skip to main content

Title: Seven confluence principles: a case study of standardized statistical analysis for 26 methods that assign net atomic charges in molecules
This article studies two kinds of information extracted from statistical correlations between methods for assigning net atomic charges (NACs) in molecules. First, relative charge transfer magnitudes are quantified by performing instant least squares fitting (ILSF) on the NACs reported by Cho et al. ( ChemPhysChem , 2020, 21 , 688–696) across 26 methods applied to ∼2000 molecules. The Hirshfeld and Voronoi deformation density (VDD) methods had the smallest charge transfer magnitudes, while the quantum theory of atoms in molecules (QTAIM) method had the largest charge transfer magnitude. Methods optimized to reproduce the molecular dipole moment ( e.g. , ACP, ADCH, CM5) have smaller charge transfer magnitudes than methods optimized to reproduce the molecular electrostatic potential ( e.g. , CHELPG, HLY, MK, RESP). Several methods had charge transfer magnitudes even larger than the electrostatic potential fitting group. Second, confluence between different charge assignment methods is quantified to identify which charge assignment method produces the best NAC values for predicting via linear correlations the results of 20 charge assignment methods having a complete basis set limit across the dataset of ∼2000 molecules. The DDEC6 NACs were the best such predictor of the entire dataset. Seven confluence principles are introduced explaining why confluent more » quantitative descriptors offer predictive advantages for modeling a broad range of physical properties and target applications. These confluence principles can be applied in various fields of scientific inquiry. A theory is derived showing confluence is better revealed by standardized statistical analysis ( e.g. , principal components analysis of the correlation matrix and standardized reversible linear regression) than by unstandardized statistical analysis. These confluence principles were used together with other key principles and the scientific method to make assigning atom-in-material properties non-arbitrary. The N@C 60 system provides an unambiguous and non-arbitrary falsifiable test of atomic population analysis methods. The HLY, ISA, MK, and RESP methods failed for this material. « less
Award ID(s):
Publication Date:
Journal Name:
RSC Advances
Page Range or eLocation-ID:
44121 to 44148
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract The restrained electrostatic potential (RESP) approach is a highly regarded and widely used method of assigning partial charges to molecules for simulations. RESP uses a quantum-mechanical method that yields fortuitous overpolarization and thereby accounts only approximately for self-polarization of molecules in the condensed phase. Here we present RESP2, a next generation of this approach, where the polarity of the charges is tuned by a parameter, δ, which scales the contributions from gas- and aqueous-phase calculations. When the complete non-bonded force field model, including Lennard-Jones parameters, is optimized to liquid properties, improved accuracy is achieved, even with this reduced setmore »of five Lennard-Jones types. We argue that RESP2 with δ  ≈ 0.6 (60% aqueous, 40% gas-phase charges) is an accurate and robust method of generating partial charges, and that a small set of Lennard-Jones types is a good starting point for a systematic re-optimization of this important non-bonded term.« less
  2. Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical modelsmore »of deoxynucleosides, even at a high level of theory, are not optimal structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.« less
  3. A classical interatomic potential for iron/iron-fluoride systems is developed in the framework of the charge optimized many-body (COMB) potential. This interatomic potential takes into consideration the effects of charge transfer and many-body interactions depending on the chemical environment. The potential is fitted to a training set composed of both experimental and ab initio results of the cohesive energies of several Fe and FeF 2 crystal phases, the two fluorine molecules F 2 and the F 2 −1 dissociation energy curve, the Fe and FeF 2 lattice parameters of the ground state crystalline phase, and the elastic constants of the bodymore »centered cubic Fe structure. The potential is tested in an NVT ensemble for different initial structural configurations as the crystal ground state phases, F 2 molecules, iron clusters, and iron nanospheres. In particular, we model the FeF 2 /Fe bilayer and multilayer interfaces, as well as a system of square FeF 2 nanowires immersed in an iron solid. It has been shown that there exists a reordering of the atomic positions for F and Fe atoms at the interface zone; this rearrangement leads to an increase in the charge transfer among the atoms that make the interface and put forward a possible mechanism of the exchange bias origin based on asymmetric electric charge transfer in the different spin channels.« less
  4. The accurate and fast measurement of nitrate in seawater is important for monitoring and controlling water quality to prevent ecologic and economic disasters. In this work we show that the in situ detection of nitrate in aqueous solution is feasible at nanomolar concentrations through surface enhanced Raman spectroscopy (SERS) using native nanostructured gold substrates without surface functionalization. Spectra were analyzed as collected or after standard normal variate (SNV) normalization, which was shown through Principal Component Analysis (PCA) to reduce spectral variations between sample sets and improve Langmuir adsorption model fits. An additional normalization approach based on the substrate silicon templatemore »showed that silicon provided an internal standard that accounted for the spectral variance without the need for SNV normalization. Nitrate adsorption was well-described by the Langmuir adsorption model, consistent with an adsorbed monolayer, and a limit of detection of 64 nM nitrate was obtained in ultrapure water, representing environmentally relevant concentrations. Free energy calculations based on the Langmuir adsorption constants, approximating equilibrium adsorption constants, and calculated self-energy arising from image charge, accounting for electrostatic interactions with a polarizable nanostructured substrate, suggest that nitrate adsorption was partially driven by an entropy gain presumably due to dehydration of the gold substrate and/or nitrate ion. This work is being extended to determine if similar statistical and normalization methods can be applied to nitrate detection in complex natural waters where non-target ions and molecules are expected to interfere.« less
  5. Metal-molecule-metal junctions based on alkane thiol (C n T) and oligophenylene thiol (OPT n ) self-assembled monolayers (SAMs) and Au electrodes are expected to exhibit similar electrical asymmetry, as both junctions have one chemisorbed Au–S contact and one physisorbed, van der Waals contact. Asymmetry is quantified by the current rectification ratio RR apparent in the current–voltage ( I – V ) characteristics. Here we show that RR < 1 for C n T and RR > 1 for OPT n junctions, in contrast to expectation, and further, that RR behaves very differently for C n T and OPT n junctionsmore »under mechanical extension using the conducting probe atomic force microscopy (CP-AFM) testbed. The analysis presented in this paper, which leverages results from the previously validated single level model and ab initio quantum chemical calculations, allows us to explain the puzzling experimental findings for C n T and OPT n in terms of different current rectification mechanisms. Specifically, in C n T-based junctions the Stark effect creates the HOMO level shifting necessary for rectification, while for OPT n junctions the level shift arises from position-dependent coupling of the HOMO wavefunction with the junction electrostatic potential profile. On the basis of these mechanisms, our quantum chemical calculations allow quantitative description of the impact of mechanical deformation on the measured current rectification. Additionally, our analysis, matched to experiment, facilitates direct estimation of the impact of intramolecular electrostatic screening on the junction potential profile. Overall, our examination of current rectification in benchmark molecular tunnel junctions illuminates key physical mechanisms at play in single step tunneling through molecules, and demonstrates the quantitative agreement that can be obtained between experiment and theory in these systems.« less