Atoms In Molecules Approach Research Articles

Theoretical study of chlordecone and surface groups interaction in an activated carbon model under acidic and neutral conditions

Activated carbons (ACs) are widely used in the purification of drinking water without almost any knowledge about the adsorption mechanisms of the persistent organic pollutants. Chlordecone (CLD, Kepone) is an organochlorinated synthetic compound that has been used mainly as agricultural insecticide. CLD has been identified and listed as a persistent organic pollutant by the Stockholm Convention. The selection of the best suited AC for this type of contaminants is mainly an empirical and costly process. A theoretical study of the influence of AC surface groups (SGs) on CLD adsorption is done in order to help understanding the process. This may provide a first selection criteria for the preparation of AC with suitable surface properties. A model of AC consisting of a seven membered ring graphene sheet (coronene) with a functional group on the edge was used to evaluate the influence of the SGs over the adsorption. Multiple Minima Hypersurface methodology (MMH) coupled with PM7 semiempirical Hamiltonian was employed in order to study the interactions of the chlordecone with SGs (hydroxyl and carboxyl) at acidic and neutral pH and different hydration conditions. Selected structures were re-optimized using CAM-B3LYP to achieve a well-defined electron density to characterize the interactions by the Quantum Theory of Atoms in Molecules approach. The deprotonated form of surface carboxyl and hydroxyl groups of AC models show the strongest interactions, suggesting a chemical adsorption. An increase in carboxylic SGs content is proposed to enhance CLD adsorption onto AC at neutral pH conditions.

Towards the origin of effective An(III)/Ln(III) separation by tridentate N-donor ligands: a theoretical study on atomic charges and polarisabilities for Cm(III)/Gd(III) separation

ABSTRACTSoft N-donor ligand have shown to separate An(III) from Ln(III). The origin of the selectivity has not been entirely identified, and similar ligands show very different separation qualities. In this study we present a theoretical investigation of several relevant N-donor ligands in terms of atomic charges and polarisabilities obtained from an atoms in molecules approach. These allow new insights into the bonds between the ligands’ nitrogen atoms and the metal cation and explain a major part of the selectivity towards actinide ions. We deduct the superiority of 2,6-bis(1,2,4-triazine-3-yl)pyridines in separation quality compared to similar ligands for the Cm(III)/Gd(III) separation. Furthermore, improvements of existing ligands are developed that allow not only a direct experimental confirmation but also a systematic experimental study of the interactions and their influence on the selectivity.

Theoretical investigation of HNgNH3(+) ions (Ng = He, Ne, Ar, Kr, and Xe).

The equilibrium geometries, harmonic frequencies, and dissociation energies of HNgNH3(+) ions (Ng = He, Ne, Ar, Kr, and Xe) were investigated using the following method: Becke-3-parameter-Lee-Yang-Parr (B3LYP), Boese-Matrin for Kinetics (BMK), second-order Møller-Plesset perturbation theory (MP2), and coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)). The results indicate that HHeNH3(+), HArNH3(+), HKrNH3(+), and HXeNH3(+) ions are metastable species that are protected from decomposition by high energy barriers, whereas the HNeNH3(+) ion is unstable because of its relatively small energy barrier for decomposition. The bonding nature of noble-gas atoms in HNgNH3(+) was also analyzed using the atoms in molecules approach, natural energy decomposition analysis, and natural bond orbital analysis.

Competing mechanisms for the reaction of dichloropropynylborane with 2-tert-butylbutadiene. Diels–Alder reaction versus alkynylboration

Density functional theory and the quantum theory of atoms in molecules approach were used to study two competing process: the Diels–Alder reaction and the 1,4-alkynylboration.

The influence of Ser-154, Cys-113, and the phosphorylated threonine residue on the catalytic reaction mechanism of Pin1.

Pin1 is an enzyme that specifically catalyzes the cis-trans isomerization of proline amide bonds in peptides that contain a phosphorylated threonine or serine residue in the position preceding proline. In the cell, the isomerization reaction is associated with cellular signaling and has been related to diseases such as Alzheimer and cancer. The catalytic mechanism by which Pin1 accelerates the isomerization reaction, however, is still unknown. In this study, we use molecular dynamics simulation in combination with the QM/MM methodology to disclose the influence of the residues Ser-154 and Cys-113 in the enzyme and the phosphorylated threonine residue in the peptide on the reaction mechanism. To account for the correct electrostatic interaction between the three residues and the reactive center, we derive atomic charges that account for the varying electrostatic field in the catalytic cavity. Different methods based on reproducing the molecular electrostatic potential or an atoms in molecules approach were investigated. Finally, the reaction mechanism is analyzed with the mean reaction force and the influence of the three residues is disclosed. Our results show that Pin1 specifically catalyzes the isomerization of the trans conformer in a jump-rope type of motion, as suggested by us and confirmed experimentally by others. This is accomplished by anchoring the threonine phosphate residue on one end of the peptide through electrostatic interactions with the basic triad of the enzyme and at the other end through specific enzyme-peptide hydrogen bonds. Cys-113 reduces the structural contribution to the activation free energy through the stabilization of the cis conformer, and Ser-154 in combination with Gln-131 assist in the isomerization reaction of the trans isomer.

Theoretical studies of bonding properties and vibrational spectra of chosen ladder-like silsesquioxane clusters

In this work the DFT calculations were carried out by means of Gaussian 09 program using B3LYP XC functional and 6-311G(d) basis set for chosen ladder-like silsesquioxane model clusters. Vibrational frequencies computations and infrared spectra were obtained subsequently for above mentioned structures. The results of topological analysis of total electron density obtained in SCF calculations (Quantum Theory of Atoms in Molecules approach) and structural analysis based on Bond Valence Method are presented in order to analyze length and ramification of ladder-like structures and various functional group influence.The calculated infrared spectra show that peak derived from vibrations of Si–O “chains” is shifting towards lower frequencies with increasing length of the ladder while at the same time, the overall strains (BVM) are diminishing.

Selectivity of azine ligands toward lanthanide(III)/actinide(III) differentiation: a relativistic DFT based rationalization.

Polyazines emerge as highly selective ligands toward actinide versus lanthanide separation. Electronic structures of several mono- and polyazine f-complexes of general formula MX3L (M(+3) = Ce, Nd, Eu, U, Am, and Cm; X = RCp(-) or NO3(-); L = N-donor ligand) related to Ln(III)/An(III) differentiation have been investigated using scalar relativistic ZORA/DFT calculations. In all cases, DFT calculations predict shorter An-N bonds than Ln-N ones whatever the azine used, in good agreement with available experimental data. The An-N bonds are also characterized by higher stretching frequencies than Ln-N bonds. The electronic structures of all species have been studied using different population analyses, among them natural population (NPA) and the quantum theory of atoms in molecule approach (QTAIM), as well as using different bond indices. The ability for Ln(III)/An(III) differentiation of the terdentate bipyrazolate BPPR ligand in the M(BPPR)(NO3)3 complexes (M(3+) = Ce, Eu, U and Am ; R = H, 2,2-dimethylpropyl) where BPP = 2,6-bis(dialkyl-1H-pyrazol-3-yl)pyridine has been studied, with a special emphasis on the total metal-ligand bonding energy (TBE). The ZORA/DFT approach was found to properly reproduce the higher selectivity of the polyazine BPP ligand compared to monoazines, especially for the Eu(III)/Am(III) pair operating in spent nuclear fuel, using computed TBEs as criterion. Moreover, the orbital part of the total bonding energy appears also to rationalize well the observed selectivity.

P-substituted phosphine–boranes: Gas phase acidities, basicities and dihydrogen release. A comparison to amine–boranes

We present the gas phase stabilities, acidities and basicities for several previously uninvestigated phosphine–boranes, and compare them to respective amine–boranes. Although both species seem to be very similar, it was found that only acidities correlate in a reasonable manner (R2=0.874). According to MP2/6-311+G(d,p) calculations the P-substitutions increase the stability of the H3P⋯BH3 complex up to 14kcal/mol. Phosphorine–borane was the only complex less stable than the unsubstituted H3P⋯BH3. Replacing the phosphine with respective amine decreases the acidity but raises the basicity of the complexes. A complex that can be described as R1R2R3P⋯BH2+⋯H2 forms upon protonation and the dihydrogen removal from such species is an exergonic process. Typical ΔG for the dissociation reaction ranges from 0.1 to −2.6kcal/mol but there are notable exceptions. For example, the protonated benzyl phosphine–borane contains a B⋯H–H⋯π interaction which is replaced with stronger B–Cπ interaction upon hydrogen removal thus leading to more favorable H2 removal. The bonds and interactions present in protonated species have been studied using Bader’s Atoms in Molecules approach.

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

Hydrogen bonds and their strength were analysed based on their X–H proton–donor bond properties and the parameters of the H–Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

Electron density distribution in the ethylene complexes with Pd-containing bimetallic clusters

The complexes of PdM bimetallic clusters (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, Ag, Cd) with ethylene are calculated at the density functional theory level with the quantum theory of atoms in molecule approach for the electron density distribution analysis. Formation of the metal–carbon coordination bonds in the studied complexes is determined by the (3, − 1) critical point appearance between the corresponding atoms. The energy of these interactions is estimated as a measure of the PdM clusters adsorptivity. All the C–C, C–Pd and C–M bonds are classified by the characters of the electron density Laplacian at the bond critical point and by the electron energy density. It is shown that the ethylene molecule is strongly activated by adsorption on the PdM clusters. The estimated binding energy between PdM and C2H4 is in the range of 58.3–97.8 kcal/mol going from the PdCd(C2H4) to the PdNi(C2H4) complexes, respectively.

The structure and bonding properties of chosen phenyl ladder-like silsesquioxane clusters

The poly(phenyl silsesquioxanes) were synthesized at 30–36°C via direct co-hydrolysis and condensation using sequential one batch, two-step reactions in the presence of potassium carbonate as the base catalyst and in the mixture THF/H2O. The structure and properties of the obtained materials were analyzed using NMR, TGA, SEC, XRD and FTIR methods. For chosen ladder-like phenyl silsesquioxane model clusters the DFT calculations by means of Gaussian09 program using B98 (DFT) method and a set 6-31G (d) of basis functions were carried out and respective infrared spectra were constructed and compared with the experimentally obtained ones. The results of topological analysis of total electron density obtained in SCF calculations (Quantum Theory of Atoms in Molecules approach) and structural analysis based on Bond Valence Method were used in detailed analysis of bonding properties in these clusters.

Electron-density studies on hydrogen bonding in chromone derivatives. Part II: comparative study

The experimental electron density of a chromone derivative was determined from a multipole refinement of 100 K X-ray synchrotron data and complemented by theoretical calculations with experimental and optimized geometry. Atomic and topological properties were obtained using the Quantum Theory of Atoms in Molecules approach. The examination of topological parameters unambiguously showed π-delocalization within the H-bonded ring. The application of source function analysis confirmed the intramolecular N–H···O hydrogen bond to be a resonance-assisted hydrogen bond. The topological study confirmed the covalent nature of N–H···O interaction and the electrostatic nature of weak C–H···O interactions.

Charge Density Analysis of a Pentaborate Ion in an Ammonium Borate: Toward the Understanding of Topological Features in Borate Minerals

Structural and charge density distribution studies have been carried out on a single crystal data of an ammonium borate, [C(10)H(26)N(4)][B(5)O(6)(OH)(4)](2), synthesized by solvothermal method. Further, the experimentally observed geometry is used for the theoretical charge density calculations using the B3LYP/6-31G** level of theory, and the results are compared with the experimental values. Topological analysis of charge density based on the Atoms in Molecules approach for B-O bonds exhibit mixed covalent/ionic character. Detailed analysis of the hydrogen bonds in the crystal structure in the ammonium borate provides insights into the understanding of the reaction pathways that could result in the formation of borate minerals. The net atomic charges and electrostatic potential isosurfaces also give additional input to evaluate chemical and physical properties in such systems.

Insights into Metal Borohydride and Aluminohydride Bonding: X-Ray and Neutron Diffraction Structures and a DFT and Charge Density Study of [Na(15-crown-5)][EH4] (E = B, Al)

The neutron and X-ray structures of [Na(15-crown-5)][BH(4)] and [Na(15-crown-5)][AlH(4)], respectively, are reported, along with a topological analysis of their DFT-computed charge densities that explores the bonding between the anionic complex hydride [EH(4)](-) (E = B, Al) and the counterion [Na(15-crown-5)](+). In each case, the interaction is weak and mainly electrostatic in nature; however, notable differences are observed in the manner in which [BH(4)](-) and [AlH(4)](-) bind to the metal, which explains their different coordination modes. A range of unconventional E-H···H-C contacts is revealed to play an important role in the overall bonding and crystal packing of both complexes. These interactions can be classified as weak dihydrogen bonds based on the atoms in molecules approach.

The quantum‐chemical study of organic octupolar chromophore triaminotrinitrobenzene and the dimer: Topological analysis and nonlinear optical characteristics

AbstractThe nonempirical calculations of the structure and molecular polarizabilities of octupolar 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB) molecule and 2TATB dimer, formed of two chromophores through H‐bonding between Oxygens of nitro groups and hydrogens of amino groups of the neighboring molecule, were calculated by TDHF/aug‐cc‐pVDZ′ method. The characterization of 2TATB formation is carried out in the framework of topological Atoms in Molecules approach. The analysis of electron charge density distribution has given evidence to the existence of two equivalent intermolecular NH…O bonds with the bond length of 2.458 Å; the intramolecular H‐bonds between oxygens and hydrogens of alternating nitro‐ and amino groups are also detected. The study of the solvent effect on the TATB electric properties, performed in the framework of conventional polarizable continuum model, demonstrated weak dependence of molecular polarizabilities on the solvent polarity. The polarizability of 2TATB dimer is nearly twice as large as that of TATB, whereas the modulus of the first hyperpolarizability of 2TATB is ∼2.3 times greater than that of TATB, thus exhibiting the cooperative effect. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Convergence of the multipole expansion for 1,2 Coulomb interactions: The modified multipole shifting algorithm

A force field that accounts for the quantum chemical reality of interacting atoms must include Coulomb interactions between bonded atoms. The short-range nature of such 1,2 interactions necessitates atomic multipole moments in addition to point charges. However, the close proximity of bonded atoms would normally lead to a divergent multipolar expansion. A special algorithm presented here, within the scope of the previously presented multipole shifting method [M. Rafat and P. L. A. Popelier, J. Chem. Phys. 124, 144102 (2006)], shows that convergence can nevertheless be achieved by a suitable selection of multipole displacements. The algorithm is applied to improve the convergence of the multipolar expansion within the quantum theory of atoms in molecules approach.

Theoretical analysis of electronic and structural properties of anhydrous calcium oxalate

The results of theoretical analysis of the elec- tronic and crystal structural properties and bonding in relation to thermal decomposition process in anhydrous calcium oxalate are presented. The methods used in this analysis—topological analysis of electron density (Bader's Quantum Theory of Atoms in Molecules approach) obtained from DFT calculations performed by Wien2k package (Full Potential Linearized Augmented Plane Wave Method); bond order model (CioslowskiM as well as Brown's Bond Valence Model (bonds valences and strength', and bond and crystal strains, calculated from crystal structure and bonds lengths data) are described. The analysis of the obtained results shows that these methods allow us to explain the way of thermal decomposition process of anhydrous calcium oxalate to calcium carbonate as a decomposition product, and to describe the structural transition taking place during such process (from mono- clinic anhydrous CaC2O4 to rhombohedral calcite struc- ture). In the light of the results of our similar calculations performed previously for other anhydrous oxalates (zinc, cadmium silver, cobalt, and mercury) the proposed theo- retical approach can be considered as promising and reli- able tool, which allow analyzing the properties of the structure and bonding and hence predicting the most probable way of thermal decomposition process for given crystal structure.

An Analysis of Substituent Effects in Ethane Derivatives: The Quantum Theory of Atoms in Molecules Approach

MP2/6-311++G(d,p) calculations were performed on ethane and its simple derivatives. Different substituents such as: Li, Na, BeH, BH(2), OH, NH(2), F and NO(2) were considered. The mono- and disubstituted derivatives of ethane were analyzed. The quantum theory of "atoms in molecules" was applied to localize bond critical points and to analyze relationships between their locations and characteristics of the species. The numerous correlations were found showing the crucial influence of substituent effects. It was also revealed that such parameters as the carbon-carbon distance, or the electron density at C-C bond critical point do not show the systematic changes caused by substituent effects. This means that some of QTAIM parameters, especially the positions of BCPs may be useful to detect numerous sensitive effects if the latter ones do not affect the traditionally analyzed geometrical parameters of a molecule, such as bond lengths.

Interplay between Hydrogen-Bond Formation and Multicenter π-Electron Delocalization: Intramolecular Hydrogen Bonds

The specific case of intramolecular hydrogen bonds assisted by pi-electron delocalization is thoroughly investigated using multicenter delocalization analysis. The effect of the pi-electron delocalization on the intramolecular hydrogen-bond strength is determined by means of the relative molecular energies of "open" and "closed" structures, calculated at the B3LYP/6-311++G(d,p) level of theory. These relative energies are compared to variations in the multicenter electron delocalization indices and covalent hydrogen-bond indices, which are shown to correlate very well with the relative strength of the intramolecular hydrogen bonds studied. The multicenter electron delocalization indices and covalent bond indices have been computed using the quantum theory of atoms in molecules approach. The hydrogen bonds are formed with oxygen, nitrogen, or sulfur as acceptor atom, which are also the atoms considered to be bonded to the donor hydrogen. Malonaldehyde is taken as reference; the substitution of oxygen by other atoms at the acceptor and donor positions and the effect of the aromaticity have been studied. The results shown here match perfectly with the qualitative expectations derived from the resonance models. In addition, they provide a quantitative picture of the role played by the pi-electron delocalization on the relative strength of intramolecular hydrogen bonds.

Interplay Between Hydrogen Bond Formation and Multicenter π-Electron Delocalization: Intermolecular Hydrogen Bonds

The interplay between aromatic electron delocalization and intermolecular hydrogen bonding is thoroughly investigated using multicenter delocalization analysis. The effect on the hydrogen bond strength of aromatic electron delocalization within the acceptor and donor molecules is determined by means of the interaction energies between monomers, calculated at the B3LYP/6-311++G(d,p) level of theory. This magnitude is compared to variations of multicenter electron delocalization indices and covalent hydrogen bond indices, which are shown to correlate perfectly with the relative values of the interaction energies for the different complexes studied. The multicenter electron delocalization indices and covalent bond indices have been computed using the quantum theory of atoms in molecules approach. All the hydrogen bonds are formed with oxygen as the acceptor atom; however, the atom bonded to the donor hydrogen has been either oxygen or nitrogen. The water-water complex is taken as reference, where the donor and acceptor molecular environments are modified by substituting the hydrogens and the hydroxyl group by phenol, furan, and pyrrole aromatic rings. The results here shown match perfectly with the qualitative expectations derived from the resonance model.