Overlap Of Electron Densities Research Articles

Density functional theory study on the formation mechanism of CaClOH in municipal solid waste incineration fly ash.

Municipal solid waste incineration (MSWI) fly ash is defined as a kind of hazardous waste because of its high levels of multiple pollutants. The main component of MSWI fly ash is CaClOH, and the characteristics have not achieved consensus. And density functional theory (DFT) was used to calculate the formation process of CaClOH in this study, which mainly included HCl adsorption on CaO (0 0 1) surface and Ca(OH)2 (0 0 1) surface and the surface reaction process. The reaction mechanism was investigated. The results showed that the maximum adsorption energies of HCl on CaO and Ca(OH)2 surfaces reached - 195.17kJ/mol and - 83.48kJ/mol, respectively, representing strong chemisorption. The chemisorption process was shown as the adsorption of H atom on O site, and the adsorption capacity was reflected in the adsorption range of O site. The significant electron density overlap between O site and H atom meant that a new chemical bond formed, which made the adsorption structure stable. The adsorption energy of multi-HCl adsorption on the crystal surfaces was not proportional to the number of HCl molecule, indicating that the adsorption processes were influenced by each other. After surface reaction, the H-Cl bond was broken completely, and the structure of CaO and Ca(OH)2 changed to new structures. According to transition state (TS) search, the formation of CaClOH had a higher priority, easier than that of CaCl2, explaining the presence of CaClOH in fly ash. The study provides helpful information for the solidification treatment of fly ash.

Importance of kink energy in calculating the formation energy of a graphene edge

The formation energy of an arbitrary graphene edge or that of other 2D materials has been estimated as a summation of the armchair (AC) and zigzag (ZZ) edge sites. Such an estimation assumes that each site is independent from its neighboring sites, which is unlikely due to the overlap of electron densities. Here, we show that to accurately calculate the formation energy of graphene edges with various functional groups the energy of the junction between AC and ZZ sites, the ``kink energy,'' is essential. It is significant that the kink energies of graphene edges with different functional groups are all negative, namely, kink formation stabilizes the chiral graphene edges.

Insights into methane to syngas on stoichiometric and defect Ce2(SO4)3 crystal surface

We present a first principles study using periodic density functional theory on the reaction between Ce2(SO4)3 oxygen carrier and CH4 during chemical looping partial oxidation. The (001) surface has an appropriate bond strength and oxygen vacancy (Ov) formation energy (Evac). Further analysis shows that CH4 has a weak adsorption performance on (001) surface, while CHx (x = 0–3) radicals have a strong electron density overlap. The lattice oxygen atoms tend to leave the crystal surface during adsorption process, which is conducive to the syngas formation. Compared with (102) surface, (001) surface has a lower dehydrogenation and syngas formation energy barrier. CH3 → CH2 + H serves as the rate-determining step on (102) surface, while on (001) surface is CH2 → CH + H (TS3). Ov effects are emphasized through the comparison of (102), (001) and Ov (001) surface. The corresponding energetic results show that the Ov facilitates the adsorption and dehydrogenation process. But when the Ov concentration is larger than 1.96%, increasing the Ov concentration does not continue to reduce the energy barrier of TS3. In summary, (001) surface has a better reaction performance, and Ov play a critical role in both adsorption and dehydrogenation process.

Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization.

In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K cation in the calculation.

DFT study of hydrogen interaction with transition metal doped graphene for efficient hydrogen storage: effect of d-orbital occupancy and Kubas interaction.

Hydrogen adsorption on pristine graphene (PG), graphene with defect (GD), and transition metal (TM) (Ag, Au, Cu, and Fe) doped graphene is systematically investigated for potential hydrogen storage using density functional theory. The stability of the TM atom doped graphene has been analysed by studying the binding energy and the electron density distribution. The TM atom-doped GD shows better binding energy and electron density overlap than PG; therefore, the TM/GD system has been considered and analysed for hydrogen adsorption. The hydrogen adsorption property is studied by examining the adsorption energy, mode of H2, density of states (DOS), charge density difference, and Löwdin charges before and after adsorption to find a better TM/GD system for hydrogen storage. The Fe/GD system shows higher hydrogen adsorption energy and hydrogen in its stable Kubas mode. Furthermore, two to five H2 molecule adsorption and desorption is studied. The increase in the number of H2, which changes the DOS at the Fermi level, suggests that one can predict H2 concentration by measuring conductivity changes. The present work is focused on studying the interaction between H2 and TM/GD systems, which will help understand the basic adsorption mechanism for practical hydrogen storage.

Quantum Chemical Roots of Machine-Learning Molecular Similarity Descriptors.

In this work, we explore the quantum chemical foundations of descriptors for molecular similarity. Such descriptors are key for traversing chemical compound space with machine learning. Our focus is on the Coulomb matrix and on the smooth overlap of atomic positions (SOAP). We adopt a basic framework that allows us to connect both descriptors to electronic structure theory. This framework enables us to then define two new descriptors that are more closely related to electronic structure theory, which we call Coulomb lists and smooth overlap of electron densities (SOED). By investigating their usefulness as molecular similarity descriptors, we gain new insights into how and why Coulomb matrix and SOAP work. Moreover, Coulomb lists avoid the somewhat mysterious diagonalization step of the Coulomb matrix and might provide a direct means to extract subsystem information that can be compared across Born-Oppenheimer surfaces of varying dimension. For the electron density, we derive the necessary formalism to create the SOED measure in close analogy to SOAP. Because this formalism is more involved than that of SOAP, we review the essential theory as well as introduce a set of approximations that eventually allow us to work with SOED in terms of the same implementation available for the evaluation of SOAP. We focus our analysis on elementary reaction steps, where transition state structures are more similar to either reactant or product structures than the latter two are with respect to one another. The prediction of electronic energies of transition state structures can, however, be more difficult than that of stable intermediates due to multi-configurational effects. The question arises to what extent molecular similarity descriptors rooted in electronic structure theory can resolve these intricate effects.

Derivatives of Bis(trifluoromethyl)biphenyl and Various Donor Noieties Exhibiting Dual State Emission

A series of bis(trifluoromethyl)biphenyl derivatives bearing carbazole, dimethylacridan, and phenothiazine donor moieties were designed and synthesized via Ullman coupling reaction. The compounds were found to be capable of forming molecular glasses with glass transition temperatures ranging from 152 °C to 244 °C. Significant dual-state emission was revealed for the synthesized compounds. Radiative decay of singlet and triplet states emerged from restricted molecular motion in solid state. The phenothiazinyl-substituted bis(trifluoromethyl)biphenyl derivative induces particular interest, as it exhibits room-temperature phosphorescence. This makes it promising for oxygen sensing applications. The theoretical work revealed that carbazolyl disubstituted bis(trifluoromethyl)biphenyl has the largest deviation of the planes of donor and acceptor fragments from 90°, which leads to larger overlap of electron density in the ground and excited states and larger oscillator strength. The calculated values of dipole moment and charge transfer during excitation were found to be the lowest for phenothiazinyl disubstituted bis(trifluoromethyl)biphenyl. This result explains the experimental fact that the solvent polarity has the least effect on the fluorescent spectrum of this compound.

Mechanistic Insight into Chemical Reactions of Acyclic Diboryloxy Carbenes: the Activation Strain Model Study

AbstractTo understand the origin of the activation barriers of the acyclic dioxycarbene and its heavier congeners, [(HCDippN)2BO]2G14 (G14=group 14 element), density functional theory calculations were used to study their reactivity with dihydrogen and ethene. Our computational results reveal that the insertion reaction of [(HCDippN)2BO]2G14 with H2 is energetically unfeasible from a kinetic viewpoint. On the other hand, only [(HCDippN)2BO]2C and [(HCDippN)2BO]2Si can readily undergo the [1+2] cycloaddition reaction with ethene. The activation strain model (ASM) was used to analyze the present computational results. The theoretical analyses indicate that when a small molecule (H2 or H2C=CH2) reacts with a big molecule ([(HCDippN)2BO]2G14), the former molecule must undergo a substantial deformation to gain a better overlap of electron density with the latter molecule. This circumstance, in turn, causes a large strain energy (ΔESTR,H2 or ΔESTR,C2H4) to influence the corresponding activation barrier. Accordingly, the heavier the central group 14 atom in [(HCDippN)2BO]2G14 is, the larger the atomic radius of G14 is, the higher the activation energies for the insertion reaction of [(HCDippN)2BO]2G14 with dihydrogen and the [1+2] cycloaddition reaction of [(HCDippN)2BO]2G14 with ethene will be, and the lower the reactivity of [(HCDippN)2BO]2G14 will be. This finding could help experimental chemists to design novel carbenes possessing fascinating substituents for carbenic chemistry.

Nonlocal Subsystem Density Functional Theory.

By invoking a divide-and-conquer strategy, subsystem DFT dramatically reduces the computational cost of large-scale, ab initio electronic structure simulations of molecules and materials. The central ingredient setting subsystem DFT apart from Kohn-Sham DFT is the nonadditive kinetic energy functional (NAKE). Currently employed NAKEs are at most semilocal (i.e., they only depend on the electron density and its gradient), and as a result of this approximation, so far large-scale simulations only included systems composed of weakly interacting subsystems. In this work, we advance the state-of-the-art by introducing fully nonlocal NAKEs in subsystem DFT simulations for the first time. A benchmark analysis based on the S22-5 test set shows that nonlocal NAKEs considerably improve the computed interaction energies and electron densities compared to commonly employed GGA NAKEs, especially when increasing intersubsystem electron density overlap is considered. Most importantly, we resolve the long-standing problem of too attractive interaction energy curves typically resulting from the use of GGA NAKEs.

Cyclohexane-Based Scaffold Molecules Acting as Anion Transport, Anionophores, via Noncovalent Interactions.

A theoretical study of a variety of cyclohexane-based anion transporters interacting with the chloride anion has been conducted using density functional theory. The calculations have been performed in the gas phase but also, in order to describe the solvation effects on the interaction, two different solvents-chloroform and dimethylsulfoxide-have been taken into account. Gas-phase interaction energies within the complexes are found to be up to 400 kJ/mol, while, when solvent effects are considered, the interaction energy values decreased drastically concomitantly with an elongation in the interatomic distances. Atoms in molecules and natural bond analysis corroborate the trends found for the intermolecular energies and Cl···H distances, suggesting strong donations from the Cl- anion into the σ*H-N antibonding orbitals, as well as with noncovalent interaction plots showing large areas of electron density overlap within the chloride anion surroundings.

Classical Pauli repulsion: An anisotropic, atomic multipole model.

Pauli repulsion is a key component of any theory of intermolecular interactions. Although Pauli or exchange repulsion has its origin in the quantum mechanical nature of electrons, it is possible to describe the resulting energetic effects via a classical model in terms of the overlap of electron densities. In fact, closed shell intermolecular repulsion can be explained as a diminution of election density in the internuclear region resulting in decreased screening of nuclear charges and increased nuclear-nuclear repulsion. We provide a concise anisotropic repulsion formulation using the atomic multipoles from the Atomic Multipole Optimized Energetics for Biomolecular Applications force field to describe the electron density at each atom in a larger system. Mathematically, the proposed model consists of damped pairwise exponential multipolar repulsion interactions truncated at short range, which are suitable for use in compute-intensive biomolecular force fields and molecular dynamics simulations. Parameters for 26 atom classes encompassing most organic molecules are derived from a fit to Symmetry Adapted Perturbation Theory exchange repulsion energies for the S101 dimer database. Several applications of the multipolar Pauli repulsion model are discussed, including noble gas interactions, analysis of stationary points on the water dimer potential surface, and the directionality of several halogen bonding interactions.

Vibrational spectra of halide-water dimers: Insights on ion hydration from full-dimensional quantum calculations on many-body potential energy surfaces

Full-dimensional vibrational spectra are calculated for both X-(H2O) and X-(D2O) dimers (X = F, Cl, Br, I) at the quantum-mechanical level. The calculations are carried out on two sets of recently developed potential energy functions (PEFs), namely, Thole-type model energy (TTM-nrg) and many-body energy (MB-nrg), using the symmetry-adapted Lanczos algorithm with a product basis set including all six vibrational coordinates. Although both TTM-nrg and MB-nrg PEFs are derived from coupled-cluster single double triple-F12 data obtained in the complete basis set limit, they differ in how many-body effects are represented at short range. Specifically, while both models describe long-range interactions through the combination of two-body dispersion and many-body classical electrostatics, the relatively simple Born-Mayer functions employed in the TTM-nrg PEFs to represent short-range interactions are replaced in the MB-nrg PEFs by permutationally invariant polynomials to achieve chemical accuracy. For all dimers, the MB-nrg vibrational spectra are in close agreement with the available experimental data, correctly reproducing anharmonic and nuclear quantum effects. In contrast, the vibrational frequencies calculated with the TTM-nrg PEFs exhibit significant deviations from the experimental values. The comparison between the TTM-nrg and MB-nrg results thus reinforces the notion that an accurate representation of both short-range interactions associated with electron density overlap and long-range many-body electrostatic interactions is necessary for a correct description of hydration phenomena at the molecular level.

Surface plasmon dependence on the electron density profile at metal surfaces.

We use an extension of the hydrodynamic model to study nonlocal effects in the collective plasmon excitations at metal surfaces and narrow gaps between metals, including the surface spill-out of conduction band electrons. In particular, we simulate metal surfaces consisting of a smooth conduction-electron density profile and an abrupt jellium edge. We focus on aluminum and gold as prototypical examples of simple and noble metals, respectively. Our calculations agree with the dispersion relations measured from planar surfaces for these materials. Systems involving small gaps display a regime of tunnelling electrons, which is partially captured by the overlap of electron densities. This extension of the hydrodynamic model to cope with inhomogeneous density profiles provides a relatively fast and accurate way of describing the optical response of metal surfaces at subnanometer distances.

Density Functional Theory Study on the Mechanism of Absorption of CO2 by the Ionic Liquid 1-Butyl-3-Methylimidazolium Acetate

The absorption of CO2 on 1-butyl-3-methylimidazolium acetate ([Bmim] [Ac]) with different substituents are calculated systematically at the GGA/PW91 level. Three hydrogen bonds are formed between [Ac]– and the cations of 1-n-[Bmim][Ac] ([NBmim]+) and 1-tert-[Bmim][Ac] ([TBmim]+). The interaction between CO2 and [NBmim][Ac] via a C – O bond is much weaker than that with [TBmim][Ac] by its forming an O…O…C…C four-membered ring. The chemisorption of CO2 on the ion pair [NBmim][Ac] is much weaker than that on [TBmim][Ac], as indicated from an absorption energy analysis. The frontier molecular orbitals show the electron density overlap between absorbed CO2 and the [Ac]– in CO2 – [NBmim][Ac] is much weaker than that in [TBmim][Ac]. As a result, the chemisorption of CO2 on [NBmim][Ac] is much weaker than that on [TBmim][Ac]. Ionic liquids based on [NBmim]+ can be used repeatedly, and the adsorbed CO2 would be more easily desorbed.

First principle study of the electronic properties of the magnetocaloric compound Gd5Si4

The electronic structure and magnetic properties of the Gd 5 Si 4 compound have been investigated by the first principles full-potential linearized augmented plane wave (FP-LAPW) method based on density functional theory (DFT) using the WIEN2k code. The Coulomb corrected local-spin density approximation (LSDA + U) in the self-interaction correction (SIC) has been used for the exchange-correlation potential. Based on the calculated results, the ground state of Gd 5 Si 4 is found to be ferromagnetic (FM). The optimized structural parameters and magnetic properties including the lattice constants and magnetic moments are in good agreement with experimental data. The magnetic moments of the Gd atoms in Gd 5 Si 4 are smaller than that of the elemental gadolinium. The magnetic moment of Gd 5 Si 4 is found to be 37.8 μB/f.u. DOS results show that the magnetic properties of the compound depend on the hybridization between Si -3p and Gd -5d states which have an effective role in the RKKY interaction. The existence of the very flat bands at -7 eV for spin up and at +3 eV for spin down that is mainly Gd -4f characters shows that the LSDA + U method provides the better description of our systems. The obvious overlap of electron densities between the Gd1 and Si atoms indicates a covalent-like bonding between them.

Comparative homology modeling-inspired protein engineering for improvement of catalytic activity of Mugil cephalus epoxide hydrolase

The epoxide hydrolase (EH) of a marine fish, Mugil cephalus, was engineered to improve the catalytic activity based on comparative homology modeling. The 3-D crystal structure of the EH from Aspergillus niger was used as a template. A triple point mutant, F193Y for spatial orientation of the nucleophile (D199), W200L for removing electron density overlap between W200 and Y348, and E378D for good charge relay in the active site, was developed. The initial hydrolysis rate, the reaction time to reach 98 %ee, and yield were enhanced up to 35-fold, 26-fold and 32%, respectively, by homology modeling-inspired site-directed mutagenesis of M. cephalus EH.

Computational and Spectroscopic Studies of Dichlorofluoroethane Hydrate Structure and Stability

Clathrate hydrates consisting of HCFC (hydrochlorofluorocarbon) guest molecules within host water cages represent a promising new medium for water desalination. The HCFC used in this study, 1,1-dichloro-1-fluoroethane (R141b), forms a structure II hydrate phase at mild conditions (0 °C, 0 atm). We present a detailed molecular picture of the structure and dynamics of guest R141b molecules within water cages, obtained from ab initio calculations, molecular dynamics simulations, and Raman spectroscopy. Such information will be needed to understand and control the nucleation and growth of these hydrates for industrial applications. Density functional theory calculations were used to provide an energetic and molecular orbital description of R141b stability in both large and small cages in a structure II hydrate. Additionally, the hydrate of an isomer, 1,2-dichloro-1-fluoroethane, does not form at ambient conditions due to extensive overlap of electron density between guest and host. Results for the isomer hydr...

Comparison of overlap-based models for approximating the exchange-repulsion energy

Different ways of approximating the exchange-repulsion energy with a classical potential function have been investigated by fitting various expressions to the exact exchange-repulsion energy for a large set of molecular dimers. The expressions involve either the orbital overlap or the electron-density overlap. For comparison, the parameter-free exchange-repulsion model of the effective fragment potential (EFP) is also evaluated. The results show that exchange-repulsion energy is nearly proportional to both the orbital overlap and the density overlap. For accurate results, a distance-dependent correction is needed in both cases. If few parameters are desired, orbital overlap is superior to density overlap, but the fit to density overlap can be significantly improved by introducing more parameters. The EFP performs well, except for delocalized pi systems. However, an overlap expression with a few parameters seems to be slightly more accurate and considerably easier to approximate.

Methane loss from (CH 3) 3O +: An asynchronous, concerted 1,2-alkane elimination

To advance our understanding of 1,2-eliminations, ab initio and density functional theories are used to characterize the elimination of CH 4 from (CH 3) 3O +. The reaction begins with the extension of a CO bond. Near the transition state, the carbon of the moving methyl (C Me) begins to approach a hydrogen (H t) in another methyl, and the original CH t bond begins to stretch. Finishing the transfer of H t after the transition state is passed completes the elimination. At the transition state, more than half of the positive charge is on the moving methyl, so the initial phase of methane elimination resembles the beginning of heterolytic dissociation to +CH 3 + CH 3OCH 3, a reaction that also occurs. There is no electron density overlap between the C and O at the transition state, but there is significant overlap density between C Me and H t. This and the charge distribution lead to classification of methane elimination as a concerted but highly asynchronous process rather than as being ion-neutral complex-mediated, in contrast to many alkane eliminations. The concertedness of this process probably arises from the threshold for partial dissociation of this system to an ion-neutral complex being much higher than the endothermicity for methane elimination.

Toward a Quantitative Description of Crystal Packing in Terms of Molecular Pairs: Application to the Hexamorphic Crystal System, 5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile

Elements of a theory of crystal packing are presented in the form of a systematic analysis of crystal packing molecular pairs, i.e., neighboring molecule−molecule pairs in the crystal, rather than in terms of selected intermolecular atom−atom contacts. Intermolecular energies, based on the molecular electron density distribution and partitioned over Coulombic, polarization, dispersion, and repulsion contributions, are calculated for such pairs by the Pixel-semiclassical density sums (SCDS) method, recently updated for a better treatment of the dependence between electron density overlap and repulsion energy. The advantages of the pairs treatment are illustrated by a study of the six known polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, in which diffuse interactions between aromatic rings over a wide range of stacking modes are shown to contribute more to the cohesive energy than do lateral interactions between polar moieties, often described as weak hydrogen bonds.