Topological Analysis Of Electron Density Research Articles

Theoretical studies on the reactions of NO 2 with CH 3SO, CH 3SS, CH 3SO 2 and CH 3S(S)O

The reactions of NO 2 with CH 3SO, CH 3SS, CH 3SO 2 and CH 3S(S)O have been studied at MP2/6-311++G(d, p)//B3LYP/6-311++G (d, p) level. Geometries of the reactants, intermediates (IM), transition states (TS) and products have been optimized and geometries of the transition states are found for the first time. The different structures among four transition states have been discussed by the method of topological analysis of electronic density. The calculated results show that these reactions can proceed via singlet-state or triplet-state potential energy surface (PES). Because of the high energy barrier of triplet PES, the singlet PES reaction is dominant. The reaction mechanisms of NO 2 with CH 3SO, CH 3SS, CH 3SO 2, CH 3S(S)O are similar. On the singlet-state PES, one of O atom of NO 2 attacks the reactants first formed an intermediate, then the intermediate decomposed to CH 3SO 2, CH 3S(S)O, CH 3SO 3, CH 3S(S)O 2 and NO. And because of the low dissociation energy of the processes, these four reactions could occur easily.

Theoretical Investigation on the Nature of Intramolecular Interactions in Aminocyclopentadienyl Ruthenium Hydride Complexes

Aminocyclopentadienyl ruthenium hydride complexes were optimized at the second-order Møller−Plesset (MP2) level of theory with 6-31G(d) and 6-311++G(d,p) basis sets to investigate the nature of intramolecular interactions. The computations show that both Ru−H···H−N dihydrogen bond interactions and Ru···H−N interactions are responsible for the stability of these complexes. The BSSE-corrected interaction energies, computed at the B3LYP and MP2 levels of theory with 6-31G(d), 6-311++G(d,p), and 6-311++G(2d,2p) basis sets, indicate that the dihydrogen bond interaction energy accounts for only 20% of the total interaction energy. Therefore, the Ru···H−N interactions play a key role in stabilizing the aminocyclopentadienyl ruthenium hydride complexes. Topological analysis of electron density at bond critical points confirms the formation of the dihydrogen bonds between oppositely charged hydrogen atoms. Analysis of charge distributions (Mulliken charges) shows there is a strong electronic attraction between Ru and the hydrogen atom.

Hydrogen bonds at metal surfaces: Universal scaling and quantification of substrate effects

Simple bio-molecules demonstrate a propensity to form hydrogen-bonded networks. Here, individual hydrogen-bond energies are determined through topological analysis of the theoretical electron density for a variety of systems, demonstrating the existence of a universal relationship between hydrogen-bond length and strength. Comparison of local hydrogen-bond strength to global stabilisation allows the quantification of contributions to intermolecular interactions within surface overlayers in unprecedented detail.

A topological analysis of electron density and chemical bonding in cyclophosphazenes PnNnX2n (X = H, F, Cl; n = 2, 3, 4)

The restricted Hartree-Fock method was used to determine the cycle size effects on the geometric parameters of several inorganic templates, cyclophosphazenes PnNnX2n (X = H, F, Cl; n = 2, 3, 4). A topological analysis of local electronic properties at the electron density critical points of bonds allowed us to quantitatively characterize the chemical bond in cyclophosphazenes and its dependence on the cycle size and substituents at phosphorus. The calculated distributions of the electron density Laplacian and electron pair localization functions revealed the special features of the electronic structure of the nitrogen and phosphorus atoms. These results explain the nature of noncovalent interactions between the P atoms of one cyclophosphazene molecule and the N atoms of the other.

A computational study on the enhanced stabilization of aminophenol derivatives by internal hydrogen bonding

The stabilization of aminophenol derivatives and their radicals due to internal hydrogen bonding has been analyzed by means of density functional theory and by topological electron density analysis. The calculations have been carried out at the B3LYP level of theory, using several basis sets, and by means of the CBS-4M composite approach. A strong O–H⋯NH 2 hydrogen bond is found to stabilize the aminophenol with the lone-pair of the nitrogen atom co-planar with the aromatic ring, contrasting with the optimized structure found for aniline. The effect of electron donors and electron acceptors on the strength of the internal hydrogen bond is also analyzed. For one of the species studied, 2,6-diaminophenol, the computed O–H bond dissociation enthalpy is only 300 kJ/mol, the lowest value found so far for phenol and other compounds containing the O–H bond, almost 25 kJ/mol lower than those found experimentally for pyrogallol and for vitamin E. The explanation for such a small value comes from the enhanced stabilization of the corresponding radical species by internal hydrogen bonding, combined with a decrease of the steric effects caused by rotation of the amino groups.

DFT Study of the Monomers and Dimers of 2-Pyrrolidone: Equilibrium Structures, Vibrational, Orbital, Topological, and NBO Analysis of Hydrogen-Bonded Interactions

A computational study of the monomers and hydrogen-bonded dimers of 2-pyrrolidone was executed at different DFT levels and basis sets. The above dimeric complexes were treated theoretically to elucidate the nature of the intermolecular hydrogen bonds, geometry, thermodynamic parameters, interaction energies, and charge transfer. The processes of dimer formation from monomers and concerted reactions of double proton transfer were considered. The evolution of geometry, vibrational frequencies, charge distribution, and AIM properties in going from monomers to dimers was systematically followed. The solvent effects upon dimer formation were investigated in terms of the self-consistent reaction field (SCRF Onsager model). For the monomers and three dimers, vibrational frequencies were calculated and the changes in frequencies of the vibrations most sensitive to complexation were discussed. The orbital interactions were shown to lengthen the X-H (X = N, O) bond and lower its vibrational frequency (a red shift). To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis. Topological analysis of electron density at bond critical points (BCP) was executed for complex molecules using the Bader's atoms in molecules (AIM) theory. The interaction energies were calculated, and the basis set superposition errors (BSSE) were estimated systematically. Satisfactory correlations between the structural parameters, interaction energies, and electron density characteristics at BCP were found.

Revisiting the Electronic Structure of Phosphazenes

Natural bond orbital (NBO) and topological electron density analyses have been used to investigate the electronic structure of phosphazenes [N3P3R6] (R = H, F, Cl, Br, CH3, CF3, N(C2H4); 2R = O2C6H4), [N4P4Cl8], and H[NPCl2]4H. Using the former, the two most likely phosphazene bonding alternatives, negative hyperconjugation and ionic bonding have been critically evaluated. Ionic bonding, as suggested by topological analysis, was found to be the dominant bonding feature, although contributions from negative hyperconjugation are necessary for a more complete bonding description. Substituent effects on the P-N bond have been assessed and cases of bond length alternation have been rationalized using this combined bonding model, which supersedes previous models involving d-orbital participation, leading to an explanation for the observed bond length alternation found in some linear polyphosphazenes. In addition, common aromaticity indicators, nucleus independent chemical shifts (NICS) and para-delocalization indices (PDI), have been determined for the cyclophosphazenes.

Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study

The intrinsic stability of Watson-Crick d(AT) and r(AU) hydrogen bonds was analyzed by employing a variety of quantum-mechanical techniques, such as energy calculations, determination of reactivity indexes, and analysis of electron density topology. The analyses were performed not only for equilibrium gas-phase geometries, but also on hundreds of conformations derived from molecular dynamics (MD) and database analysis. None of our results support the idea that r(AU) hydrogen bonds are intrinsically more stable than those of d(AT). Instead, our data are in accordance with the traditional view that the greater stability of RNA relative to DNA is attributable to a variety of effects (e.g., stacking, sugar puckering, solvation) rather than to a significant difference in the hydrogen bonding of DNA and RNA base pairs.

Atomic interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis

A topological analysis of the experimental electron density in racemic ethylenebis(1-indenyl)zirconium dichloride, C20H16Cl2Zr, measured at 100 (1) K, has been performed. The atomic charges calculated by the numerical integration of the electron density over the zero-flux atomic basins demonstrate the charge transfer of 2.25 e from the Zr atom to the two indenyl ligands (0.19 e to each) and two Cl atoms (0.93 e to each). All the atomic interactions were quantitatively characterized in terms of the electron density and the electronic energy-density features at the bond critical points. The Zr-C2 bond paths significantly curved towards the C1-C2 bond were found; no other bond paths connecting the Zr atom and indenyl ligand were located. At the same time, the pi-electrons of the C1-C2 bond are significantly involved in the metal-ligand interaction. The electron density features indicate that the indenyl coordination can be approximately described as eta1 with slippage towards eta2. The ;ligand-opposed' charge concentrations around the Zr atom were revealed using the Laplacian of the electron density and the one-particle potential; they were linked to the orbital representations. Bonds in the indenyl ligand were characterized using the Cioslowski-Mixon bond-order indices calculated directly from the experimental electron density.

Unconventional interaction in N(P)-related systems

Non-conventional intramolecular and intermolecular interactions have been investigated employing glycine (VIIp), NH 3⋯HCl, NH 3⋯H 2O and PH 3⋯H 2O as model systems. Geometries and harmonic frequencies were determined at a correlated ab initio level, which shows a elongating of the Cl–H or O–H bond of the proton donor and a red-shifting of the corresponding Cl–H or O–H bond stretching frequency. NBO analysis indicates there is a significant charge transfer from the proton acceptor to the proton donor. However, this type of interaction cannot be called hydrogen bond according to a comparative analysis of electron density topology in the four systems.

Studies on the Stablest Geometries and CP Bonding Nature in P‐ylide CH2PH3and P‐ylide‐like Radical ·CHPH3

AbstractStudies on the geometries, electronic structures and bonding nature of P‐ylide CH2PH3and P‐ylide‐like radical ·CHPH3have been carried out at the level of MP4(SDTQ)/6‐311++G(d,p) and B3LYP/6‐311++G(d,p). The CP bonding nature of them was discussed by means of topological analysis of electronic density. The following conclu‐sions were obtained: the CP bonding nature of the P‐ylide‐like radical is similar to that of the P‐ylide, and π bonds exist in both of them. But there are two electrons in the π bond of P‐ylide, while there is only one electron in the π bond of P‐ylide‐like radical,i.e., there is a single‐electron π bond in the P‐ylide‐like radical. The electron in the π bond of P‐ylide‐like radical appears mainly near the carbon atom. The bond CP in P‐ylide‐like radical is weaker than that in the corresponding product, ·CH2PH2.

Treatments of non-nuclear attractors within the theory of atoms in molecules

This Letter describes simple procedures to deal with non-nuclear attractors which are found in some results arising from topological population analyses of the molecular electron density. The proposed treatments have been applied to determine atomic electron populations and bond orders in the acetylene and dilithium molecules, achieving satisfactory chemical results. A detailed discussion of our proposals is reported.

Mechanistic aspects of hydrogen abstraction for phenolic antioxidants. Electronic structure and topological electron density analysis

Density functional calculations using the B3LYP functional are used to provide insight into the hydrogen abstraction mechanism of phenolic antioxidants. The energy profiles for 13 ortho, meta, para and di-methyl substituted phenols with hydroperoxyl radical have been determined. An excellent correlation between the enthalpy (DeltaH) and activation energy (DeltaEa) was found, obeying the Evans-Polanyi rule. The effects of hydrogen bonding on DeltaEa are also discussed. Electron donating groups at the ortho and para positions are able to lower the activation energy for hydrogen abstraction. The highly electron withdrawing fluoro substituent increases the activation energies relative to phenol at the meta position but not at the para position. The electron density is studied using the atoms in molecules (AIM) approach. Atomic and bond properties are extracted to describe the hydrogen atom abstraction mechanism. It is found that on going from reactants to transition state, the hydrogen atom experiences a loss in volume, electronic population and dipole moment. These features suggest that the phenol hydroperoxyl reactions proceed according to a proton coupled electron transfer (PCET) as opposed to a hydrogen atom transfer (HAT) mechanism.

Topological Analysis of Electron Densities: Is the Presence of an Atomic Interaction Line in an Equilibrium Geometry a Sufficient Condition for the Existence of a Chemical Bond?

AbstractContrary to the published acknowledgement, Professor R. F. W. Bader in no way contributed to any of arguments presented in this paper; he has indicated that all of the criticisms raised by the authors were previously discussed and rebuted in J. Chem. Phys. A 1998, 102, 7314.A copy of an earlier version of the manuscript was sent to Professor Bader last spring, and the e‐mail correspondence that followed made it very clear that he disagreed strongly with the conclusions. The authors nevertheless found the discussion useful, since it clarified the nature of the disagreement. Professor Bader's queries also prompted the authors to calculate the dissociation energy of the He@adam inclusion complex and to determine the structure of the transition state as discussed in the article. The authors apologize for omitting to ask for Professor Bader's permission to include his name among the acknowledgements.

MP2 studies of copper complexes with bis(methoxycarbimido)amine and its anion

The geometries of square-planar Cu(mici) 2 n−2 , mici −=HN–C(OCH 3)–N–C(OCH 3)–NH, and Cu(Hmici) 2 n , Hmici=HN–C(OCH 3)–NH–C(OCH 3)–NH, complexes with the copper oxidation state n=1 or 2 are optimized using MP2 treatment. The corresponding electronic structures are investigated in terms of Mulliken population analysis and AIM topological analysis of electron density. In agreement with experimental data, the preferred conformations of the complexes depend on the ligand (mici − prefers the methoxy-group at the central nitrogen whereas Hmici at the side nitrogen atoms) and not on the oxidation state of the central atom. The mechanical strain equilibrium in the metallacycle is changed mainly due to different π bonding of central C–N bonds of the ligands. The shielding by methoxy-groups is the main reason of the preferred site of deprotonation.

Accuracy of topological analysis of gridded electron densities

Topological analysis of electron densities sampled on 3D grids have been performed on two different crystalline compounds—ammonium dihydrogen phosphate and urea—using the software package InteGriTy and the results are compared to that of analytical derivation from the software Newprop and TOPOND. Both critical points and integrated quantities are considered with emphasis put on bond critical points and atomic charges.

Topological analysis of electron densities: is the presence of an atomic interaction line in an equilibrium geometry a sufficient condition for the existence of a chemical bond?

The structure, energetics, and electron density in the inclusion complex of He in adamantane, C10H16, have been studied by density functional theory calculations at the B3LYP6-311++G(2p,2d) level. Topological analysis of the electron density shows that the He atom is connected to the four tertiary tC atoms in the cage by atomic interaction lines with (3,-1) critical points. The calculated dissociation energy of the complex He@adamantane(g)=adamantane(g) + He(g) of DeltaE=-645 kJ mol(-1) nevertheless shows that the He-tC interactions are antibonding.

MP2 studies of the bis(methoxycarbimido)amine ligand and its anion

Various conformations of bis(methoxycarbimido)amine, [HN C(OCH 3)] 2NH (Hmici), and of it anion, [HN C(OCH 3)] 2N − (mici −), have been optimized at MP2 level of theory. Their electronic structures have been investigated in terms of Mulliken population analysis and topological analysis of electron density. The experimentally observed conformations are not the most stable ones and the determining role of the central atom for the geometry and electronic structure of Hmici and mici − complexes may be concluded. The preferential methoxy group positions may be explained by energy arguments of the free ligands. Shielding (especially by methoxy groups) should increase the electron density at the central H atom in Hmici.

Quantum chemical study of the preferential ortho-addition of phenoxyl radicals to nitroso spin-traps II. AIM analysis

The addition of phenoxyl radicals to aromatic nitroso compounds preferentially proceeds in the phenoxyl ortho-position. Using AIM topological analysis of electron density of phenoxyl radical, its methyl- and chloro-derivatives and 2,3,5,6-tetramethyl-1-nitrosobenzene evaluated at MP2/6-311G** level of theory, the electron density at the carbon atom of the phenoxyl radical (the highest in ortho-position) is confirmed as the driving force of this reaction in agreement with previously used Mulliken population analysis.

Comparative study of non-planar cyclotetraphosphazenes and their isostructural hydrocarbon analogues

Using MP2/cc-pVDZ treatment, the optimal conformations of cyclo-(NPH 2) 4 and cyclo-(CCH 2) 4 are investigated. Only C 4 v , D 2 d (with N atoms alternating above and below the four P atoms plane) and two different C 2 h stable cyclo-(NPH 2) 4 structures (the D 2 d one being the most stable) have been found. Only two different D 2 d and one C 2 h (with CH 2 in the mirror plane) stable cyclo-(CCH 2) 4 structures (the C 2 h one being the most stable) have been found. The deviations of bond length characteristics from the D 4 h conformation are higher in the phosphazene than in its hydrocarbon analogue but the reverse relation is true for the bond angles. This is in agreement with the picture of two perpendicular π bonds in phosphazenes and only one in their hydrocarbon analogues. Topological analysis of electron density has confirmed this picture.