NBO 6.0: Natural bond orbital analysis program

We describe principal features of the newly released version, NBO 6.0, of the natural bond orbital analysis program, that provides novel “link‐free” interactivity with host electronic structure systems, improved search algorithms and labeling conventions for a broader range of chemical species, and new analysis options that significantly extend the range of chemical applications. We sketch the motivation and implementation of program changes and describe newer analysis options with illustrative applications. © 2013 Wiley Periodicals, Inc.     

Natural resonance structures and aromaticity of the nucleobases

Natural resonance theory (NRT) and nucleus- independent chemical shift (NICS) analyses have been applied to the standard nucleobases adenine, guanine, cytosine, uracil, and thymine. The molecular electron densities were obtained from density functional theory calculations at the B3LYP level and ab initio calculations at the HF, MP2, and CCD levels. Compared with the dominance of the two Kekulé structures in benzene, the structural modifications in the forms of endocyclic heteroatoms and exocyclic substituents introduce various degrees of charge separation in nucleobases. As a result, the leading resonance structures for cytosine, uracil, and thymine are found to be covalent structures, but their weightings decrease to ~30% in the NRT expansion. For adenine and guanine, the covalent structures have weightings of ~20%, and the leading ionic resonance structures have weightings of as high as about 8%. Methods that include electron correlation effects, B3LYP, MP2, and CCD, give smaller weightings for the covalent structures than HF. However, MP2 and CCD results often include “strange” resonance structures with connections between unbonded vicinal atoms, making DFT at the B3LYP level the better choice for calculating these molecules’ electron density. The NICS at the ring center shows that the six-membered rings in cytosine, uracil, thymine, and guanine are nonaromatic with NICS within − 3 to − 1 ppm, while it is − 7.3 ppm for the six-membered ring in adenine. The NICS of the five-membered rings of adenine and guanine is around − 12 ppm, a slight decrease from the value of − 15.0 ppm for pyrrole.     

Chemical applications of topology and group theory

The 60 even permutations of the ligands in the five-coordinate complexes, ML ₅, form the alternating group A ₅, which is isomorphic with the icosahedral pure rotation group I. Using this idea, it is shown how a regular icosahedron can be used as a topological representation for isomerizations of the five-coordinate complexes, ML ₅, involving only even permutations if the five ligands L correspond either to the five nested octahedra with vertices located at the midpoints of the 30 edges of the icosahedron or to the five regular tetrahedra with vertices located at the midpoints of the 20 faces of the icosahedron. However, the 120 total permutations of the ligands in five-coordinate complexes ML ₅ cannot be analogously represented by operations in the full icosahedral point group I _h, since I _his the direct product I×C₂ whereas the symmetric group S ₅ is only the semi-direct product A ₅S₂. In connection with previously used topological representations on isomerism in five-coordinate complexes, it is noted that the automorphism groups of the Petersen graph and the Desargues-Levi graph are isomorphic to the symmetric group S ₅ and to the direct product S ₅×S ₂, respectively. Applications to various fields of chemistry are briefly outlined.     

Intermolecular interactions in uracil–nitrous acid complexes: structures,binding energy,topological properties,and nuclear magnetic resonance study

Molecular interactions between uracil and nitrous acid (U–NA) [C₄N₂O₂H₄? NO₂H] have been studied using B3LYP, B3PW91, and MP2 methods with different basis sets. The optimized geometries, harmonic vibrational frequencies, charge transfer, topological properties of electron density, nucleus‐independent chemical shift (NICS), and nuclear magnetic resonance one‐ and two‐bonds spin–spin coupling constants were calculated for U–NA complexes. In interaction between U and NA, eight cyclic complexes were obtained with two intermolecular hydrogen bonds N(C)HU…N(O) and OH_NA…O_U. In these complexes, uracil (U) simultaneously acts as proton acceptor and proton donor. The most stable complexes labeled, UNA1 and UNA2, are formed via NH bond of U with highest acidity and CO group of U with lowest proton affinity. There is a relationship between hydrogen bond distances and the corresponding frequency shifts. The solvent effect on complexes stability was examined using B3LYP method with the aug‐cc‐pVDZ basis set by applying the polarizable continuum model (PCM). The binding energies in the gas phase have also been compared with solvation energies computed using the PCM. Natural bond orbital analysis shows that in all complexes, the charge transfer takes place from U to NA. The results predict that the Lone Pair (LP)(O)_U → σ*(O? H) and LP(N(O)_NA → σ*(N(C)? H)_U donor–acceptor interactions are most important interactions in these complexes. Atom in molecule analysis confirms that hydrogen bond contacts are electrostatic in nature and covalent nature of proton donor groups decreases upon complexation. The relationship between spin–spin coupling constant (^1hJ_H…_Y and ^2hJ_H…_Y) with interaction energy and electronic density at corresponding hydrogen bond critical points and H‐bonds distances are investigated. NICS used for indicating of aromaticity of U ring upon complexation. © 2013 Wiley Periodicals, Inc.     

Natural bond orbital analysis: A critical overview of relationships to alternative bonding perspectives

We sketch the basic principles of natural bond orbital (NBO) theory, including critical discussion of its relationship to alternative bonding concepts and selected illustrations of its application to a broad spectrum of chemical bonding motifs. Particular emphasis is placed on the close NBO connections to prequantal bonding, and electromerism concepts, as well as the deep roots in quantal eigenvalue, superposition, and Pauli exclusion concepts that are manifested in many aspects of NBO donor–acceptor analysis. With respect to leading alternative perspectives, we identify similarities and differences that distinguish NBO theory from the corresponding precepts of valence bond theory, molecular orbital theory, and Bader's quantum theory of atoms in molecules, with critical discussion of the assumptions underlying characteristic differences in each case. © 2012 Wiley Periodicals, Inc.     

Chemical applications of group theory and topology

The following procedure is described for investigating the qualitative dynamics of simple chemical systems: 1) A so-called influence diagram is generated representing the relationships between the reference reactants (phase-determining intermediates); 2) This influence diagram is used to generate a truth table indicating possible transitions between state vectors representing the signs of the time derivatives of of the reference reactant concentrations; 3) The truth table is used to determine a state transition diagram representing the flow topology around unstable equilibrium points; 4) The characteristic equation of the adjacency matrix of the influence diagram is solved in order to determine the presence of such unstable equilibrium points. The two types of qualitative dynamics possible for chemical systems containing two reference reactants and one feedback circuit are bifurcation between two attracting regions (bistability) and limit cycle oscillation. However, in two reference reactant systems oscillation requires an additional self-activating loop to generate the unstable equilibrium point required for its realization. Bistability and limit cycle oscillation are also two of the possible types of qualitative dynamics for chemical systems containing three reference reactants. However, chemical systems with three reference reactants and two or more feedback circuits can also contain interlocking limit cycles, which can lead to toroidal oscillations or chaos. The influence diagrams are given for the systems exhibiting these various types of dynamic behavior along with a summary of the important properties of all 729 possible influences for simple chemical systems containing three reference reactants.     

Orthogonal natural atomic orbitals form an appropriate one-electron basis for expanding CASSCF wave functions into localized bonding schemes and their weights

Localized bonding schemes and their weights have been obtained for the pi-electron system of nitrone by expanding complete active space self-consistent field wave functions into a set of Slater determinants composed of orthogonal natural atomic orbitals (NAOs) of Weinhold and Landis (Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective, 2005). Thus, the derived bonding schemes are close to orthogonal valence bond structures. The calculated sequence of bonding scheme weights accords with the sequence of genuine resonance structure weights derived previously by Ohanessian and Hiberty (Chem Phys Lett 1987, 137, 437), who employed nonorthogonal atomic orbitals. This accord supports the notion that NAOs form an appropriate orthogonal one-electron basis for expanding complete active space self-consistent field wave functions into meaningful bonding schemes and their weights.     

Fock space multireference coupled cluster theory: Study of shape resonance

The complex absorbing potential along with correlated independent particle potential (CIP) Fock space multireference coupled cluster method is used for the study of resonances. We have studied shape resonance of e^?‐ F₂, e^?‐ N₂O and e^?‐CO molecules. In particular, we have studied e^?‐ F₂ scattering at different bond lengths to know whether is bound at the equilibrium bond length of F₂. © 2013 Wiley Periodicals, Inc.     

A nuclear magnetic resonance study of toluene-polyisobutylene solutions. 2. Vrentas-Duda theory

The self-diffusion coefficients of toluene in polyisobutylene have been analyzed using the Vrentas-Duda free volume diffusion model. The diffusion coefficients were determined at different temperatures and concentrations, using the pulsed field gradient nuclear magnetic resonance technique. The data were satisfactorily described by the model and the size of the polymer jumping unit was extracted. Comparisons were made with the Fujita free volume theory and the Fujita free volume parameters were extracted from the Vrentas-Duda free volume parameters. From the diffusion data that now available, it can be concluded that for most polymers the jumping unit is about 1.5 times the polymer monomer molecular weight. The activation energy of the toluene diffusion in polyisobutylene is compared with the activation energies of other penetrants in the same polymer. The diffusion data presented in this work show that the energy per mole required to overcome the attractive forces which constrain a diffusing species to its neighbors should be considered to be zero, in order to be able to extract the free volume parameters (from viscosity and diffusion data) with an acceptable uncertainty. ©1995 John Wiley & Sons, Inc.     

In-Situ Electronegativity and the Bridging of Chemical Bonding Concepts

One challenge in chemistry is the plethora of often disparate models for rationalizing the electronic structure of molecules. Chemical concepts abound, but their connections are often frail. This work describes a quantum-mechanical framework that enables a combination of ideas from three approaches common for the analysis of chemical bonds: energy decomposition analysis (EDA), quantum chemical topology, and molecular orbital (MO) theory. The glue to our theory is the electron energy density, interpretable as one part electrons and one part electronegativity. We present a three-dimensional analysis of the electron energy density and use it to redefine what constitutes an atom in a molecule. Definitions of atomic partial charge and electronegativity follow in a way that connects these concepts to the total energy of a molecule. The formation of polar bonds is predicted to cause inversion of electronegativity, and a new perspective of bonding in diborane and guanine−cytosine base-pairing is presented. The electronegativity of atoms inside molecules is shown to be predictive of pK_a.     

NMR of Natural Products as Potential Drugs

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.     

A nuclear magnetic resonance study of dynamics in toluene-polyisobutylene solutions: 1. Penetrant diffusion and Fujita theory

The self-diffusion coefficients of toluene in polyisobutylene (PIB) solutions were determined using the pulsed field gradient nuclear magnetic resonance technique. The volume fraction of toluene in the polymer was varied from 0.045 up to 0.712 and the temperature was varied from 225 K up to 368 K. The concentration dependence of the data was interpreted using the Fujita free volume theory and the temperature dependence was interpreted with the WLF equation. These models describe separately the concentration and temperature dependencies of the toluene self-diffusion coefficients very well and the resulting free volume parameters are in good agreement with the ones extracted from the analysis of viscosity data on the same system. ©1995 John Wiley & Sons, Inc.