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1. Direct and Simple Experimental Crystallographic Method to Calculate Partial Charges with Atomistic Correspondence to ab-initio Methods

   Prakash, P.; Byrne, A. N.; Keller, T. M.; Zdilla, M. J. (August 2020, American Crystallographic Association National Meeting 2020)

   Derivation of partial charges in small and large scale molecular systems is important for modeling of various experimental and theoretical properties like dipole moments, auto-correlation functions, charge disparity, understanding of dispersion, benchmark of classical MD simulations and electrostatic potential energy surface mapping. A correspondence between theoretical calculations (based on single/small number of molecules) is usually established with macroscopic IR/Raman spectra or dipole moment measurements. Such comparisons are indirect and lack a fine mapping of electrostatic potential from theory to experiment. In a new approach developed as the experimental part of this work, partial charges are calculated from crystallographic model refinement. The experimental method exhibits a satisfactory correspondence with partial charges obtained using quantum chemistry calculations. Particularly, gas phase partial charges from CHELPG method and condensed phase Lowdin charges correlate well and validate this experimental method. 

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2. Predicting mixing free energy using mutual ghosting

   https://doi.org/10.1039/D2ME00109H  

   Shetty, Shreya; Agarwala, Puja; Gomez, Enrique D.; Milner, Scott T. (October 2022, Molecular Systems Design & Engineering)

   The excess free energy of mixing Δ G ex governs the phase behavior of mixtures and controls material properties. It is challenging, however, to measure Δ G ex in simulations. Previously, we developed a method that combines molecular dynamics (MD) simulations with thermodynamic integration along the path of transformation of chains to predict the Flory Huggins interaction parameter χ for polymer mixtures and block copolymers. However, this method is best applied when the constituent molecules of the blends are structurally related. To overcome this limitation, we have developed a new method to predict Δ G ex for mixtures. We perform simulations to induce phase separation within a mixture by gradually weakening the interaction between different species. To compute Δ G ex we measure the thermodynamic work required to modify the interactions and the interfacial energy between the separated phases. We validate our method by applying it first to equimolar mixtures of labeled and unlabeled Lennard-Jones (LJ) beads, and labeled and unlabeled benzene, which results in good agreement with ideal solution theory. Then we compute the excess free energy of mixing for equimolar mixtures of benzene and pyridine, using both united-atom (UA) and all-atom (AA) potentials. Our results using UA potentials predict a value for Δ G ex about four times the experimental value, whereas using AA potentials gives results consistent with experiment, highlighting the need for good potentials to faithfully represent mixture behavior. 

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3. Measurement of partial atomic charges by least-squares refinement of variable electron density crystallographic models.

   Michael J. Zdilla, Taylor M. (August 2020, American Crystallographic Association Annual Meeting 2020)

   Of interest in understanding electronic structure, bulk physical properties, enthalpies of phase changes, dipole moments, and numerous other properties of molecules, is the determination of realistic partial atomic charges on atoms. Atoms may take on partial positive or negative charges due to polar covalent bonds, coordinate covalent bonds, or due to formal charges imposed by Lewis structure constraints. Traditional crystallographic refinement treats each atom as a neutral, spherical atom however. We present a ongoing developments of a mode of crystallographic model refinement that permits refinement of electron density at individual atoms in order to arrive at partial atomic charges of atoms in a crystallographic model. Comparison to calculated partial charges (CHELPG, NBO, Mulliken) from quantum calculations (DFT, MP2) in both the gas phase and crystalline state will be presented. 

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4. NETWORK THEORETIC APPROACH TO ATOMISTIC MATERIAL MODELING USING SPECTRAL SPARSIFICATION

   Woerner, Peter; Nair, Aditya; Taira, Kunihiko; Oates, William (October 2017, Proceedings of the ASME 2017 Conference on Smart Materials, Adaptive Structures and Intelligent Systems)

   Network theory is used to formulate an atomistic material network. Spectral sparsification is applied to the network as a method for approximating the interatomic forces. Local molecu- lar forces and the total force balance is quantified when the inter- nal forces are approximated. In particular, we compare spectral sparsification to conventional thresholding (radial cut-off dis- tance) of molecular forces for a Lennard–Jones potential and a Coulomb potential. The spectral sparsification for the Lennard– Jones potential yields comparable results while spectral sparsi- fication of the Coulomb potential outperforms the thresholding approach. The results show promising opportunities which may accelerate molecular simulations containing long-range electri- cal interactions which are relevant to many multifunctional ma- terials. 

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5. Seven confluence principles: a case study of standardized statistical analysis for 26 methods that assign net atomic charges in molecules

   https://doi.org/10.1039/d0ra06392d  

   Manz, Thomas A. (December 2020, RSC Advances)

   null (Ed.)

   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 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. 

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