Molecular Electronegativity Research Articles

Recent progress in quantifying substituent effects

This paper summarizes significant progress in quantifying organic substituent effects in the last 20 years. The main content is as follows: (1) The principle of electronegativity equalization has gained wide acceptance, and has been used to calculate the intramolecular charge distribution and inductive effect of groups. A valence electrons equalization method was proposed to compute the molecular electronegativity on the basis of geometric mean method, harmonic mean method, and weighted mean method. This new calculation method further extended the application of the principle of electronegativity equalization. (2) A scale method was established for experimentally determining the electrophilic and nucleophilic ability of reagents, in which benzhydryliumions and quinone methides were taken as the reference compounds, and the research field was extended to the gas phase conditions, organometallic reaction and radicals system. Moreover, the nucleophilicity parameters N and electrophilicity parameters E for a series of reagents were obtained. The definition and quantitative expression of electrophilicity index ω and nucleophilicity index ω - were proposed theoretically, and the correlation between the parameters from experimental determination and the indexes from theoretical calculation was also investigated. (3) The polarizability effect parameter was initially calculated by empirical method and further developed by quantum chemistry method. Recently, the polarizability effect index of alkyl (PEI) and groups (PEIX) were proposed by statistical method, and got wide applications in explaining and estimating gas-phase acidity and basicity, ionization energy, enthalpy of formation, bond energy, reaction rate, water solubility and chromatographic retention for organic compounds. (4) The excited-state substituent constant σccex obtained directly from the UV absorption energy data of substituted benzenes, is different from the polar constants in molecular ground state and the radical spin-delocalization effects constants in molecular radical state. The proposed constant σccex correlated well with the UV absorption energy of many kinds of organic compounds, such as 1,4-disubstituted benzenes, substituted stilbenes, and disubstituted N -benzylidenebenzenamine. (5) The establishment of the steric shielding effect distinguished the three traditional steric effects. The stereoselectivity index Ci was proposed to quantify the stereoselectivity of the addition reaction of carbonyl with nucleophilic reagent. The shielding parameter was defined to quantitatively express the specific surface of the reaction center screened by a group. Further, the Topological Steric Effect Index (TSEI) of a group was proposed on the basis of the relative specific volume of reaction center screened by the atoms of substituents. These parameters can be applied in estimating the intramolecular dihedral angles, stereoselectivity of reaction, enthalpies of formation of alkenes and alkylbenzene, acidity of substitutedimidazolium ionic liquid, and the reaction rate of alkane and hydroxyl radical. In addition, some suggestions and prospects for further studies on quantifying the organic substituent effects were presented in this paper.

Density functional investigation of the molecular structures, vibrational spectra and molecular properties of sulfonated pyridyl imine ligands and their palladium complexes

The equilibrium geometries and harmonic vibrational frequencies of thesulfonated pyridyl-imine ligands (L1–L6) and their palladium (II) complexes (C1–C6) were calculated using density functional theory at the B3LYP level. The complete vibrational assignments of ligand L1, and its palladium (II) complex C1, were performed based on the total energy distribution (TED) of the vibrational modes and the calculated isotopic frequency shifts.In order to investigate the electronic properties of ligands and complexes, quantum chemical parameters, such as the highest occupied molecular orbital energy (εHOMO), the lowest unoccupied molecular orbital energy (εLUMO), energy gap (Δε), dipole moment (μ), electronegativity (χ) and hardness (η) were calculated. Chemical hardness was used to predict their relative stability and reactivity.

Ab Initio Density Functional Theory Investigation of the Interaction between Carbon Nanotubes and Water Molecules during Water Desalination Process

Density functional theory calculations using B3LYP/3‐21G level of theory have been implemented on 6 carbon nanotubes (CNTs) structures (3 zigzag and 3 armchair CNTs) to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2‐3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.

On the performance of local density approximation in describing the adsorption of electron donating/accepting molecules on graphene

In order to asses performance of the LDA in describing physisorption on graphene, adsorptions of TCNE, TCNQ, TNF, TTF, and DMPD as well as four benzene derivatives on C54H18 and C110H30 were explored with a variety of DFTs such as MPWB1K, M06-2X, PBE-D and LSDA. Although it is well known that the LDA considerably overestimate non-covalent interaction, the LSDA predicted adsorption energies except for TCNE on C110H30 are systematically lower than those from the M06-2X by 0.4–3.2kcal/mol, and they are more significantly lower than those from the PBE-D for all the molecules by 3–6kcal/mol. However, the LSDA adsorption energy sequence is consistent with that from the PBE-D, TNF∼TCNQ>TCNE∼DMPD>TTF. Moreover, the domain interaction between the electron donor and acceptor molecules with graphene through cooperative π⋯π, C–H⋯π and N–H⋯π were visualized with sign(λ2)×ρ, and the relationships between the binding energy with London force, molecular electronegativity, and frontier orbital level were extensively discussed.

Computational Prediction of CNS Drug Exposure Based on a Novel In Vivo Dataset

To develop a computational model for predicting CNS drug exposure using a novel in vivo dataset. The brain-to-plasma (B:P) ratio of 43 diverse compounds was assessed following intravenous administration to Swiss Outbred mice. B:P ratios were subjected to PLS modeling using calculated molecular descriptors. The obtained results were transferred to a qualitative setting in which compounds predicted to have a B:P ratio > 0.3 were sorted as high CNS exposure compounds and those below this value were sorted as low CNS exposure compounds. The model was challenged with an external test set consisting of 251 compounds for which semi-quantitative values of CNS exposure were available in the literature. The dataset ranged more than 1700-fold in B:P ratio, with 16 and 27 compounds being sorted as low and high CNS exposure drugs, respectively. The model was a one principal component model based on five descriptors reflecting molecular shape, electronegativity, polarisability and charge transfer, and allowed 74% of the compounds in the training set and 76% of the test set to be predicted correctly. A qualitative computational model has been developed which accurately classifies compounds as being high or low CNS exposure drugs based on rapidly calculated molecular descriptors.

QSPR-based estimation of the half-lives for polychlorinated biphenyl congeners

In this study, the depuration half-lives of 62 polychlorinated biphenyl (PCB) congeners in juvenile rainbow trout (Oncorhynchus mykiss) were estimated from their structural features based on QSPR methodology. A genetic algorithm (GA) was applied as a variable subset selection strategy and QSPR models established upon multiple linear regression (MLR), multilayer perceptron neural network (MLP NN) and support vector regression (SVR) procedures. Robustness and predictive stability of the constructed models were evaluated through internal and external validation methods. The high numerical values of and , and low RMSE in the case of the MLP NN model, confirm the supremacy of this model as well as nonlinear dependency of molecular structural features to the PCB congeners half-lives. In the best developed QSPR model the following four descriptors are used; lopping centric index (Lop), mean topological charge index of order 1 (JGI1), Geary autocorrelation lag-8/weighted by atomic Sanderson electronegativities (GATS8e) and highest eigenvalue of Burden matrix/weighted by atomic masses (BEHm3). Analysis of the descriptors involved in these models revealed that 2D molecular structural features, compactness and electronegativities are the main factors contributing to the half-lives of PCBs. The structural information presented in this work can be used for further evaluation of half-lives of PCBs and other similar structural compounds in the environment.

DFT Study of Interaction of Azoles with Cu(111) and Al(111) Surfaces: Role of Azole Nitrogen Atoms and Dipole–Dipole Interactions

Azoles and their derivatives are among the often used organic corrosion inhibitors for copper. For this reason, the adsorption of four azole molecules—imidazole, 1,2,3-triazole, tetrazole, and pentazole—on Cu(111) and Al(111) surfaces has been studied and characterized using density functional theory (DFT) calculations. We find that the molecules weakly adsorb in an upright geometry onto the top site of Cu(111) via single nitrogen atom; except for triazole the bonding with two nitrogen atoms to a bridge site becomes slightly preferred at very low coverage. Molecular electronic structure is only weakly perturbed upon adsorption and the molecule–surface interaction involves the hybridization between molecular σ orbitals and metal states, yet the main contribution to bonding comes from the electrostatic dipole interactions due to a large dipole moment of azole molecules. Also, the lateral intermolecular repulsion can be significant and very long ranged. With increasing the number of nitrogen atoms in azole ring the molecular electronegativity and chemical hardness linearly increase. The harder the molecule the more difficult the hybridization with metal states, which can explain why with the increasing number of nitrogen atoms in azole ring the molecule–Cu(111) bond strength decreases linearly, being 0.69, 0.55, 0.43, and 0.22 eV for imidazole, 1,2,3–triazole, tetrazole, and pentazole, respectively. The same bonding trend with very similar adsorption energies is also found on Al(111).

Triazole, Benzotriazole, and Naphthotriazole as Copper Corrosion Inhibitors: I. Molecular Electronic and Adsorption Properties

The gas-phase adsorption of 1,2,3-triazole, benzotriazole, and naphthotriazole-considered as corrosion inhibitors-on copper surfaces was studied and characterized using density functional theory (DFT) calculations. We find that the molecule-surface bond strength increases with increasing molecular size, thus following the sequence: triazole<benzotriazole<naphthotriazole. This trend is explained in terms of molecular electronegativity and chemical hardness, which decrease monotonously as the molecular size increases. While the electronegativity of triazole is almost degenerate with the work function of Cu(111) surface, the electronegativity of larger acenotriazoles is smaller. The difference in electronegativity between the Cu(111) and the acenotriazoles thus increases with increasing the molecular size, which, together with decreasing the molecular hardness, results in larger molecule-to-metal electron charge transfer and stronger molecule-surface bonds.

Estimation of the ionization potential for polyhalogenated hydrocarbons by weakest bound potential method

The weakest bound potential method was proposed to estimate the ionization potential (IP) of polyhalogenated methanes, that is, the model IP = aχve + bPEIfi + c was developed, in which χve is molecular electronegativity calculated by valence electrons equilibration method, and polarizability effect index (PEI)fi is the influence of polarizability effect. The result indicates that the model is reasonable and effective to predict the IP for polyhalogenated methanes. Besides, the quantum chemistry method, the MOPAC AM1 method, and the density functional theory (B3LYP) method were employed to calculate the IP values of the same polyhalogenated methanes, and those results were less than that of the weakest bound potential method. Furthermore, the experimental values of 67 polyhalogenated hydrocarbons were correlated with the parameters χve and PEIfi. The regression results show a good correlation (R = 0.988), and the average absolute error between the experimental values and the calculated values is only 0.10 eV. Copyright © 2011 John Wiley &amp; Sons, Ltd.

Second and third-order nonlinear optical properties and molecular parameters of azo chromophores: Semiempirical analysis

The static and frequency dependent average polarizability (〈 α〉), first- and second-hyperpolarizabilities (〈 β〉 and 〈 γ〉) and highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energies of nonlinear optical chromophores with nitro acceptors 1– 5 have been investigated by using the Austin Model 1 (AM1), Modified Neglect of Diatomic Overlap (MNDO), MNDO with d orbitals (MNDO-d), Parameterization Method 3 (PM3), Recife Model 1 (RM1) and Parameterization Method 6 (PM6) methods within a time-dependent Hartree–Fock (TDHF) approaches. The electronic properties of chromophores 1– 5 have been reported by employing two-state model calculated at Zerner's spectroscopic version of the Intermediate Neglect of Differential Overlap singly excited configuration interaction (ZINDO/S-SCI) method. Also, the molecular hardness ( η) and electronegativity ( χ) parameters have been obtained by using molecular frontier orbital energies. The 〈 α〉, 〈 β〉, 〈 γ〉 HOMO, LUMO energies, η and χ parameters have been investigated with respect to the choice of different semiempirical methods.

Quantitative Structure–Retention Relationship Study on Nitrogen-Containing Polycyclic Aromatic Compounds by Using Molecular Electronegativity Interaction Vector

The molecular structures of 117 nitrogen-containing polycyclic aromatic compounds (N-PACs) were described by a method of molecular structural characterization (MSC) called molecular electronegativity interaction vector (MEIV). The samples were divided into a training set and a test set. For the training set, a quantitative structure–retention relationship (QSRR) model was built up by multiple linear regression (MLR) and the model was evaluated by performing the cross validation with the leave-one-out (LOO) procedure. The correlation coefficient (R) and the cross-verification correlation coefficient (RCV) of the model were 0.992 and 0.991, respectively. Moreover, the model was evaluated by the test set and satisfactory results with a correlation coefficient (Rtest) of 0.993 were obtained. The results suggested good stability and predictability of the model.

Reduction potentials of para‐substituted nitrobenzenes—an infrared, nuclear magnetic resonance, and density functional theory study

Formal reduction potentials, E°′, of a series of 12 para‐substituted nitrobenzenes (R―C6H4―NO2, where R═NH(CH3), NH2, OCH3, CH3, H, OCO(CH3), Cl, CF3, CO(CH3), CO(H), CN, and NO2) were measured and related to experimental parameters and the calculated descriptors: the lowest unoccupied molecular orbital (LUMO) energy (ELUMO), electron affinity (EA), electrophilicity index (ω), and relative group electronegativity (χR). Excellent correlation was obtained in the linear relationship between E°′ and both ELUMO (R2 &gt; 0.99) and ω, followed by EA, χR, experimental δ1H nuclear magnetic resonance (NMR), infrared asymmetric NO2 stretching frequency (νas), and lastly, δ13C NMR. Calculated ELUMO was found to provide the most convenient theoretical means for predicting experimental E°′ while, together with ω, also giving the highest degree of accuracy. Copyright © 2011 John Wiley &amp; Sons, Ltd.

The Nature of the Idealized Triple Bonds Between Principal Elements and the σ Origins of Trans-Bent Geometries-A Valence Bond Study.

We describe herein a valence bond (VB) study of 27 triply bonded molecules of the general type X≡Y, where X and Y are main element atoms/fragments from groups 13-15 in the periodic table. The following conclusions were derived from the computational data: (a) Single π-bond and double π-bond energies for the entire set correlate with the "molecular electronegativity", which is the sum of the X and Y electronegativites for X≡Y. The correlation with the molecular electronegativity establishes a simple rule of periodicity: π-bonding strength generally increases from left to right in a period and decreases down a column in the periodic table. (b) The σ frame invariably prefers trans bending, while π-bonding gets destabilized and opposes the trans distortion. In HC≡CH, the π-bonding destabilization overrides the propensity of the σ frame to distort, while in the higher row molecules, the σ frame wins out and establishes trans-bent molecules with 2(1)/2 bonds, in accord with recent experimental evidence based on solid state (29)Si NMR of the Sekiguchi compound. Thus, in the trans-bent molecules "less bonds pay more". (c) All of the π bonds show significant bonding contributions from the resonance energy due to covalent-ionic mixing. This quantity is shown to correlate linearly with the corresponding "molecular electronegativity" and to reflect the mechanism required to satisfy the equilibrium condition for the bond. The π bonds for molecules possessing high molecular electronegativity are charge-shift bonds, wherein bonding is dominated by the resonance energy of the covalent and ionic forms, rather than by either form by itself.

Equalized Electronegativity Based on the Valence Electrons and Its Application

We take the contribution of all valence electrons into consideration and propose a new valence electrons equilibration method to calculate the equalized electronegativity including molecular electronegativity, group electronegativity, and atomic charge. The ionization potential of alkanes and mono-substituted alkanes, the chemical shift of 1H NMR, and the gas phase proton affinity of aliphatic amines, alcohols, and ethers were estimated. All the expressions have good correlations. Moreover, the Sanderson method and Bratsch method were modified on the basis of the valence electrons equilibration theory. The modified Sanderson method and modified Bratsch method are more effective than their original methods to estimate these properties.

Effects of different basis sets and donor‐acceptor groups on linear and second‐order nonlinear optical properties and molecular frontier orbital energies

AbstractThe calculation of molecular hyperpolarizability, molecular frontier orbital energies of some donor‐acceptor oxadiazoles (5a–f, 8a–f, and 9a–f) have been investigated using ab initio methods and different basis sets. Ab initio optimizations were performed at the Hartree–Fock (HF) and density functional (Beckee‐3–Lee–Yang–Parr; B3LYP) levels of theory with 6‐31G basis set. The polarizability (&lt;α&gt;), anisotropy of polarizability (Δα), and ground‐state dipole moment (μ), first hyperpolarizability (β), and molecular frontier orbital (HOMO, highest occupied molecular orbital and LUMO, lowest unoccupied molecular orbital) energies of 5a–f, 8a–f, and 9a–f have been calculated at the HF and B3LYP methods with 6‐31G, 6‐31G(d), 6‐31+G(d), 6‐31++G(d,p), 6‐311G, 6‐311G(d), 6‐311+G(d), and 6‐311++G(d,p) basis sets. Also, the molecular hardness (η) and electronegativity (χ) parameters have been obtained using molecular frontier orbital energies. The &lt;α&gt;, Δα, μ, β, HOMO, LUMO energies, η and χ parameters have been investigated as dependence on the choice of method and basis set. The variation graphics of &lt;α&gt;, Δα, μ, β, η, and χ parameters using HF and B3LYP methods with different basis sets are presented. We have examined the frontier molecular orbital pictures of 5a–f, 8a–f, and 9a–f using B3LYP/6‐31++G(d,p) level. The 5a–f, 8a–f, and 9a–f display significant linear, second‐order molecular nonlinearity, and molecular parameters and provide the basis for future design of efficient nonlinear optical materials having the 1,3,4‐oxadiazole core. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

The consistency analysis of different semiempirical calculations on second- and third-order nonlinear optical properties of donor–acceptor chromophores containing α-cyan

The static and frequency dependent average polarizability (< α>), first- and second-hyperpolarizabilities (< β> and < γ>) and HOMO and LUMO energies of donor–acceptor chromophores containing α-cyan ( 1a– c) have been investigated by using the AM1, MNDO, MNDO-d, PM3, RM1 and PM6 methods within a time-dependent Hartree–Fock (TDHF) approaches. The electronic properties of 1a– c have been reported by employing two-state model calculated at ZINDO/S-SCI, PM3-SCI and RM1-SCI methods. Also, the molecular hardness ( η) and electronegativity ( χ) parameters have been obtained by using molecular frontier orbital energies. The < α>, < β>, < γ> HOMO, LUMO energies, η and χ parameters have been investigated with respect to the choice of different semiempirical methods. The variation graphics of β, β 0, η and χ parameters according to the different semiempirical methods are presented. Furthermore, the variation graphics of β 0 with regard to the μ eg , Δ μ and λ eg are displayed. The frontier molecular orbital and electrostatic potential pictures of 1a– c using ZINDO/S-SCI level have been examined. The results of 1a– c display significant second- and third-order molecular nonlinearity.

Prediction of blood–brain partitioning: A model based on molecular electronegativity distance vector descriptors

The objective of this paper is to build a reliable model based on the molecular electronegativity distance vector (MEDV) descriptors for predicting the blood–brain barrier (BBB) permeability and to reveal the effects of the molecular structural segments on the BBB permeability. Using 70 structurally diverse compounds, the partial least squares regression (PLSR) models between the BBB permeability and the MEDV descriptors were developed and validated by the variable selection and modeling based on prediction (VSMP) technique. The estimation ability, stability, and predictive power of a model are evaluated by the estimated correlation coefficient ( r), leave-one-out (LOO) cross-validation correlation coefficient ( q), and predictive correlation coefficient ( R p ). It has been found that PLSR model has good quality, r = 0.9202, q = 0.7956, and R p = 0.6649 for M1 model based on the training set of 57 samples. To search the most important structural factors affecting the BBB permeability of compounds, we performed the values of the variable importance in projection (VIP) analysis for MEDV descriptors. It was found that some structural fragments in compounds, such as –CH 3, –CH 2–, CH–, C , C–, –CH<, C<, N–, –NH–, O, and –OH, are the most important factors affecting the BBB permeability.

Density functional energetics and frontier orbitals analysis for the derivatives of the nonclassical triplet-pentagon-fusion fullerene C 64X (X = Si and Ge)

The structures, frontier orbitals, electronegativities, and static linear polarizabilities of the nonclassical triplet-pentagon-fusion fullerene derivatives C 64X (X = Si and Ge) are studied using the density functional theory. The binding energies of four C 64X (X = Si and Ge) isomers explore that, the Si atom or Ge atom locates on the triplet-pentagon-fusion vertex of C 64, to form the most stable structure, namely, C 64Si-1 or C 64Ge-1. The frontier orbital theory strongly confirms the possibility for synthesizing C 64X-1 (X = Si and Ge). The reactive heats, energy gaps, molecular electronegativities, and mean polarizabilities all show that C 64Si-1 might be more stable and easier to synthesize than C 64Ge-1.

QSPR model for bioconcentration factors of nonpolar organic compounds using molecular electronegativity distance vector descriptors

A five-variable model (model M2) was developed for the bioconcentration factors (BCFs) of nonpolar organic compounds (NPOCs) by using molecular electronegativity distance vector (MEDV) to characterize the structures of NPOCs and variable selection and modeling based on prediction (VSMP) to select the optimum descriptors. The estimated correlation coefficient (r (2)) and the leave-one-out cross-validation correlation coefficients (q (2)) of model M2 were 0.9271 and 0.9171, respectively. The model was externally validated by splitting the whole data set into a representative training set of 85 chemicals and a validation set of 29 chemicals. The results show that the main structural factors influencing the BCFs of NPOCs are -cCc, cCcc, -Cl, and -Br (where "-" refers to a single bond and "c" refers to a conjugated bond). The quantitative structure-property relationship (QSPR) model can effectively predict the BCFs of NPOCs, and the predictions of the model can also extend the current BCF database of experimental values.

QSPR study on GC relative retention time of organic pesticides on different chromatographic columns

In the present study, Lu index and distance-based atom type topological index (DAI) previously developed in our team, were introduced and combined with molecular electronegativity chi ep to characterize quantitative structure-property relationship of GC relative retention time (RRT) for several types of structurally diverse organic pesticides on the four kinds of chromatographic columns. Using multiple linear regression technique, four several-variable models are obtained with the estimations correlation coefficient (R(2)) being between 0.9655 and 0.9285, and the correlation coefficient (R(2)cv) in the leave-one-out cross-validation procedure are between 0.9560 and 0.9143, respectively. The results in this study indicate that the three topological indices Lu index, DAI, and molecular electronegativity chi ep can predict the gas chromatographic RRT of organic pesticides with diverse hetero-atoms.