Partial Equalization Of Orbital Electronegativity Research Articles

Interpretable AI and Machine Learning Classification for Identifying High-Efficiency Donor-Acceptor Pairs in Organic Solar Cells.

To enhance the efficiency of organic solar cells, accurately predicting the efficiency of new pairs of donor and acceptor materials is crucial. Presently, most machine learning studies rely on regression models, which often struggle to establish clear rules for distinguishing between high- and low-performing donor-acceptor pairs. This study proposes a novel approach by integrating interpretable AI, specifically using Shapely values, with four supervised machine learning classification models, namely, support vector machines, decision trees, random forest, and gradient boosting. These models aim to identify high-efficiency donor-acceptor pairs based solely on chemical structures and to extract important features that establish general design principles for distinguishing between high- and low-efficiency pairs. For validation purposes, an unsupervised machine learning algorithm utilizing loading vectors obtained from the principal component analysis is employed to identify crucial features associated with high-efficiency donor-acceptor pairs. Interestingly, the features identified by the supervised machine learning approach were found to be a subset of those identified by the unsupervised method. Noteworthy features include the van der Waals surface area, partial equalization of orbital electronegativity, Moreau-Broto autocorrelation, and molecular substructures. Leveraging these features, a backward-working model can be developed, facilitating exploration across a wide array of materials used in organic solar cells. This innovative approach will help navigate the vast chemical compound space of donor and acceptor materials essential in creating high-efficiency organic solar cells.

QSAR of Chalcones Utilizing Theoretical Molecular Descriptors.

The paper is an attempt for QSAR modeling based on topological, electrostatic, quantum chemical, constitutional, geometrical and physicochemical indices computed from the structures of 59 set of synthesized chalcone derivatives tested for the cell cycle inhibition of mitotic G2/M phase using multiple linear regression method. Impact of such computed structural descriptors towards antimitotic and antiproliferative activities was analysed by ridge regression (RR) studies. The RR model explained that the topological indices alone can produce significant influence upon the pharmacological responses while combination of topological, electrostatic and quantum chemical descriptors can enhance the degree of impact towards antimitotic and antiproliferative activities of these compounds. Furthermore, QSAR models were formulated utilizing only topological and the combination of topological, electrostatic and quantum chemical descriptors respectively by multiple linear regression method and the validation of the model was performed by searching the predictability of the QSAR models. Satisfactory results were obtained in terms of model quality expressed as R(2) = 0.826, QLoo(2) = 0.710, Rpred(2) = 0.771 respectively for the topological indices. Combination of topological, electrostatic and quantum chemical descriptors resulted in an increase of R(2) = 0.965, QLoo 2 = 0.891, Rpred(2) = 0.849. The generated model predicted that BCUT descriptors (Charge) using modified partial equalization of orbital electronegativity (MPEOE), autocorrelation descriptors, information content descriptor and HOMO descriptor are very much crucial for modeling highly active chalcone compounds. Quantitative structure-activity relationships modeling of 59 set of synthesized chalcone derivatives were tested for the inhibition of mitotic G2/M phase using ridge regression and multiple linear regression methodologies. The generated model predicted that BCUT descriptors (Charge) using modified partial equalization of orbital electronegativity (MPEOE), autocorrelation descriptors, information content descriptor and HOMO descriptor are very much crucial for producing mitotic spindle inhibition of chalcone compounds.

Development of ecotoxicity QSAR models based on partial charge descriptors for acrylate and related compounds

Using Gasteiger's partial equalization of orbital electronegativity (PEOE) method, we constructed ecotoxicity prediction equations based on two-dimensional descriptors for α,β-unsaturated carbonyl compounds. After examining electrostatic effects on the calculated ecotoxicities of 10 α,β-unsaturated ketones and aldehydes (A-group compounds) by using the Mulliken atomic charges on the carbonyl oxygen atoms, we investigated the efficacy of the PEOE descriptors for the same 10 compounds and the correlation between the PEOE descriptors and the Mulliken charge. We then constructed QSAR models for acute fish and Daphnia toxicities by using the PEOE descriptors for acrylic acids and compounds with acrylate-like substructures (CH-group compounds). In the constructed models, the adjusted squared correlation coefficients between measured and calculated toxicities with the lowest Akaike information criterion were 0.77 and 0.79, respectively. The applicability of the constructed models was then evaluated for various methacrylates and similar compounds (CH3-group compounds). Both the fish and the Daphnia toxicities of some of the CH3-group compounds were underestimated by these models. Nevertheless, we concluded that the QSAR models based on the PEOE descriptors were practical for predicting acute toxicity, especially for α,β-unsaturated carbonyl compounds with an α-hydrogen. Combining hydrophobicity and PEOE descriptors led to accurate predictions for fish toxicity.

Development predictive QSAR models for artemisinin analogues by various feature selection methods: A comparative study

Quantitative structure–activity relationship (QSAR) models were derived for 179 analogues of artemisinin, a potent antimalarial agent. The activities of these compounds were investigated by means of multiple linear regression (MLR). To select relevant descriptors, several methods including stepwise selection, successive projection algorithm and an ant colony optimization algorithm (called memorized_ACS) were employed. A wide variety of molecular descriptors belonging to various structural properties were calculated for each molecule. Two matrixes (D1 and D2) of molecular properties were built. The D1 matrix included the calculated descriptors and the D2 matrix contained the first to third orders of the calculated descriptors and the logarithm of absolute values of the calculated descriptors. For both data matrixes, significant QSAR models were obtained by the memorized_ACS algorithm. The reactive and PEOE (partial equalization of orbital electronegativity) descriptors represented the highest impact on the antimalarial activity. The PEOE descriptors belong to partial charge descriptors and the reactive descriptor is an indicator of the presence of the reactive groups in the molecule. The best MLR model has a training error of 0.71 log RA units (r 2 = 0.81) and a prediction error of 0.48 log RA units (r 2 = 0.88).

Fast access to total energies

A new computational method for the fast calculation of total energies is presented. Using classical Huckel molecular orbital (HMO [1]) theory and the partial equalization of orbital electronegativity (PEOE [2]) methodology it could be shown that heats of formation of large molecules might become accessible through quite simple means. The new approach uses classical HMO calculation for the determination of bond orders, partial charges and bond energies in π-conjugated components. Furthermore, 2-dimensional Huckel problems are formulated and solved for isolated σ- and π-bonds. Assuming no charge interaction between σ- and π-orbitals, all non-conjugated parts of the considered molecule are iteratively allowed for charge transfer according to PEOE, which leads to the following scheme (Figure ​(Figure11): Figure 1 Correlating results from this procedure for a set of 201 organic molecules with total energies calculated by PM3 [3] lead to a very good agreement and a stability index of R2=0.991. An incorporation into force fields for the inclusion of steric terms such as electrostatic interactions and van-der-Waals forces is planned.

Molecular Simulation to Aid in the Understanding of the Aβ(1–42) Peptide of Alzheimer's Disease

The Aβ(1–42) peptide of Alzheimer's disease was studied by molecular modeling. The coordinates of the peptide were experimentally generated from solution-NMR spectroscopy, and the conformations were energy minimized using a combination of connectivity-based iterative partial equalization of orbital electronegativity with the MM + force field. There is a central folded domain in the Aβ peptide. This part is an apolar α-helix. The remaining residues form β-sheets. Aggregation requires that β-sheets interact by noncovalent bonding forces. The unsoluble, aggregated complexes are energetically stable and have ordered structures. A perspective in drug research is to design compounds that inhibit the hydrophobic cores of the individual Aβ peptides, blocking so the associations between the β-strains.

A Fast Method for Calculating Geometry-Dependent Net Atomic Charges for Polypeptides

A new method for calculating geometry-dependent atomic charges (GDACs) for polypeptides is presented. It overcomes the limitations of the partial equalization of orbital electronegativity (PEOE) and modified PEOE (MPEOE) methods, which depend only on connectivity, not geometry. Introduction of distance-dependent damping factors helps to include the effect of environment in determining the variation of bond distance (without explicit contribution of the correlated variation of bond angles), and thereby to reduce the number of parameters required to represent different atomic species. Since the correlation between the geometry and the dipole moments of molecules is crucial for this method, ab initio molecular orbital calculations were carried out to obtain the geometries and dipole moments with the 6-31G** basis set at the level of B3LYP theory. When bond distances are fixed prior to a charge calculation, the methodology outlined here leads to a direct calculation of the permanent molecular charge distribut...

Influence of γ-hydrogens (hydrogens three bonds away) in calculating13C chemical shifts of acyclic alkanes and alcohols

The 13C NMR chemical shifts of acyclic alkanes and alcohols are reproduced by an equation having two parameters, the charge on the carbon atom as calculated by iterative partial equalization of orbital electronegativity and the effective number of hydrogen atoms three bonds away from the carbon atom under consideration. The data sets consist of 183 carbons of all alkane isomers up to C8 and 184 carbons of aliphatic alcohol isomers up to C8 . The alkane carbons are correlated with a correlation coefficient of 0.994 and a standard deviation of 1.06 ppm and the alcohol carbons with a correlation coefficient of 0.997 and a standard deviation of 1.37 ppm. The influence of effective number of hydrogen atoms three bonds away is discussed in terms of 1,4 steric interactions in the molecules. Copyright © 1999 John Wiley & Sons, Ltd.

Determination of Potential Parameters for Amino Acid Zwitterions

An empirical potential energy function for description of the interactions between amino acid zwitterions has been developed. Potential energy surfaces of molecular ion pairs, methylammonium ion−acetate ion, glycine zwitterion−methyl ammonium ion, and glycine zwitterion−acetate ion, were obtained with 6-31G** ab initio molecular orbital calculations. The point charges of the ions were obtained with the modified partial equalization of orbital electronegativity (M-PEOE) method, the coefficients of the attractive part of the nonbonded potential were calculated from charge-dependent effective atomic polarizabilities, and the coefficients of the repulsive part of the nonbonded potential were obtained from the equilibrium conditions of molecules in molecular crystals and by reproducing the lattice energies of amino acid molecular crystals. The hydrogen-bond model proposed by No et al. was introduced, and the potential parameters of the model were determined in order that the potential energy function could reproduce both the ab initio potential energy surfaces and the experimental structures of some amino acid molecular crystals. The minimum-energy crystal structures obtained through crystal packing computations with the empirical potential energy function agreed well with X-ray crystal structures.

Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. IV. Application to hypervalent sulfur‐ and phosphorus‐containing molecules

AbstractThe parameters for an empirical point charge calculation method, Mulliken Population Constrained Potential Derived–Modified Partial Equalization of Orbital Electronegativity (MPCPD–MPEOE) method, for hypervalent sulfur, phosphorus, and the atoms bonded to these atoms, were determined. A new empirical method, MPCPD, which has inherent advantages over both the Mulliken population and potential derived methods, is proposed here. The MPCPD net atomic charges are transferable and reproduce the electrostatic potential. The electrical properties were calculated with the MPCPD and MPCPD–MPEOE charges. These properties agreed well with experimental results and with 6‐31G** ab initio results. The MPEOE parameters for the sulfur atom in aromatic molecules and trivalent phosphorus in phosphite molecules were also determined. The dipole moments calculated with the MPCPD–MPEOE point charges agreed well with experimental results. All the parameters obtained in this work are consistent with those obtained in our previous work. © 1995 by John Wiley & Sons, Inc.

Molecular modelling of photoactive pigments in the solid state: Investigations of polymorphism

The application of molecular mechanics calculations to the study of solid state organic photoconductors has been investigated. Using X-ray crystallographic information for a series of four N.N′-dialkylperylene pigments, 1–4, lattices of these molecules were modelled using the Dreiding force field. Comparison of the resulting lattices with the experimental data demonstrated that both molecular and physical features of the perylenes could be accurately reproduced in these calculations. When systematic deviations in molecular geometry occurred, these errors could be attributed to the generic nature of the force field. We have extended the computational studies to the problem of polymorphism since this is known to have a profound effect on photoconduction. To model enthalpic polymorphs of N,N′-dimethylperylene, 1, the symmetry relationships and atomic coordinates from the crystal structure of N,N′-di-n-pentylperylene, 4, were utilized. By truncating the pentyl substituents to methyl groups and applying external stresses to the resulting lattice during minimization it was possible to identify two likely polymorphs of 1. The inclusion of Gasteiger's partial equalization of orbital electronegativity (PEOE) charges on the perylenes was not found to be beneficial in locating suitable polymorphs. These computational methods have been successful in modelling perylene pigments in the solid state and have been shown to be useful in investigating polymorphism.

An empirical method to calculate average molecular polarizabilities from the dependence of effective atomic polarizabilities on net atomic charge

An empirical method for the calculation of average molecular polarizability is introduced. In this method, the effective atomic polarizabilities are described as a function of net atomic charges which are obtained with the modified partial equalization of orbital electronegativity (M-PEOE) method. The effective atomic polarizability is derived with the aid of the Thomas-Fermi model of multiply-charged spherical ions. The calculated polarizabilities agree well with experimental data. Nonbonded potential parameters are also calculated as a function of net atomic charges from the effective atomic polarizabilities

Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes

AbstractThe PEOE (partial equalization of orbital electronegativity) procedure has been modified slightly and reparametrized for haloalkanes to calculate partial atomic charges suitable for evaluation of dipole moments and electrostatic energies in conjunction with molecular mechanics (MM2) calculations. Dipole moments of 66 haloalkanes are calculated with an average absolute deviation of 0.14 D from experimental values. The conformational energies of 40 compounds have been calculated and the agreement with experimental data is generally good and compares well with calculations by the IDME (induced dipole moment and energy) method. In addition, carbon and proton charges correlate well with C‐1s core binding energies and 1H‐NMR (nuclear magnetic resonance) shifts for halomethanes. The most striking benefit of treating electrostatics through a set of partial charges compared to the standard MM2 bond dipole approach is demonstrated by calculations on 1,4‐disubstituted cyclohexanes, for which standard MM2 fails to predict the most stable conformation.

A quantitative empirical treatment of 13C NMR chemical shift variations on successive substitution of methane by halogen atoms

AbstractThe 13C NMR chemical shifts of halogen‐substituted methanes are reproduced by a linear two‐parameter equation. The parameters consist of the charge on the carbon atom, as calculated by iterative partial equalization of orbital electronegativity, and the square of the mean molecular polarizability.

Extension of the method of iterative partial equalization of orbital electronegativity to small ring systems

By using a limited set of hybridization states the method of iterative partial equalization of orbital electronegativity has been extended to molecules containing three- and four-membered rings. The values of charges thus calculated have been successfully correlated with 13C- 1H coupling constants, as well as with acidity constants, and can be used for the calculation of dipole moments.

Prediction of proton magnetic resonance shifts: The dependence on hydrogen charges obtained by iterative partial equalization of orbital electronegativity

AbstractProton chemical shifts correlate linearly with charges on hydrogen obtained by a method for iterative partial equalization of orbital electronegativity. The compounds studied comprise a wide variety of classes of molecules; all points fall on a single correlation line, showing the general importance of electronic effects in proton chemical shifts and the physical significance of the atomic charges. On the other hand, as there is no general correlation between charges on carbon and on hydrogen atoms, proton chemical shifts cannot be used as probes for charge densities on carbon atoms. Deviations from the correlation line can be attributed to anisotropy effects and provide an estimate for their magnitude.

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

A method is presented for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems. Atoms are characterized by their orbital electronegativities. In the calculation only the connectivities of the atoms are considered. Thus only the topology of a molecule is of importance. Through an iterative procedure partial equalization of orbital electronegativity is obtained. Excellent correlations of the atomic charges with core electron binding energies and with acidity constants are observed. This establishes their value in predicting experimental data.