Atomic and bond topological properties of the tripeptide L-alanyl-L-alanyl-L-alanine based on its experimental charge density obtained at 20 K

A 20 K high resolution X-ray data set of L-Ala-L-Ala-L-Ala*1/2 H2O was measured using an ultra-low temperature laboratory setup, that combines area detection and a closed cycle helium cryostat. The charge density determination includes integration of atomic basins and topological analysis according to Bader's quantum theory of atoms in molecules. Two tripeptide units are found in the asymmetric unit, allowing the assessment of transferability of bond topological and atomic properties taking also into consideration previous data of oligopeptides. With respect to invariom modeling the limits of such transferability are investigated and the results of this study show the validity of the nearest/next-nearest neighbour approximation and support the use of database approaches for electron density modeling of macromolecules.     

A reactive bond orbital investigation of the Diels-Alder reaction between 1,3-butadiene and ethylene: Energy decomposition, state correlation diagram, and electron density analyses

The reactive bond orbital (RBO) method (Hirao, Chem Phys Lett 2007, 443, 141) is extended and applied to the Diels-Alder reaction between 1,3-butadiene and ethylene, with the aim of understanding the nature of their interaction. The roles of distortion, electrostatic, exchange, polarization, and charge transfer (CT) interaction energies at the transition state of the reaction are evaluated by means of RBO energy decomposition analysis. The effects of the hypothetical interactions on electron density redistribution are also identified by analysis based on the RBO method. CT is shown to play essential roles in the new bond formation between the reacting molecules and their internal bond order alterations. However, each of the CT interactions from butadiene to ethylene and from ethylene to butadiene does not necessarily contribute to the bond-order alteration process effectively. A state correlation diagram approach based on the RBO method is also proposed, and its usefulness in understanding the origin of the barrier in the Diels-Alder reaction is demonstrated.     

Interactions of glutathione tripeptide with gold cluster: influence of intramolecular hydrogen bond on complexation behavior

Understanding the nature of the interaction between metal nanoparticles and biomolecules has been important in the development and design of sensors. In this paper, structural, electronic, and bonding properties of the neutral and anionic forms of glutathione tripeptide (GSH) complexes with a Au(3) cluster were studied using the DFT-B3LYP with 6-31+G**-LANL2DZ mixed basis set. Binding of glutathione with the gold cluster is governed by two different kinds of interactions: Au-X (X = N, O, and S) anchoring bond and Au···H-X nonconventional hydrogen bonding. The influence of the intramolecular hydrogen bonding of glutathione on the interaction of this peptide with the gold cluster has been investigated. To gain insight on the role of intramolecular hydrogen bonding on Au-GSH interaction, we compared interaction energies of Au-GSH complexes with those of cystein and glycine components. Our results demonstrated that, in spite of the ability of cystein to form highly stable metal-sulfide interaction, complexation behavior of glutathione is governed by its intramolecular backbone hydrogen bonding. The quantum theory of atom in molecule (QTAIM) and natural bond orbital analysis (NBO) have also been applied to interpret the nature of interactions in Au-GSH complexes. Finally, conformational flexibility of glutathione during complexation with the Au(3) cluster was investigated by means of monitoring Ramachandran angles.     

Inclusion of thymol into cucurbiturils: density functional theory approach with dispersion correction and natural bond orbital analysis

Journal of Inclusion Phenomena and Macrocyclic Chemistry - Stability of inclusion complexes of thymol (a natural flavour) with cucurbit[n]urils was interpreted by using density functional theory...     

N, P, and As ylides and aza- and arsa-Wittig reactions from topological analyses of electron density

The nature of bonding between N, P, and As constituent atoms in ylide systems with the R(3)XYR' formula (X = N, P, As; Y = N, P, As; R = F, H; R' = H, CH(3)) has been characterized by ab initio (MP2/6-311++G**) and density functional theory (B3LYP/6-311++G**) calculations. Its electronic structure has been analyzed through electron density with the quantum theory of atoms in molecules and the electron localization function (ELF). The characteristics of the central bond are inspected with the calculated rotational barriers. The results show that N has a behavior different from that of the remaining pnicogen atoms (P, As), where the bond is much stronger. Fluorine substituents strengthen the X-Y bond, reduce the bond distance, and increase the electron density in the central bond so that the substituent pulls charge from the bond in the pnicogen X atom. For the N-pnicogen ylides, the results showed different bonding characters between F and X atoms; depending on the position of the F atom, the difference of the bond character is sensed by the basin synaptic order, as it is deduced from the analysis of the ELF basins. The energy profiles of the rotational barriers have been calculated at the MP2/6-311++G** level, indicating that the electronegativity of the substituents is a relevant factor that has consequences in the characteristics of the X-Y bond.     

Localization maps by orbital partitioning of the electron density

Summary We define a localization measure for one-determinantal wave-functions based on the partitioning of the total electron density to orbital contributions. The set of occupied orbitals is the more localized the fewer terms are necessary to describe the total density. This measure varies from point to point in space which leads to characteristic localization maps for molecules.Supported in part by the grant Hungarian Research Fund OTKA 517/1990     

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.     

An orbital localization criterion based on the topological analysis of the electron localization function

This work proposes a new molecular orbital localization procedure. The approach is based on the decomposition of the overlap matrix in accordance with the partitioning of the three‐dimensional physical space into basins with clear chemical meaning arising from the topological analysis of the electron localization function. The procedure is computationally inexpensive, provides a straightforward interpretation of the resulting orbitals in terms of their localization indices and basin occupancies, and preserves the σ/π‐separability in planar N‐electron systems. The localization algorithm is tested on selected molecular systems. © 2012 Wiley Periodicals, Inc.     

Static and dynamic second hyperpolarizability calculated by time-dependent density functional cubic response theory with local contribution and natural bond orbital analysis

The static and dynamic second hyperpolarizability gamma has been investigated by time-dependent density functional cubic response theory. The third-order coupled perturbed Kohn-Sham equations were solved to obtain the third-order perturbed charge density. Calculations on a number of small molecules (N(2), CO(2), C(2)H(4), CO, HF, H(2)O, and CH(4)), paradisubstituted oligoacetylene chains, benzene, and eight paradisubstituted benzenes were performed to verify the implementation and to assess the accuracy of the nonhybrid and hybrid time-dependent density functional theory computations. Nitroaniline and a derivative were taken as examples to investigate the distribution of the "gamma density" and to demonstrate the feasibility of analyzing cubic response functions in terms of contributions from natural bond orbitals (NBOs) and natural localized molecular orbitals (NLMOs). The results highlight the contributions from atoms and bonds on different functional groups to the total value of gamma based on the NBO/NLMO analysis, which might be helpful for new nonlinear optical materials design.     

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     

Study of static and dynamic first hyperpolarizabilities using time-dependent density functional quadratic response theory with local contribution and natural bond orbital analysis

We apply time-dependent density-functional quadratic response theory to investigate the static and dynamic second-order polarizabilities (first hyperpolarizability) beta. A new implementation using Slater-type basis functions, numerical integration, and density fitting techniques is reported. The second order coupled perturbed Kohn-Sham equations are solved and the second-order perturbed charge density is obtained. It is useful to highlight atomic and bond contributions to understand the relation between molecular structure and properties. Four moderately sized molecules (para-nitroaniline and derivatives thereof) are investigated to assess the accuracy of the time-dependent density-functional theory computations and to investigate the distribution of the second-order charge density as well as the "beta density." Our results highlight the contributions from atoms and bonds on different functional groups to the total value of beta with Mulliken-type and natural bond orbital (NBO) analyses, and demonstrate in some cases how contributions from a particular bond may be identified easily by visual inspection of the beta density. In addition, the position of side group substitution on carbon-carbon bonds significantly affects the hyperpolarizability. A contribution analysis as performed here might be helpful for the design of new materials with desired properties.     

Application of natural bond orbital analysis to delocalization and aromaticity in C-substituted tetrazoles.

Energies of two tautomeric forms of 10 tetrazole derivatives substituted at C5 were established by DFT/B3LYP calculations carried out at the 6-311++G level. In each case the calculated energy of the 2H-tautomer was lower than that of the 1H. Furthermore, three geometric aromaticity indices of both forms were calculated, as were the values of nuclear independent nuclear shift and aromatic stabilization energy. The electronic properties were evaluated with the help of the natural bonding orbital theory. Following this a new pi-delocalization parameter, the root-mean square of pi-electron density localized on the atoms of the five-membered tetrazole ring, SDn, was introduced. It was concluded that the electronic delocalization can be described equally well by three different parameters: SDn, the extent of the transfer of electron density from the p(z) orbital of one nitrogen to the rest of the pi electron system, and population of two antibonding pi orbitals. Arguably, the information provided by the electronic parameters is similar to that contained in the geometric (structural) aromaticity indices except for tetrazole substituted by -BH(2).     

Spectroscopic, electronic structure and natural bond orbital analysis of o-fluoronitrobenzene and p-fluoronitrobenzene: a comparative study

Experimental FTIR, FT-Raman and FT-NMR spectroscopic studies of o-fluoronitrobenzene and p-fluoronitrobenzene have been carried out. A detailed quantum chemical calculations have been performed using DFT/B3LYP method with 6-311++G** and 6-31G** basis sets. Complete vibrational analyses of the compounds were performed. The temperature dependence of thermodynamic properties has been analysed. The atomic charges, electronic exchange interaction and charge delocalisation of the molecule have been performed by natural bond orbital (NBO) analysis. Molecular electrostatic surface potential (MESP), total electron density distribution and frontier molecular orbitals (FMOs) are constructed at B3LYP/6-311++G** level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecules have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecules in chloroform solvent and in gas phase were calculated by using the Gauge-Independent Atomic Orbital (GIAO) method and are found to be in good agreement with experimental values. The theoretical parameters obtained at B3LYP levels have been compared with the experimental values.     

The effect of electron correlation on the topological and atomic properties of the electron density distributions of molecules

The topological properties of the electron density and the properties of an atom in a molecule are calculated by means of second-order Møller-Plesset perturbation theory (MP2) and compared with the results of configuration interaction calculations (C12) which include all single and double substitutions from the Hartree-Fock reference configuration. A software package for analyzing the effects of electron correlation on the topological properties of the electron density of molecules is described. H₂CO is used to provide a numerical example and to indicate that the number of bond critical points is unaffected by the inclusion of electron correlation. Correlation leads to only a small shift in the positions of bond critical points and a small change in the electron density at bond critical points. It is further shown that the energy of an atom in a molecule can be calculated to an accuracy of 1 kcal/mol and the electron population of an atom to about 0.001e. A statistical method is used to show that the deviation of the MP2 correlation correction relative to the CI2 correlation correction for a variety of atomic properties is about 25%.