Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.     

Trends in Conjugated Chalcogenophenes: A Theoretical Study

Heavy atom substitution in chalcogenophenes is a versatile strategy for tailoring and ultimately improving conjugated polymer properties. While thiophene monomers are commonly implemented in polymer designs, relatively little is known regarding the molecular properties of the heavier chalcogenophenes. Herein, we use density functional theory (DFT) calculations to examine how group 16 heteroatoms, including the radioactive polonium, affect polychalcogenophene properties including bond length, chain twisting, aromaticity, and optical properties. Heavier chalcogenophenes are more quinoidal in character and consequently have reduced band gaps and larger degrees of planarity. We consider both the neutral and radical cationic species. Upon p-type doping, bond length rearrangement is indicative of a more delocalized electronic structure, which combined with optical calculations is consistent with the polaron-model of charge storage on conjugated polymer chains. A better understanding of the properties of these materials at their molecular levels will inevitably be useful in material design as the polymer community continues to explore more main group containing polymers to tackle issues in electronic devices.     

autoCAS: A Program for Fully Automated Multiconfigurational Calculations

We present our implementation autoCAS for fully automated multiconfigurational calculations, which we also make available free of charge on our webpages. The graphical user interface of autoCAS connects a general electronic structure program with a density-matrix renormalization group program to carry out our recently introduced automated active space selection protocol for multiconfigurational calculations (Stein and Reiher, J. Chem. Theory Comput., 2016, 12, 1760). Next to this active space selection, autoCAS carries out several steps of multiconfigurational calculations so that only a minimal input is required to start them, comparable to that of a standard Kohn–Sham density-functional theory calculation, so that black-box multiconfigurational calculations become feasible. Furthermore, we introduce a new extension to the selection algorithm that facilitates automated selections for molecules with large valence orbital spaces consisting of several hundred orbitals. © 2019 Wiley Periodicals, Inc.     

PyCDFT: A Python package for constrained density functional theory

We present PyCDFT, a Python package to compute diabatic states using constrained density functional theory (CDFT). PyCDFT provides an object-oriented, customizable implementation of CDFT, and allows for both single-point self-consistent-field calculations and geometry optimizations. PyCDFT is designed to interface with existing density functional theory (DFT) codes to perform CDFT calculations where constraint potentials are added to the Kohn–Sham Hamiltonian. Here, we demonstrate the use of PyCDFT by performing calculations with a massively parallel first-principles molecular dynamics code, Qbox, and we benchmark its accuracy by computing the electronic coupling between diabatic states for a set of organic molecules. We show that PyCDFT yields results in agreement with existing implementations and is a robust and flexible package for performing CDFT calculations. The program is available at https://dx.doi.org/10.5281/zenodo.3821097 .     

Very Long‐Range Effects: Cooperativity between Anion–π and Hydrogen‐Bonding Interactions

The interplay between two important non‐covalent interactions involving aromatic rings (namely anion–π and hydrogen bonding) is investigated. Very interesting cooperativity effects are present in complexes where anion–π and hydrogen bonding interactions coexist. These effects are found in systems where the distance between the anion and the hydrogen‐bond donor/acceptor molecule is as long as ～11 Å. These effects are studied theoretically using the energetic and geometric features of the complexes, which were computed using ab initio calculations. We use and discuss several criteria to analyze the mutual influence of the non‐covalent interactions studied herein. In addition we use Bader’s theory of atoms‐in‐molecules to characterize the interactions and to analyze the strengthening or weakening of the interactions depending upon the variation of the charge density at the critical points.     

Geometric and electronic structure of methane adsorbed on a Pt surface

The electronic structure of methane adsorbed on Pt(977) is investigated using angle-resolved x-ray absorption spectroscopy (XAS) in combination with density functional theory spectrum calculations. XAS, which probes the unoccupied states atom specifically, shows the appearance of the symmetry-forbidden gas-phase lowest unoccupied molecular orbital due to s-p rehybridization. In addition new adsorption-induced states appear just above the Fermi level. A systematic investigation, where computed XA spectra are compared with the experiment, indicates elongation of the C-H bond pointing toward the surface to 1.18+/-0.05 A. The bond elongation arises due to mixing between bonding and antibonding C-H orbitals. Computed charge density difference plots show that no covalent chemical bond is formed between the adsorbate and substrate upon adsorption. The changes in electronic structure arise in order to minimize the Pauli repulsion by polarizing charge away from the surface toward the carbon atom of the methane molecule.     

Probing the electronic structure,chemical bonding,and excitation spectra of [CuE]+/0/− (E = 14 group element) diatomics employing DFT and ab initio methods

The electronic structure, chemical bonding, and excitation spectra of neutral, cationic, and anionic diatomic molecules of Cu and 14 group elements formulated as [CuE]^+/0/? (E = C, Si, Ge, Sn, Pb) were investigated by density functional theory (DFT) and time‐dependent (TD)‐DFT methods. The electronic and bonding properties of the diatomics analyzed by natural bond orbital (NBO) analysis approch revealed a clear picture of the chemical bonding in these species. The spatial organization of the bonding between Cu and E atoms in the [CuE]^+/0/? (E = Si, Ge, Sn, Pb) molecules can easily be recognized by the cut‐plane electron localization function representations. Particular emphasis was given on the absorption spectra of the [CuE]^+/0/? which were simulated using the results of TD‐DFT calculations employing the hybrid Coulomb‐attenuating CAM‐B3LYP functional. The absorption bands have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made. © 2012 Wiley Periodicals, Inc.     

Bond critical points in the electronic structures of the main group diatomic hydrides of lithium through bromine

The bond critical points and associated electronic properties of the diatomic hydrides of the twenty-one main group elements from lithium to bromine have been calculated with large basis sets. As part of a systematic study of the polarity of chemical bonds, the position of the bond critical point, the charge density at the bond critical point, the Laplacian of the charge density at the bond critical point, and the molecular dipole moment of each molecule have been calculated. Particular attention has been paid to the effect of bond length elongation and contraction on the electronic properties. Variation of the bond length reveals that with atoms of low electronegativity, the bond critical point of AH tends to follow atom A, whereas with atoms of high electronegativity, the bond critical point tends to follow the hydrogen atom as the bond lengthens. Furthermore, it is shown that some properties of the diatomic hydrides vary monotonically within each row of the periodic table, while others effect a classification according to the character of the bond.     

Experimental and theoretical charge density study of chemical bonding in a Co dimer complex

The charge density of Co2(CO)6(HC[triple bond]CC6H10OH) (1) in the crystalline state has been determined using multipolar refinement of single-crystal X-ray diffraction data collected (i) with a synchrotron source at very low temperatures (15 K) and (ii) using a conventional source with the crystal at intermediate temperature (100 K). The X-ray charge density model is augmented by complete active space and density functional theory calculations. Topological analyses of the different charge distributions show that the two Co atoms are not bonded to each other in the quantum theory of atoms in molecules (QTAIM) sense of the word. However, the behavior of the source function and the total energy density indicate that there is some bond-like character in the Co-Co interaction. The bridging alkyne fragment provides an unusual bonding situation, with extremely small electron density differences between the two Co-C bond critical points and the "CoC2" ring critical point. Thus, the structure is close to a topological catastrophe point. Comparison of the results obtained from the two diffraction data sets and ab initio theory suggests that the topology of the experimental electron density in this special atomic environment is highly sensitive to subtle effects of measurement errors and potential shortcomings of the multipole model, or to effects of the crystal field. Thus, even the two identical molecules in the asymmetric unit show altered bonding patterns.     

Molecules for organic electronics studied one by one

The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-bodipy molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V.     

Daubechies wavelets as a basis set for density functional pseudopotential calculations

Daubechies wavelets are a powerful systematic basis set for electronic structure calculations because they are orthogonal and localized both in real and Fourier space. We describe in detail how this basis set can be used to obtain a highly efficient and accurate method for density functional electronic structure calculations. An implementation of this method is available in the ABINIT free software package. This code shows high systematic convergence properties, very good performances, and an excellent efficiency for parallel calculations.     

Three-center-two-electron and four-center-four-electron bonds. A study by electron charge density over the structure of methonium cations

We study the electronic density charge topology of CH(5)(+) species 1 (C(s)()), 2 (C(s)()), and 3 (C(2)(v)) at ab initio level using the theory of atoms in molecules developed by Bader. Despite the reports of previous studies concerning carbocationic species, the methane molecule is protonated at the carbon atom, which clearly shows its pentacoordination. In addition to the fact that hydrogen atoms in the methonium molecule behave in a very fluxional fashion and that the energy difference among the species 1, 2, and 3 are very low, is important to point out that two different topological situations can be defined on the basis of our study of the topology of the electronic charge density. Then, the species 1 and 2 present a three-center-two-electron (3c-2e) bond of singular characteristics as compared with other carbocationic species, but in the species 3, the absence of a 3c-2e bond is noteworthy. This structure can be characterized through the three bond critical points found, corresponding to saddle points on the path bonds between the C-H(2,3,5) that lie in the same plane. These nuclei define a four-center interaction where the electronic delocalization produced among the sigma(C-H) bonds provide a stabilization of the three C-H bonds involved in this interaction (the remaining two C-H bonds are similar to those belonging to the nonprotonated species). Our results show that bonding situations with a higher number of atom arrays are possible in protonated hydrocarbons.     

O–H···C hydrogen bond in the methane–water complex

Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH₄ complex formed by water and methane molecules, in which water is a proton donor and methane carbon (sp³) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial С–H bond of methane directed along the line of the O–H···C hydrogen bridge and the antibonding σ* orbital of the О–H bond of the water molecule. Topological analysis of electron density in the HOH···CH₄ complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O–H···C interaction are typical for Н-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an Н bond of O–H···σ(С–H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).     

THEORETICAL STUDIES ON THE SUBSTITUTION EFFECT OF FLUORINE ON ETHANE

<正> The substitution effect of fluorine on ethane has been investigated by means of studying the properties of the charge distribution at the bond critical points with the theory of atoms in molecule.It is found that the major substitution effects of fluorine atom are positive a inductive and polarity effect.At the same time,fluorine atom partially provides π electrons to other chemical bonds by means of hy-perconjugation in molecules with two fluorine atoms and one or two carbon atoms in the same plane,and these effects are reflected in the quantity of bond ellipticity,Laplacian and the charge density of charge distribution at the bond critical points.The substitution of hydrogen by fluorine in ethane strengthens all the bonds in substituted ethanes.Other effects originating from the substitution of hydrogen by fluorine have also been discussed.     

Ab initio study of molecular structures and excited states in anthocyanidins

The structural and electronic characters of four types of hydroxyl group-substituted anthocyanidins (pelargonidin, cyanidin, delphinidin, and aurantinidin) were examined using quantum chemical calculations. For these cationic molecules, both the planar and non-planar structures in the electronic ground state were determined at the B3LYP/D95 level of theory. We revealed that the planar structure is slightly more stable than the non-planar structure for each molecule. For the optimized planar structures, single excitation-configuration interaction (SE-CI) based on the restricted Hartree-Fock (RHF) wave function was evaluated and the electronic character in the low-excited states was discussed in terms of the MO theory. Symmetry adapted cluster (SAC)/SAC-CI calculations were also carried out to estimate the excitation energies precisely. The results showed that hydroxylation of the phenyl group causes a change in the excitation energies without taking the solvent effects into account. The results are in agreement with spectral experiments and previous MO calculations.