Charge Assignment Research Articles

Constructing surface models of silicate glasses using molecular dynamics to understand the effect of pH on the hydration properties.

In this work, we use realistic silicate glass surface models, with molecular dynamics simulations, and present an algorithm for proper atomic partial charge assignment, consistent with measurable internal dipoles. The immersion energy is calculated for different silicate glass compositions in solutions of varying pH. We use molecular dynamics to elucidate the differences in the structure of water between mono- and divalent cations. The immersion energy of the glass surface is found to increase with an increase in ionic surface density and pH. This can be attributed to the stronger interaction between water and cations, as opposed to the interactions between water and silanol groups. The developed models and methods provide new insights into the structure of glass-solution interfaces and the effect of cation surface density in common nanoscale environments.

Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters.

The three-dimensional reference interaction site model molecular solvation theory with the Kovalenko-Hirata closure relation has been shown to produce excellent solvation characteristics for a large class of (bio)chemical systems in solution. Correct calculation of hydration free energy is central to successful application of any solvation model. In order to find out the best possible force-field parameters to be used for hydration free energy calculation with the aforementioned theory, we have developed an extended database containing a large number of experimental solvation free energies available in the current literature and used a plethora of theoretical models for assessment. The general Amber force field was found to perform satisfactorily, whereas special care should be taken in solute charge assignment with the universal force field.

Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases.

Organic photovoltaics (OPV) have been theoretically studied within the usual parameters: open circuit voltage (Voc), short circuit current (Jsc), and fill factor (FF). The first two refer mostly to electronic properties, whereas the last contains all other possible contributions to cell efficiency, importantly including molecular geometrical and topological structures, both within a single molecule as amongst a system of molecules. In order to study the effects of molecular morphology of the heterostructures used in OPVs, molecular dynamic simulations (MDS) are imperative, and therefore parameterization of force fields to account for the description of planarity between aromatic rings, both intra- and inter-molecules, is of key importance. In this work, we present quantum mechanical analysis of geometry for the ground, and singlet and triplet excited states, of two simple prototypical molecules used to parametrize the corresponding force-fields. Central for this parameterization is the assignment of local charges within molecules; we studied and compared six different methods to assign atomic charges. With the parameters obtained, we performed molecular dynamics simulations of nanosystems of these molecules. Planarity effects and comparison between different methods for deriving atomic charges are investigated. These results can be applied in future MDS to interpret and characterize charge-transfer models in molecules suitable for OPV design. Graphical Abstract Depiction of a replicated system of BTT and BPT molecules after simulation.

B\u2192s\u03bc+\u03bc\u2212 anomalies and related phenomenology in mathrm{U}{(1)}_{{mathrm{B}}_3-{mathrm{x}}_{mu }{mathrm{L}}_{mu }-{mathrm{x}}_{tau }{mathrm{L}}_{tau }} flavor gauge models

We propose a generation dependent lepton/baryon gauge symmetry, mathrm{U}{(1)}_{B_3-{x}_{mu }{L}_{mu }-{x}_{tau }{L}_{tau }}equiv mathrm{U}{(1)}_X (with xμ + xτ = 1 for anomaly cancellation), as a possible solution for the b → sμ+μ− anomalies. By introducing two Higgs doublet fields, we can reproduce the observed CKM matrix, and generate flavor changing Z′ interactions in the quark sector. Thus one can explain observed anomalies in b → sℓ+ℓ− decay with the lepton non-universal U(1)X charge assignments. We show the minimal setup explaining b→sℓ+ℓ− anomalies, neutrino masses and mixings and dark matter candidate, taking into account experimental constraints of flavor physics such as charged lepton flavor violations and the {B}_s-{overline{B}}_s mixing. Finally we discuss collider physics focusing on Z′ production at the Large Hadron Collider and relic density of our dark matter candidate.

A very heavy sneutrino as viable thermal dark matter candidate in U(1)\u2032 extensions of the MSSM

We study the Standard Model singlet (“right-handed”) sneutrino {tilde{nu}}_R dark matter in a class of U(1)′ extensions of the MSSM that originate from the breaking of the E6 gauge group. These models, which are referred to as UMSSM, contain three right-handed neutrino superfields plus an extra gauge boson Z′ and an additional SM singlet Higgs with mass ≃ MZ′, together with their superpartners. In the UMSSM the right sneutrino is charged under the extra U(1)′ gauge symmetry; it can therefore annihilate via gauge interactions. In particular, for {M}_{{tilde{nu}}_R}simeq {M}_{Zprime }/2 the sneutrinos can annihilate by the exchange of (nearly) on-shell gauge or Higgs bosons. We focus on this region of parameter space. For some charge assignment we find viable thermal {tilde{nu}}_R dark matter for mass up to ∼ 43 TeV. This is the highest mass of a good thermal dark matter candidate in standard cosmology that has so far been found in an explicit model. Our result can also be applied to other models of spin−0 dark matter candidates annihilating through the resonant exchange of a scalar particle. These models cannot be tested at the LHC, nor in present or near-future direct detection experiments, but could lead to visible indirect detection signals in future Cherenkov telescopes.

Automated simultaneous assignment of bond orders and formal charges

Bond orders and formal charges are fundamental chemical descriptors. In cheminformatic applications it is necessary to be able to assign these properties to a given molecular structure automatically, given minimal input information. Here we describe a method for determining the bond order and formal charge assignments from only the atom types and connectivity. Our method utilises a graph theoretical description of electron positions. Each electron position assignment is scored according to lookup tables of atomic and bond dissociation energies derived from quantum chemical calculations. We tested three different optimisation methods—local optimisation, an A* pathfinding method, and an FPT optimisation method utilising tree decompositions—for finding the best electron position assignment, from which the bond orders and formal charges are extracted. We show that our method can assign bond orders and formal charges at a high degree of accuracy across a wide range of molecules from two different databases, and that the FPT algorithm provides the best combination of speed and accuracy.

A unified geometric framework for boundary charges and dressings: Non-Abelian theory and matter

Boundaries in gauge theories are a delicate issue. Arbitrary boundary choices enter the calculation of charges via Noether's second theorem, obstructing the assignment of unambiguous physical charges to local gauge symmetries. Replacing the arbitrary boundary choice with new degrees of freedom suggests itself. But, concretely, such boundary degrees of freedom are spurious—i.e. they are not part of the original field content of the theory—and have to disappear upon gluing. How should we fit them into what we know about field-theory? We resolve these issues in a unified and geometric manner, by introducing a connection 1-form, ϖ, in the field-space of Yang–Mills theory. Using this geometric tool, a modified version of symplectic geometry—here called ‘horizontal’—is possible. Independently of boundary conditions, this formalism bestows to each region a physical notion of charge: the horizontal Noether charge. The horizontal gauge charges always vanish, while global charges still arise for reducible configurations characterized by global symmetries. The field-content itself is used as a reference frame to distinguish ‘gauge’ and ‘physical’; no new degrees of freedom, such as group-valued edge modes, are required. Different choices of reference fields give different ϖ's, which are cousins of gauge-fixings like the Higgs-unitary and Coulomb gauges. But the formalism extends well beyond gauge-fixings, for instance by avoiding the Gribov problem. For one choice of ϖ, would-be Goldstone modes arising from the condensation of matter degrees of freedom play precisely the role of the known group-valued edge modes, but here they arise as preferred coordinates in field space, rather than new fields. For another choice, in the Abelian case, ϖ recovers the Dirac dressing of the electron.

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.

Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chemical space by addressing limitations in chemotype transferability. OPLS3e accomplishes this by incorporating new parameter types that recognize moieties with greater chemical specificity and integrating an on-the-fly parametrization approach to the assignment of partial charges. As a consequence, OPLS3e leads to greater accuracy against performance benchmarks that assess small molecule conformational propensities, solvation, and protein-ligand binding.

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid.

Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the syn conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We focus on the carboxyl torsional potential and configurations of microhydrated acetic acid from molecular dynamics simulations, probing the effects of solvent, force field (GAFF vs GAFF2), and partial charge assignment of acetic acid. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach

A key factor in computational drug design is the consistency and reliability with which intermolecular interactions between a wide variety of molecules can be described. Here we present a procedure to efficiently, reliably and automatically assign partial atomic charges to atoms based on known distributions. We formally introduce the molecular charge assignment problem, where the task is to select a charge from a set of candidate charges for every atom of a given query molecule. Charges are accompanied by a score that depends on their observed frequency in similar neighbourhoods (chemical environments) in a database of previously parameterised molecules. The aim is to assign the charges such that the total charge equals a known target charge within a margin of error while maximizing the sum of the charge scores. We show that the problem is a variant of the well-studied multiple-choice knapsack problem and thus weakly mathcal {NP}-complete. We propose solutions based on Integer Linear Programming and a pseudo-polynomial time Dynamic Programming algorithm. We demonstrate that the results obtained for novel molecules not included in the database are comparable to the ones obtained performing explicit charge calculations while decreasing the time to determine partial charges for a molecule from hours or even days to below a second. Our software is openly available.

An anomaly-free atlas: charting the space of flavour-dependent gauged U(1) extensions of the Standard Model

Spontaneously broken, flavour-dependent, gauged U(1) extensions of the Standard Model (SM) have many phenomenological uses. We chart the space of solutions to the gauge anomaly cancellation equations in such extensions, for both the SM chiral fermion content and the SM plus (up to) three right-handed neutrinos (SMνR). Methods from Diophantine analysis allow us to efficiently index the solutions arithmetically, and produce the complete solution space in particular cases. In order to solve the general case, we build a computer program which cycles through possible U(1) charge assignments, providing all solutions for charges up to some pre-defined maximum absolute charge. Lists of anomaly-free U(1) charge assignments result, which corroborate the results of our Diophantine analysis. We make these lists, which may be queried for further desirable properties, publicly available. This previously uncharted space of anomaly-free charge assignments has been little explored until now, paving the way for future model building and phenomenological studies.

Structure and Dynamics of the Bcl-2 Promoter G-Quadruplex using the Drude Polarizable Force Field

G-quadruplexes (GQ) are noncanonical nucleic acid structures that form in guanine-rich sequences and exist in a variety of topological forms. The guanine bases in GQ arrange in a square planar configuration and stack to form tetrads via Hoogsteen hydrogen bonding and coordination of ions like K+. These highly ordered secondary structures are implicated in the regulation of gene expression and genome maintenance, and alterations to their structures contribute to diseases such as cancer. The B-cell CLL/lymphoma 2 (bcl-2) oncogene is associated with a variety of cancers and its promoter features a GQ that arises due to two consecutive substitutions of guanine with thymine. Understanding the forces driving GQ folding and stabilization is required for developing novel therapeutics that target these structures. To develop a greater understanding of the atomistic details in the bcl-2 GQ, we performed molecular dynamics simulations using the CHARMM36 additive and Drude-2017 polarizable force fields. In the classical Drude oscillator model, electronic degrees of freedom are modeled as negatively charged particles attached harmonically to all heavy atoms. This approach overcomes limitations of nonpolarizable force fields, which approximate average polarization via assignment of partial charges. We performed simulations of the mutant bcl-2 promoter GQ and created the wild-type sequence by reverting the point mutations. The wild-type sequence was then thermally denatured and allowed to re-fold to determine the structural differences between the mutant bcl-2 GQ and the native, wild-type fold. Our analysis provides insight into the stability of the bcl-2 GQ structure, backbone conformational ensembles in dihedral space, base-ion interaction energetics, and the magnitude and fluctuation of dipole moments. These simulations illustrate that polarization is integral for tetrad stability and suggests that the Drude force field is essential for simulating GQ structures.

Revisiting the number-theory dark matter scenario and the weak gravity conjecture

We revisit the number-theory dark matter scenario where one of the light chiral fermions required by the anomaly cancellation conditions of U(1)B-L explains dark matter. Focusing on some of the integer B-L charge assignments, we explore a new region of the parameter space where there appear two light fermions and the heavier one becomes a dark matter of mass ≲O(10)keV or O(10)MeV. The dark matter radiatively decays into neutrino and photon, which can explain the tantalizing hint of the 3.55keV X-ray line excess. Interestingly, the other light fermion can erase the AdS vacuum around the neutrino mass scale in a compactification of the standard model to 3D. This will make the standard model consistent with the AdS-WGC statement that stable non-supersymmetric AdS vacua should be absent.

Electrides with Dinitrogen Ligands.

Electrides are a class of materials which contain excess electrons occupying the cavities in the crystal and playing the role of anions. To achieve electron-rich conditions, it usually requires a positive total formal charge in electride materials. However, the assignment of charges relies on a detailed analysis on chemical bonding. Herein, we present a survey on potential electrides which may be overlooked if no bonding analysis is performed. By applying various structure sampling techniques in conjunction with first-principles calculation, we predicted two compounds Ba2N2:e- and Li2Ca3N6:2e-, both of which are featured by the presence of dinitrogen ligands [N2], to be potential electrides. While Li2Ca3N6:2e- with [N2]2- ions has been synthesized in the past, its electride nature was discovered for the first time based on our high-throughput screening. On the other hand, Ba2N2:e- with [N2]3- ions is a new compound entirely from first-principles structure prediction. The different valence states of dinitrogen ligands identified in these two compounds suggest a novel route to tune the concentration and anisotropic properties of anionic interstitial electrons. Our discovery does not only establish a new class of inorganic electrides but also demonstrates the predictive power of modern crystal structure sampling techniques toward rational material design.

Improved general-purpose five-point model for water: TIP5P/2018.

A new five point potential for liquid water, TIP5P/2018, is presented along with the techniques used to derive its charges from ab initio per-molecule electrostatic potentials in the liquid phase using the split charge equilibration of Nistor et al. [J. Chem. Phys. 125, 094108 (2006)]. By taking the density and diffusion dependence on temperature as target properties, significant improvements to the behavior of isothermal compressibility were achieved along with improvements to other thermodynamic and rotational properties. While exhibiting a dipole moment close to ab initio values, TIP5P/2018 suffers from a too small quadrupole moment due to the charge assignment procedure and results in an overestimation of the dielectric constant.

SO(3) family symmetry and axions

Motivated by the idea of comprehensive unification, we study a gauged SO(3) flavor extension of the extended Standard Model, including right-handed neutrinos and a Peccei-Quinn symmetry with simple charge assignments. The model accommodates the observed fermion masses and mixings and yields a characteristic, successful relation among them. The Peccei-Quinn symmetry is an essential ingredient.

Depletable channels: dynamics, behaviour, and efficiency in network design

We present a simple model, called depleatable channels, of multi-hop communication in ad hoc networks. We introduce a model for channel energy consumption, and we propose a notion of channel equivalence based on the communication service they provide, regardless of specific routing protocols. In particular, we consider equivalent two channels with identical maximum and minimum inhibiting flow, and prove that this notion of equivalence, and variants of it, coincide with standard equivalences borrowed from the theory of concurrency. Unfortunately, while the maximum flow can be computed in polynomial time, calculating the value of a minimum inhibiting flow is NP-hard. Thus, we propose a characterization of those graphs, called weak, which admit charge assignments for which the minimum inhibiting flow is strictly less than the maximum flow and show that weakness can be checked efficiently by providing an algorithm that does so in polynomial time.

Standard model extension with flipped generations

An extension of the Standard Model is presented that leads to the possible existence of new gauge bosons with masses in the range of a few TeV. Due to the fact that their couplings to Standard Model fermions are strongly suppressed, it is possible for them to be hidden from current searches. The model contains additional generations of fermions with quantum numbers resembling those of the Standard Model fermion generations but with a twist: their charge assignments are such that their electric charges and chiralities are flipped with respect to those of their corresponding Standard Model counterparts. This feature provides a way to obtain potential dark matter candidates and the interesting possibility for a Lepton number conserving dimension-five operator for Dirac neutrino masses. The model implications associated to electroweak precision parameters, flavor changing neutral currents, and diphoton rate contributions are briefly discussed. The general assumptions of this set up are also used to sketch a couple of variants of the model with peculiar features that could motivate further study.

Approximating Isotope Distributions of Biomolecule Fragments.

In mass spectrometry (MS)-based proteomics, protein and peptide sequences are determined by the isolation and subsequent fragmentation of precursor ions. When an isolation window captures only part of a precursor’s isotopic distribution, the isotope distributions of the fragments depend on the subset of isolated precursor isotopes. Approximation of the expected isotope distributions of these fragments prior to sequence determination enables MS2 deisotoping, monoisotopic mass calculation, charge assignment of fragment peaks, and deconvolution of chimeric spectra. However, currently such methods do not exist, and precursor isotope distributions are often used as a proxy. Here, we present methods that approximate the isotope distribution of a biomolecule’s fragment given its monoisotopic mass, the monoisotopic mass of its precursor, the set of isolated precursor isotopes, and optionally sulfur atom content. Our methods use either the Averagine model or splines, the latter of which have similar accuracy to the Averagine approach, but are 20 times faster to compute. Theoretical and approximated isotope distributions are consistent for fragments of in silico digested peptides. Furthermore, mass spectrometry experiments with the angiotensin I peptide and HeLa cell lysate demonstrate that the fragment methods match isotope peaks in MS2 spectra more accurately than the precursor Averagine approach. The algorithms for the approximation of fragment isotope distributions have been added to the OpenMS software library. By providing the means for analyzing fragment isotopic distributions, these methods will improve MS2 spectra interpretation.

Heavy Majorana neutrino pair productions at the LHC in minimal U(1) extended Standard Model

In our recent paper (Das et al. in Phys Rev D 97:115023, 2018) we explored a prospect of discovering the heavy Majorana right-handed neutrinos (RHNs) at the future LHC in the context of the minimal non-exotic U(1) extended Standard Model (SM), where a pair of RHNs are created via decay of resonantly produced massive U(1) gauge boson (Z^{prime }). We have pointed out that this model can yield a significant enhancement of the branching ratio of the Z^prime boson to a pair of RHNs, which is crucial for discovering the RHNs under the very severe LHC Run-2 constraint from the search for the Z^prime boson with dilepton final states. In this paper, we perform a general parameter scan to evaluate the maximum production rate of the same-sign dilepton final states (smoking gun signature of Majorana RHNs production) at the LHC, while reproducing the neutrino oscillation data. We also consider the minimal non-exotic U(1) model with an alternative charge assignment. In this case, we find a further enhancement of the branching ratio of the Z^prime boson to a pair of RHNs compared to the conventional case, which opens up a possibility of discovering the RHNs even before the Z^prime boson at the future LHC experiment.