2 Inhibitor Nirmatrelvir

Quantum mechanical second order Møller–Plesset (MP2) perturbation theory and density functional theory (DFT) Becke, 3-parameter, Lee-Yang-Parr (B3LYP) and Minnesota 2006 local functional (M06L) calculations were performed to optimize structure of nirmatrelvir and compute the Merz-Kollman electrostatic potential (MK ESP), natural population analysis (NPA), Hirshfeld, charge model 5 (CM5), and mulliken partial charges. The mulliken partial charge distribution of nirmatrelvir exhibits a poor correlation with the MK ESP charges in MP2, B3LYP, and M06L calculations respectively. The NPA, Hirshfeld, and CM5 partial charge scheme of nirmatrelvir indicate a reasonable correlation with MK ESP charge assignments in B3LYP and M06L calculations. The above correlations were not improved by the inclusion of implicit solvation model. The MK ESP and CM5 partial charges show a strong correlation between the results of MP2 and two DFT methods. The three optimized structures present a certain degree of differences from the crystal bioactive conformation of nirmatrelvir, suggesting the nirmatrelvir-enzyme complex is formed in the induced-fit model. The Reactivity of warhead electrophilic nitrile is justified by the relatively weaker strength of π bonds in the MP2 calculations. The nirmatrelvir hydrogen bond acceptors consistently show strong delocalization of lone pair electrons in three calculations, whereas hydrogen bond donors are found to have high polarization on the heavy nitrogen atoms in MP2 computations. This work helps to parametrize the force field of nirmatrelvir and improve accuracy of molecular docking and rational inhibitor design.

Low-energy effective description of dark $Sp(4)$ theories

Strongly interacting massive particles are viable dark matter candidates. We consider a dark Sp(4)Sp(4) gauge theory with N_f=2Nf=2 fermions in the pseudo-real fundamental representation and construct the chiral low-energy effective theory. We determine the flavour multiplet structure and the chiral Lagrangian, including the Wess-Zumino-Witten term for mass-degenerate and non-degenerate flavours. We then study the possible charge assignments under a U(1)'U(1)′ gauge symmetry, emphasizing on dark state stability, and provide the full Lagrangian description for Goldstone bosons and vector resonances, including the Wess-Zumino-Witten term. Finally, we use dedicated lattice simulations to determine the chiral low-energy effective theory’s validity and low-energy constants. This work represents a self-consistent study of this non-Abelian theory. It thereby provides a framework for future phenomenological exploration in connection to the dark matter problem.

What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids?

In classical nonpolarizable models, electrostatic interactions are usually described by assigning fixed partial charges to interaction sites. Despite the multitude of methods and theories proposed over the years for partial charge assignment, a fundamental question remains─what is the correct degree of polarization that a fixed-charge model should possess to provide the best balance of interactions (including induction effects) and yield the best description of the potential energy surface of a liquid phase? We address this question by approaching it from two separate and independent viewpoints: the QUantum mechanical BEspoke (QUBE) approach, which assigns bespoke force field parameters for individual molecules from ab initio calculations with minimal empirical fitting, and the Polarization-Consistent Approach (PolCA) force field, based on empirical fitting of force field parameters with an emphasis on transferability by rigorously accounting for polarization effects in the parameterization process. We show that the two approaches yield consistent answers to the above question, namely, that the dipole moment of the model should be approximately halfway between those of the gas and the liquid phase. Crucially, however, the reference liquid-phase dipole needs to be estimated using methods that explicitly consider both mean-field and local contributions to polarization. In particular, continuum dielectric models are inadequate for this purpose because they cannot account for local effects and therefore significantly underestimate the degree of polarization of the molecule. These observations have profound consequences for the development, validation, and testing of nonpolarizable models.

Z 3 scalar dark matter with strong positron fluxes

We explore a class of simplified extensions to the Standard Model containing a complex singlet scalar as a dark matter candidate accompanied by a vector-like lepton as a mediator, both charged under a new Z 3 symmetry. In its simplest form, the new physics couples only to right-handed electrons, and the model is able to accommodate the correct dark matter relic abundance around the electroweak scale up to several TeV evading the strongest constraints from perturbativity, collider and dark matter searches. Furthermore, the model is capable to enhance naturally positron fluxes by several orders of magnitude presenting a box-shape spectra. This framework opens up a lot of phenomenological possibilities depending on the quantum charge assignments of the new fields.

Scalar-singlet assisted leptogenesis with CP violation from the vacuum

In the vanilla type-I seesaw leptogenesis scenario, CP violation required to generate the lepton asymmetries in the heavy Majorana neutrino decays stem from complex Dirac-type Yukawa couplings. In this paper we explore the case in which that CP violation originates from the vacuum expectation value of a complex scalar singlet at a very high scale. This non-trivial CP-violating phase can be successfully communicated to the low-energy neutrino sector via the heavy neutrino portal. The new scalar-singlet degrees of freedom generate new contributions to the CP asymmetries relevant for leptogenesis not only at the one-loop level but also through tree-level three-body decays. These are computed here for an arbitrary number of heavy neutrinos, Higgs doublets and scalar singlets. We also take into account the new decays and scattering processes that enter the unflavoured Boltzmann equations governing the heavy-neutrino particle densities and the (B – L)-asymmetry evolution. Having established the framework of interest, we present a simple model with two RH neutrinos, two Higgs doublets and a complex scalar singlet, supplemented with a Ƶ8 flavour symmetry. This symmetry minimises the number of free parameters without compromising the possibility of spontaneous CP violation and compatibility with neutrino data. In fact, the only viable Ƶ8 charge assignment shows a preference for a non-trivial spontaneous CP-violating phase, which in turn leads to a non-vanishing CP asymmetry due to the direct link between high- and low-energy CP violation. An interesting feature of this simple setup is that the usual wave and vertex type-I seesaw contributions to the CP asymmetry vanish due to the Ƶ8 symmetry. Thus, the observed baryon-to-photon ratio can be explained thanks to the new couplings among the heavy neutrinos and the new scalar degrees of freedom.

Integer solutions to the anomaly equations for a class of chiral gauge theories

We find all the integer charge solutions to the equations for the cancellation of local gauge anomalies in a class of gauge theories that extend the Standard Model (SM) by a gauge group of the form $G\ifmmode\times\else\texttimes\fi{}\mathrm{U}(1)$, where $G$ is an arbitrary semisimple compact Lie group. The SM fermions are assumed to be neutral under $G\ifmmode\times\else\texttimes\fi{}\mathrm{U}(1)$ gauge interactions, while the new fermions transform in nontrivial representations of both the new and the SM gauge groups. Our analysis is valid also when the latter is embedded in an arbitrary semisimple compact Lie group. Theories with this structure have recently been studied as models of composite axions based on accidental symmetries and can provide a field theory resolution to the axion quality problem. We apply our results to cases of phenomenological interest and prove the existence of charge assignments with Peccei-Quinn symmetry protected up to dimension 18.

SM extension with a gauged flavor U(1)F symmetry

An extension of the Standard Model with anomaly free $U(1{)}_{F}$ flavor symmetry is studied in this paper. With this extension and the addition of the right-handed neutrino states, the solution of anomaly free charge assignments is found, which gives appealing texture zero and hierarchical Yukawa matrices. This gives us a natural understanding of the hierarchies between charged fermion masses and Cabibbo-Kobayashi-Maskawa matrix elements. Neutrino Dirac and Majorana coupling matrices also have desirable structures leading to successful neutrino oscillations with inverted neutrino mass ordering. Other interesting implications of the presented scenario are also discussed.

Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules.

Analysis and validation of a mass spectrometry (MS) experiment are usually performed by comparison to reference spectra. However, if references are missing, measured spectra cannot be properly matched. To close this gap, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed. It enables fully automatic calculations of electron ionization (EI) and positive ion collision-induced dissociation (CID) mass spectra of singly charged molecular ions. In this work, the extension to negative and multiple ion charge for the CID run mode is presented. QCxMS is now capable of calculating structures carrying any charge, without the need for pretabulated fragmentation pathways or machine learning of database spectra. Mass spectra of four single negatively charged and two multiple positively charged organic ions with molecular sizes from 12 to 92 atoms were computed and compared to reference spectra. The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the semiempirical quantum mechanical GFN2-xTB method, while for some small molecules, ab initio DFT-based MD simulations were performed. Detailed insights into the fragmentation pathways were gained, and the effects of the computed charge assignments on the resulting spectrum are discussed. Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial. Doubly charged fragments could successfully be calculated fully automatically for the first time, while higher charged structures introduced severe assignment problems. Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation.

Classification of Abelian domain walls

We discuss domain walls from spontaneous breaking of Abelian discrete symmetries $Z_N$. A series of different domain wall structures are predicted, depending on the symmetry and charge assignments of scalars leading to the spontaneous symmetry breaking (SSB). A widely-existing type of domain walls are those separating degenerate vacua which are adjacent in the field space. We denote these walls as adjacency walls. In the case that $Z_N$ terms are small compared with the $U(1)$ terms, the SSB of $U(1)$ generates strings first and then adjacency walls bounded by strings are generated after the SSB of $Z_N$. For symmetries larger than $Z_3$, non-adjacent vacua exist, we regard walls separating them as non-adjacency walls. These walls are unstable if $U(1)$ is a good approximation. If the discrete symmetry is broken via multiple steps, we arrive at a complex structure that one kind of walls wrapped by another type. On the other hand, if the symmetry is broken in different directions independently, walls generated from the different breaking chains are blind to each other.