Calculation Of Atomic Charges Research Articles

Density functional theory analysis of the local chemical bonds in the periodic tantalum dichalcogenides TaX2 (X=S, Se, Te)

The electronic structure of layered tantalum dichalcogenides 1T-TaX2 (X=S, Se, Te) have been studied both with the linear muffin tin orbitals-atomic sphere approximation (LMTO-ASA) and the Amsterdam density functional for band (ADF-band) programs. The first code (LMTO) provides band structures, density of states (DOS), and crystal orbitals Hamiltonian populations (COHP) while the second one allows accurate atomic charge calculations by means of a powerful electron density numerical integration. All those analyses were used to rationalize the electronic structures of the three 1T-TaX2 phases, in particular to enlighten the 13×13 structural modulations observed in TaS2 and TaSe2, and to put forward the influence of the local chemical Ta–Te bonds on the relative stability of the 1T-TaTe2 phase vs the distorted monoclinical one. The indirect overlap between the two bands responsible for the metallic properties of TaS2 and TaSe2 has been shown to significantly increase the tantalum d electron count compared to its formal value (d1) leading to a more realistic occupation of the threefolded t2g-like bands involved in the 13×13 instability. Owing to the low electronegative character of Te compared to S and Se, the direct overlap occurring at the Fermi level results in an electron transfer from local Ta–Te bonding states to local Ta–Te antibonding ones yielding a destabilization of the metal–chalcogen bonds.

Anticonvulsant properties of various acetylhydrazones, oxamoylhydrazones and semicarbazones derived from aromatic and unsaturated carbonyl compounds

Various acetylhydrazones, oxamoylhydrazones and semicarbazones were prepared as candidate anticonvulsants with a view to examining the viability of a putative binding site hypothesis. Atomic charge calculations were undertaken to determine the hydrogen bonding capacities of various molecules. The biological results obtained revealed that in general the acetylhydrazones and semicarbazones afforded good protection against convulsions while the oxamoylhydrazones were significantly less active. These data suggest that terminal electron-donating groups enhanced the hydrogen bonding capabilities and anticonvulsant properties of these molecules.

Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 A resolution as a first test case.

The number of protein structures refined at a resolution higher than 1.0 A is continuously increasing. Subatomic structures may deserve a more sophisticated model than the spherical atomic electron density. In very high resolution structural studies (d < 0.5 A) of small peptides, a multipolar atom model is used to describe the valence electron density. This allows a much more accurate determination of the anisotropic thermal displacement parameters and the estimate of atomic charges. This information is of paramount importance in the understanding of biological processes involving enzymes and metalloproteins. The structure of the scorpion Androctonus australis Hector toxin II has been refined at 0.96 A resolution using synchrotron diffraction data collected at room temperature. Refinement with a multipolar electron-density model in which the multipole populations are transferred from previous peptide studies led to the observation of valence electrons on covalent bonds of the most ordered residues. The refined net charges of the peptide-bond atoms were of the correct sign but were underestimated. Such protein-structure refinements against higher resolution data collected at cryogenic temperature will enable the calculation of experimental atomic charges and properties such as electrostatic potentials.

A New Topological Model for the Calculation of Partial Atomic Charges

A New Topological Model for the Calculation of Partial Atomic Charges

Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: III. Extension of thePESP method for calculation of electrostatic potential-derived atomic charges to compounds containing Li+, Na+, Mg2+, K+, Ca2+, Zn2+, and I

The PESP (Parameterized ElectroStatic Potential) method for calculating molecular electrostatic potentials, previously parameterized for H, C, N, O, F, P, S, Cl, and Br, is extended to molecules containing Li+, Na+, Mg2+, K+, Ca2+, Zn2+, and I. For a collection of 166 molecules containing 1668 atoms with at least one metal or iodine atom, PESP achieves an average absolute deviation in electrostatic potential-derived atomic charges of 0.042e− compared with ab initio MP2/6-31G** calculations, with a correlation coefficient of 0.996. For a larger data set, consisting of 311 molecules encompassing all of the 16 elements just listed (2488 total atoms), PESP achieves an average absolute deviation of 0.040e− and a correlation coefficient of 0.995. PESP calculations are an order of magnitude faster than the simplest ab initio method (STO-3G) on large molecules, while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1456–1469, 1998

The Calculation of Atomic Charges in Crystals: A Comparative Analysis for the Pseudo-Orbital Basis

The paper presents the results of atomic charge calculations in the crystals performed by means of the pseudopotential method within the pseudo-atomic-orbital basis. The calculations have been carried out for the group of binary and complex ion-molecular compounds. Four different types of population analysis have been examined including the dependence of the results on the basis used. It is shown that the pseudo-atomic-orbital basis is capable to produce reasonable values of atomic charges both for ionic and covalent compounds, and for a mixed type of chemical bonding as well.

An extended scheme for calculation of atomic charges by the modified Sanderson method and application to some polycyclic organic molecules

Abstract It has been demonstrated that the modified Sanderson formalism (MS) for calculation of atomic charge yields good correlation with C 1s core level shifts in organic molecules with carbon in the sp 3 hybridized state (Sastry, J. Electron. Spectrosc., 85 (1997) 167) as well as in monocyclic aromatic molecules (Patil et al., J. Electron Spectrosc., 85 (1997) 249). In this communication, a reinterpretation of the MS method is presented which leads to an extension of the scheme enabling application to polycyclic molecules for the first time. A linear relationship is established between partial charges on carbon and C 1s core level shifts in some polycyclic organic molecules.

Interacting induced dipoles polarization model for molecular polarizabilities: application to benzothiazole (A)-benzobisthiazole (B) oligomers AB 13A

We have outlined a method for the calculation of atomic net charges and molecular dipole-dipole,  α , dipole-quadrupole,  A , and quadrupole-quadrupole,  C , polarizabilities which we have successfully applied to benzothiazole (A)-benzobisthiazole (B) oligomers in the series AB 1A to AB 13A, and the results have been extrapolated to give predictions for polybenzobisthiazole. The calculation of  α ,  A and  C has been carried out by the interacting induced dipoles polarization model that calculates tensor effective anisotropic point polarizabilities (method of Applequist). The mean effective atomic α effpolarizabilities for the monomeric unit are of the same order of magnitude as reference calculations (PAPID program). The value of the dipole moment drops sharply from the monomeric unit to the dimeric unit. The high dipole moment of the monomeric unit forces a charge redistribution in the molecule, that reverses the sign of the mean quadrupole moment with respect to the remaining oligomers. The values of  α and  C for the oligomers are much larger than the sum of their component parts, as would be expected owing to the larger length of π conjugation. However, the values of  A are also sensitive to the molecular dipole moment. This fact explains a relative maximum in ¦ A x, xx ¦ for the polar monomeric unit. The remaining oligomers show a constant dipole moment, and a non-linear increase in ¦ A x, xx ¦ with the number of units is observed. The fractal dimension of the solvent accessible surface and the 1-octanol-water partition coefficient, P, increase with the number of units in the oligomer. Functions of N (the total number of units either A or B) have been fitted to α (mean value), α xx , ¦ A x ¦ ( x vector component), ¦ A x, xx ¦ and C xx, xx , and these may be used to predict the values for longer oligomers. The finite oligomer results have been extrapolated to predict optical properties of polybenzobisthiazole.

Resonance-Induced Hydrogen Bonding at Sulfur Acceptors in R 1 R 2C=S and R 1CS2 − Systems

The hydrogen-bond acceptor ability of sulfur in C=S systems has been investigated using crystallographic data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. The R1R2C=S bond lengths span a wide range, from 1.58 Å in pure thiones (R 1 = R 2 = Csp 3) to 1.75 Å in thioureido species (R 1 = R 2 = N) and in dithioates —CS^{-}_2. The frequency of hydrogen-bond formation at =S increases from 4.8% for C=S &gt; 1.63 Å to more than 70% for C=S &gt; 1.70 Å in uncharged species. The effective electronegativity of S is increased by conjugative interactions between C=S and the lone pairs of one or more N substituents (R 1 R 2): a clear example of resonance-induced hydrogen bonding. More than 80% of S in —CS^{-}_2 accept hydrogen bonds. C=S...H—N,O bonds are shown to be significantly weaker than their C=O...H—N,O analogues by (a) comparing mean S...H and O...H distances (taking account of the differing non-bonded sizes of S and O and using neutron-normalized H positions) and (b) comparing frequencies of hydrogen-bond formation in `competitive' environments, i.e. in structures containing both C=S and C=O acceptors. The directional properties and hydrogen-bond coordination numbers of C=S and C=O acceptors have also been compared. There is evidence for lone-pair directionality in both systems, but =S is more likely (17% of cases) than =O (4%) to accept more than two hydrogen bonds. Ab initio calculations of residual atomic charges and electrostatic potentials reinforce the crystallographic observations.

Correlation of C 1s binding energies in organic molecules with atomic charge calculated using a modified Sanderson formalism

This communication seeks to study the correlation between the C 1s binding energy (BE) in organic molecules, both in the gaseous and solid phases, and the atomic charge on the carbon using the modified Sanderson method. An extremely good correlation is found for both cases, with the relationship between charge and BE being linear. The Sanderson approach for atomic charge calculation is extremely simple and not computationally intensive, as are other approaches such as ab initio quantum-chemical calculations of varying levels of complexity. The good correlation with binding energy values reported in the literature, together with the ease of calculation of the atomic charge, make the modified Sanderson approach a promising one from the experimentalists' point of view. Other advantages of this approach are also discussed in this article.

Arylazopyridines-mercury(II) coordination and organometallic compounds: Theoretical support

Arylazopyridines (Haap,1) are mercurated by Hg(OAc)2 in methanol followed by LiCl addition. Two classes of compounds are identified: Hg(Haap)Cl2 (2), a simple coordination compound of tetrahedral geometry, and organomercury compounds, Hg(aap)Cl(3). The compounds are characterised by elemental analyses, IR and1H NMR spectra. The NMR results suggest that mercury is directed to the C-5 position (meta to pyridine-N) in the pyridine fragment of the ligand. This assumption is supported by net atomic charge calculation using the MNDO method.

Threshold Energy and Unimolecular Rate Constant for Elimination of HF from Chemically Activated CF3CF2CH3: Effect of the CF3 Substituent on the α-Carbon

Methyl and CF3CF2 radicals were combined to form chemically activated CF3CF2CH3 with 104 kcal/mol of internal energy, and the experimental rate constant for unimolecular 1,2-dehydrofluorination was 4.5 × 105 s-1. Fitting the calculated rate constant for HF elimination from RRKM theory to the experimental value provided a threshold energy, Eo, of 68.5 kcal/mol. Comparing this threshold energy to those for CF2HCH3, CH3CF2CH3, CF2ClCH3, and CF3CH3 shows that replacing the α-H of CF2HCH3 with CH3 lowered the Eo by 7 kcal/mol and replacing with CF3, Cl, or F raises the Eo about 8 kcal/mol. The CF3 substituent, an electron acceptor, increased the Eo by an amount nearly equal to that with F and Cl substituents, suggesting that halogen substituents exert a similar inductive effect at the α-carbon that loses electron density as the transition state forms. These proposals will be compared to recent calculations of the carbon's atomic charges in the reactant and transition state.

Prediction of flux through polydimethylsiloxane membranes using atomic charge calculations: Application to an extended data set

The maximum steady state flux of 171 compounds through PDMS membranes was predicted using a refinement of a previously developed empirical quantitative structure-transportability relationship (QSTR) produced using the reported flux data for 103 compounds. The model utilized partial atomic charge, solubility, and molecular weight as predictors. The predicted data set includes a variety of substituted benzenes, naphthalenes, thiophenes, benzimidazoles, pyridines, quinolines, isoquinolines, pyrimidines, triazoles and lesser numbers of other heterocyclic classes of compounds over a wide range of polarity. Maximum steady state flux was measured using isopropyl alcohol as solvent. Molecular models of all the compounds were simulated using SYBYL 6.0 molecular modeling software. The atomic charge of each individual compound was computed with the Gast-Hück method using the same software. Results show that the simple QSTR equation is capable of accurately predicting the steady state flux of a variety of compounds. Contribution of atomic charge to mass transport phenomena was further verified by the prediction of the apparent permeability calculated from the steady state flux data. Permeability decreases significantly as the atomic charge of diffusant is increased. Predicted results show that atomic charges can be used to represent the polarity and be correlated to the polarity-related properties of an electrically neutral compound.

Atomic charges and structures of some hydrogen bonded substituted anilinium chloride systems: Correlation with XPS

Using the MOPAC/AM1 method and employing an aggregate involving a cation with three hydrogen bonded chloride counterions, atomic charge calculations have been made on the basis of known crystal structures for the anilinium derivatives RR′ C 6 H 4 NH 3 + Cl −, in which R = 4- CH 3, R′ = H, and R = 2- CH 3, R′ = 6- CH 3, together with the newly determined structures which have R = 2-OCH 3, R′ = H (I) and R = 2-CH 3, R′ = H ( II) . For I, molecular formula C 7H 10NClO : space group P21 c , Z = 4 with a = 0.5374 (5), b = 1.3869 (7), c = 1.0940 (8)nm, β = 97.61(7) °, R, R w = 0.050, 0.047. For II, molecular formula C 7H 10ClN : space group Pca2 1 , Z = 4 with a = 1.5767(6), b = 0.5408 (3), c = 0.8705 (4)nm, R, R w = 0.041, 0.035. The estimated charges on the N atoms are shown to correlate with the N(1 s) binding energies, determined via XPS measurements. It is also demonstrated that these charges are largely independent of substituent ring-position.

Electrostatic properties in zeolite-type materials from high-resolution x-ray diffraction: The case of natrolite.

High-resolution x-ray-diffraction data of natrolite at room temperature give by multipolar refinement an analytical expression of the electron density which permits the calculation of net atomic charges and electrostatic potential. The observed net charges show that the structural formula of natrolite may be written ${\mathrm{Na}}_{2}$${\mathrm{Al}}_{2}$${\mathrm{Si}}_{2}$${\mathrm{O}}_{8}$(Si${\mathrm{O}}_{2}$),2${\mathrm{H}}_{2}$O. The electrostatic energy of one sodium ion inside the crystal is estimated to -21.6 eV. Calculation of the electrostatic potential excluding one sodium shows that the minimum is precisely at the removed Na position.

Comprehensive Evaluation of the Absorption, Photophysical, Energy Transfer, Structural, and Theoretical Properties of α-Oligothiophenes with One to Seven Rings

A large basis set of α-oligothiophenes with two to seven rings (α2−α7), also including thiophene, α1, have been investigated in five solvents regarding absorption, fluorescence and phosphorescence, quantum yields of fluorescence (φF) and triplet formation (φT), lifetimes of fluorescence and the triplet state, quantum yields of singlet oxygen production (φΔ), all rate constants kF, kIC, kISC, and several of the foregoing as a function of temperature. Ten different theoretical calculations across several levels including three levels of ab initio have been carried out regarding which conformer is lowest in energy and the ΔH's among all conformers of α2, α3 and α5, as well as calculations of transitions energies of the α-oligothiophenes. We have shown that the (l) 1Bu state is the lowest singlet state for all α2−α7 in any solvent, in contradiction to previous predictions for the higher members. Based on absorption and fluorescence data and calculations of atomic charges in S0 and S1, the ground state is twis...

A Detailed Study of VESPA Electrostatic Potential-Derived Atomic Charges

VESPA, an improved semiempirical method for the calculation of electrostatic potential-derived atomic charges has been tested. It is shown that this approach is even less dependent upon molecular orientation than "high density" CHELPG ab initio ESP-derived charges. The conformational dependence of VESPA charges has been investigated for rotation around the C-N bond in formamide and 11 different conformers of glycerolphosphorylcholine. The results obtained are also compared to the corresponding ab initio values. Finally, VESPA is used to calculate electrostatic potential-derived charges for bioorganic molecules. We discuss the abilities and the limitations of ESP charges in this area.

Molecular electronegativity in density functional theory (I)——Direct calculation of atomic charges in a molecule via electronegativity equalization principle

On the basis of electronegativity expressed in density functional theory and electronegativity equalization principle, a new scheme for calculating the atomic charges in a molecule has been proposed and designed, which gives a new scale of the atomic electronegativity and hardness in a certain molecular environment and takes the harmonic mean electronegativity as a reference value of the molecular electronegativity so that the multiple-regression and nonuniform parameters in the original method are avoided. This approach can be easily and widely applied to the calculation of atomic charges for a big molecule and quite good results of atomic charges in some illustrated molecules are obtained as compared with those from the ab initio STO-3G SCF calculations.

X-ray structure of isomeric 3-chloro-4-(methylthio)- and 4-chloro-3-(methylthio)quinolines

The crystal and molecular structures of two isomeric 3,4- and 4,3-chloro-(methylthio)quinolines have been determined. For 3-chloro-4-(methylthio)-quinoline (3-Cl−4-MeS−Q); triclinic, space group\(\bar P1\),a=7.199(3),b=7.919(3),c=8.921(3) A, α=89.74(3), β=74.29(3), γ=78.55(3)°. For 4-chloro-3-(methylthio)quinoline (4-Cl−3-MeS−Q): monoclinic, space group P21/n,a=12.860(4),b=5.424(2),c=13.434(4) A, β=90.84(3)°. The values of the Cl...S distance as well as those for the Cl−C−C(S) and (Cl)C−C−S angles indicate the attractive interaction between ortho-situated heteroatoms in isomer 4-Cl−3-MeS−Q contrary to the effects observed in the case of 3-Cl−4-MeS−Q. The conclusions were confirmed by calculations of atomic charges withab initio method 4-31G basis set, which show positively charged sulfur atom in 4-Cl−3-MeS−Q and negatively charged sulfur in 3-Cl−4-MeS−Q.

Aspects of Electrophilic Bromination of Alkenes in Solution. Theoretical Calculation of Atomic Charges in Bromonium Ions

Aspects of Electrophilic Bromination of Alkenes in Solution. Theoretical Calculation of Atomic Charges in Bromonium Ions