Chemical interpretation of molecular electron density distributions

In this study, the two small molecules HS(CH)(CH(2)), 1, and F(CH)(4)F, 2, are presented, which yield different chemical interpretations when one and the same density is interpreted either by means of Natural Bond Orbital and subsequent Natural Resonance Theory application or by the Quantum Theory of Atoms In Molecules. The first exhibits a S-C bond in the orbital based approach, whereas the density based Quantum Theory of Atoms In Molecules detects no corresponding bond. In F(CH)(4)F a F...F bond is detected in the density based approach, whereas in the orbital based approach no corresponding bond is found. Geometrical reasons for the presence of unexpected and the absence of expected bond critical points are discussed.     

Electron momentum density distribution in homonuclear diatomic molecules

Individual orbital contributions to the electron momentum densities of first-row homonuclear diatomic molecules are discussed. It is shown that the nodal surfaces in the orbital EMDs arise from a diffraction factor with both geometric and electronic components. The positions of the nodal surfaces convey information on the electronic structure. The results are illustrated with a Hartree-Fock-Slater calculation of the F₂(X¹Σ_g⁺) molecule.     

A molecular connectivity study of electron density in alkanes

Molecular connectivity indices have been developed which characterize contributions of neighboring atoms to the CNDO/2 calculated electronic charge of a carbon atom. An analysis of these indices reveals their ability to predict this charge to 0.001 electron.     

The bond nature of alkaline-earth homonuclear metal clusters investigated with pseudopotential CI method

The electronic stucture of Be_l, Mg_m and Ca_n ( 1? 7, m and n ? 5) metal clusters has been investigated by means of an ab initio pseudopotential method followed by multireference double-excitation configuration interaction (PP MRD CI). Two completely different situations arise on going from Be to heavier alkaline metals. The sp hybridization, which is effective in the Be case, completely disappears when aggregates of Mg and Ca are considered. The potential energy curves relative to Be, Mg and Ca clusters exhibit a very shallow minimum at large distances while a second deeper minimum is characteristic of some Be clusters. This inner minimum is generated by the large interaction of atomic p orbitals at an internuclear separation close to the BeBe distance present in the Be crystal. The bond in Be clusters largely depends on the geometrical arrangement which directly influences the possible sp hybridisation. Very small Be planar structures are always less favored with respect to clusters containing the tetrahedral unit as a part of the whole structure. However, this situation is changed when larger planar clusters are considered, and the highest binding energy per atom (12.0 kcal/mole) from all clusters considered in this work was found for the triplet ground state of the planar Be₇(D_6h) cluster.     

Transfer of electron density as a result of hydrogen bond formation

It has been found that the amount of charge transfer between donor and acceptor molecules in four sets of hydrogen‐bonded complexes may be adequately described as an exponential function of the equilibrium distance between the hydrogen atom and the nearest atom of the acceptor molecule. The exponential factors of the transfer are of the same order but somewhat larger than the factors found otherwise in the investigations of dynamic electron transfer. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Redox-active tyrosine residues: role for the peptide bond in electron transfer

Photosystem II (PSII) catalyzes the light-driven oxidation of water and reduction of plastoquinone. In PSII, redox-active tyrosine Z conducts electrons between the primary chlorophyll donor and the manganese cluster, which is the catalytic site. In this report, difference FT-IR spectroscopy is used to show that oxidation of redox-active tyrosine Z causes perturbations of the peptide bond. PSII data were acquired on control samples, as well as samples in which tyrosine was 2H4 (ring)-labeled. Comparison to model compound data, acquired both from tyrosinate and its 2H4 isotopomer, was performed. The PSII FT-IR spectrum exhibited vibrational bands that are assignable to imide and amide vibrational modes. In previous work, we have shown that oxidation of tyrosinate perturbs the terminal amino group of tyrosinate (Ayala, I.; Range, K.; York, D.; Barry, B. A. J. Am. Chem. Soc. 2002, 124, 5496-5505). Density functional calculations on tyrosinate supported the interpretation that the perturbation is due to spin delocalization onto the amino group. In tyrosine-containing dipeptides, perturbations of the peptide bond were observed. Therefore, the imide and amide perturbations observed here are attributed to spin delocalization into the peptide bond in PSII. Migration of the electron hole in PSII may be consistent with peptide bond involvement in tyrosyl radical-based electron-transfer reactions.     

On the role of localized molecular orbitals in the formation of bond dipoles

The hypothesis of the classical chemistry about bond dipoles resulting from shifts of separate pairs of electrons is proved using the non-canonical method of molecular orbitals (MOs). To this end, a relation is sought between the total charge distribution inside an individual chemical bond of a polyatomic molecule and the square of the respective single localized MO (LMO). General expressions for these MOs are obtained directly on the basis of the Brillouin theorem without invoking additional localization criteria. The two characteristics under comparison are presented in an explicit algebraic form in terms of meaningful components. Reshaping of square of the ‘own’ LMO of the given bond is shown to play the decisive role in the formation of secondary dipoles of initially homopolar bonds (e.g. of C–C and C–H bonds in substituted alkanes), as well as of bonds of relatively low initial polarity. Thus, representability of these dipoles by shifts of the ‘own’ pairs of electrons of respective bonds is supported. For bonds of a high initial polarity, the secondary dipoles are shown to originate mainly from contributions of LMOs of other bonds extending over the antibonding basis orbital of the given bond. Moreover, the actual secondary bond dipole takes an opposite direction vs. that predicted by the shift of the respective ‘own’ pair of electrons in this case. The latter result serves to account for the known low nucleofugality of highly electronegative heteroatoms in the S_N2 reactions.     

Characterization of a trihydrogen bond on the basis of the topology of the electron density

Recent DFT calculations have predicted unexpected molecular structures for the ion induced dipole clusters H(n)(-) (3 ≤ n-odd ≤ 13). Analysis of these calculations suggests the definition of a new bond, called the trihydogen bond (THB). This is placed in context by a review and classification of multihydrogen interactions as usually discussed in the literature. The results of analysis related to the trihydrogen bond are presented. These include a series of linear relations exhibited by the H(n)(-) clusters involving the charge carried by the central H(-) ion, the binding energy of the clusters, and the relative stabilization of the central anion H(-) with respect to the energy of a free H(-) atom.     

Electronegativity estimator built on QTAIM‐based domains of the bond electron density

The electron localization function, natural localized molecular orbitals, and the quantum theory of atoms in molecules have been used all together to analyze the bond electron density (BED) distribution of different hydrogen‐containing compounds through the definition of atomic contributions to the bonding regions. A function, g_AH, obtained from those contributions is analyzed along the second and third periods of the periodic table. It exhibits periodic trends typically assigned to the electronegativity (χ), and it is also sensitive to hybridization variations. This function also shows an interesting S shape with different χ‐scales, Allred–Rochow's being the one exhibiting the best monotonical increase with regard to the BED taken by each atom of the bond. Therefore, we think this χ can be actually related to the BED distribution. © 2014 Wiley Periodicals, Inc.     

Structure of molecular energy levels of homonuclear diatomic molecules

A new approach is given for the systematic prediction of the low‐lying electronic states of homonuclear diatomic molecules. The approach is based on the bond order and the energy levels of the separated atoms. The asymptotic wave functions are derived from two atomic wave functions by using new operators defined as linear combinations of certain ladder operators. We show that the low angular moment states tend to have a high bond order in the states derived from an asymptote. The observed low‐lying states of C₂, C, Sc₂, and Ti₂ molecules agree with the predictions. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 597–604, 1999     

The electron density of the water molecule

The electron density of the water molecule, as calculated by a standard program, is approximated by linear combinations of spherical Gaussians. The accuracy of the result is studied as a function of the numbers and positions of the Gaussians. Since this shows where the charge is located in the molecule it has immediate physical significance. The building-up of the density can be followed in more and more detail. From these expansions, point charge models of water are readily deduced. These are compared with models of similar kinds used by other authors. Some of the calculations have been repeated with a wavefunction of higher accuracy to investigate the stability of the results. Results show that the more accurate density requires more Gaussians to represent its greater complexity.     

Elastic forward scattering of high-energy electrons and molecular electron density

The elastic forward scattering of high-energy electrons from molecules has been studied in the second Born approximation. An integral transformation has been adopted to evaluate the second Born integrals analytically without explicit use of molecular wave functions. In the high-energy limit, the differential cross section for the forward scattering is expressed in terms of electric dipole and quadrupole moments, the second moment of charge distribution with respect to the molecular center, and transition dipole moments. All these quantities are shown to be computable from molecular electron densities in the ground state.     

On the evaluation of molecular electron affinities by approximate density functional theory

The ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH₃, NH₂, OH, and HC₂ as well as the multibonded species CN, BO, N₃, OCN, and NO₂. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EA_ad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EA_ad by 0.2 eV. It is concluded that the LDA/NL method affords EA_ad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.     

The carbenoid-type reactivity of simplest nitrile imine from a molecular electron density theory perspective

The [3 + 2] cycloaddition (32CA) reactions of the simplest nitrile imine with ethylene and electrophilic dicyanoethylene have been studied within the Molecular Electron Density Theory (MEDT) with the aim of characterising its reactivity. Topological analysis of the electron localisation function of NI shows that it has a carbenoid structure. The activation energy of the 32CA reaction of the simplest nitrile imine with dicyanoethylene is 5.6 kcal mol^?1 lower than that involving ethylene, in agreement with the high polar character of the former reaction. Bonding Evolution Theory accounts for the cb-type reactivity of nitrile imine. Along the more favourable ortho regioisomeric path associated with the 32CA reaction involving dicyanoethylene, which takes place through a non-concerted two-stage one-step mechanism, formation of the first C3-C4 single bond takes place at a C-C distance of 2.02?Å, by donating the non-bonding electron density of the carbenoid center of nitrile imine to the β-conjugated C4 carbon of dicyanoethylene.