# Theoretical Chemistry Accounts

## Current research reports and chronological list of recent articles..

TCA publishes papers in all fields of theoretical chemistry, computational chemistry, and modeling. Fundamental studies as well as applications are included in the scope.

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## Theoretical Chemistry Accounts - Abstracts

Insights into the bonding between tributylphosphine chalcogenides and zinc(II)

### Abstract

We present a first-principles systematic study on the bonding and structure of the complexes between zinc(II) chloride and tributylphosphine chalcogenides, n-Bu3PE (E = O, S, Se). These investigations are carried out within the framework of the density functional theory with and without considering the dispersion corrections evaluated at the GD3 level. Inspection of the calculated binding energies, orbitals, charge transfers and natural bond orbital analysis shows the importance of the interplay between σ- and π-type bonding within P–E and E–Zn in the formation of these complexes. Calculations reveal that the P–E–Zn angle goes from 120° to 90° when going from O to Se. In the complexes, the P–E bonds resemble those in the isolated PE diatomic anions, where an electron density excess is found on the chalcogen E whatever its nature. A bonding model for this type of organometallic complexes is proposed and discussed here for the first time.

Datum: 19.04.2018

Conceptual DFT study of the local chemical reactivity of the dilysyldipyrrolones A and B intermediate melanoidins

### Abstract

This computational study assessed 11 density functionals related to Def2TZVP basis sets, namely CAM-B3LYP, LC- $$\omega$$ PBE, M11, M11L, MN12L, MN12SX, N12, N12SX, $$\omega$$ B97, $$\omega$$ B97X, and $$\omega$$ B97XD, and the SMD solvation model for calculating the molecular properties and structures of the intermediate melanoidin pigments, dilysyldipyrrolone A (XL-W1) and dilysyldipyrrolone B (XL-W2). The global and local chemical reactivity descriptors for the systems were calculated via conceptual density functional theory (DFT). The active sites applicable to nucleophilic, electrophilic, and radical attacks were chosen by connecting them with Fukui function indices, electrophilic Parr functions, and condensed dual descriptor $$\varDelta {f}({\mathbf {r}})$$ over the atomic sites. The predicted maximum absorption wavelength obtained directly from the HOMO–LUMO was more accurate relative to the experimental values of the MN12SX and N12SX density functionals than those obtained with TDDFT calculations. This study found the MN12SX and N12SX density functionals to be most appropriate for predicting the chemical reactivity of the molecules under study.

Datum: 16.04.2018

Aromatic sulfur compounds oxidation with H 2 O 2 over fully coordinated and defect sites in Ti-beta zeolites: evaluation by density functional theory

### Abstract

The oxidative desulfurization mechanisms of aromatic sulfur compounds, including thiophene, benzothiophene, and dibenzothiophene, with H2O2 on fully coordinated and defective Ti sites on Ti-beta zeolites are investigated by means of density functional theory calculations. In this work, three current concerns are explored: First is the oxidation of sulfides into the sulfoxides and sulfones in the presence of H2O2; the second is the comparison between the sulfide oxidation mechanism on T5 and T2 defective sites in Ti-beta zeolites; and finally the comparison with the oxidation mechanism on fully coordinated Ti site on the Ti-beta zeolite. The model shows that T5 defect site in Ti-beta is the most catalytically active site for the oxidation of aromatic sulfides.

Datum: 13.04.2018

Computational approach to study the influence of Mn, Fe, and Ni as additives toward rubber–brass adhesion

### Abstract

The effect of different transition metals (manganese, iron, and nickel) as alternative for cobalt additives toward the performance of rubber adhesion to brass has been investigated by employing modeling approach at density functional theory level. Out of the three different dopants, manganese shows positive results on both sulfide surfaces with notable improvement in adhesion on copper sulfide via carbon–carbon double bond. However, it exhibits lower promotional effect on zinc sulfide than cobalt dopant. Iron, on the other hand, only enhances the adhesion on copper sulfide, while inclusion of nickel displays the lowest promotional effect.

Datum: 12.04.2018

Ground-state energy for confined H 2 : a variational approach

### Abstract

Ground-state energies for confined H2 molecule are computed using the variational method. The approach proposed here uses a molecular wave function of the valence bond type, written as the sum of the covalent term and the ionic term. The molecule is confined in an impenetrable prolate spheroidal box. The atomic orbitals are built from a previous suggestion inspired by the factorization of the Schrödinger equation. The aim of this work is to propose a new wave function to be used for the confined hydrogen molecule. The polarizability and quadrupole moment are also calculated. The results obtained are in agreement with other results present in the literature, and they lead to a discussion about the relevance of the ionic term in the wave function.

Datum: 12.04.2018

Effect of electron-withdrawing terminal group on BDT-based donor materials for organic solar cells: a theoretical investigation

### Abstract

Rational end group modification has been found as an effective strategy to improve power conversion efficiencies (PCEs) for photovoltaic materials. However, due to different electronic processes competition, various interaction factors must be taken into account to make materials design. Through density functional theory (DFT) and time-dependent DFT (TD-DFT), the effect of electron-withdrawing substitution on benzodithiophene-based donor materials from the open circuit voltage ( $$V_{\text{OC}}$$ ), light absorption, exciton dissociation to charge transport in bulk materials has been investigated. The results point to that strong electron-withdrawing end group remarkably (1) enhances $$V_{\text{OC}}$$ due to lowered HOMO energy level; (2) induces photon absorption redshift due to narrow optical gap (Eg); (3) facilitates exciton dissociation because of enhanced intramolecular charge transfer character. However, there is no direct correlation between electron-withdrawing ability and charge transport properties, since steric hindrance, noncovalent interaction and electrostatic interaction altogether have large impact on intermolecular stacking and then charge mobility. Comprehensive factors should be considered to improve PCEs for photovoltaic materials. Impressively, the designed molecule SM8 with dicyanovinyl-capped reveals excellent optical-electron properties, which may be a promising donor for high performance SM-OSCs.

Datum: 11.04.2018

Quantum chemical study on the reaction mechanism and kinetics of Cl-initiated oxidation of methyl n -propyl ether

### Abstract

Oxidation of methyl n-propyl ether (CH3CH2CH2OCH3) molecule initiated by Cl atoms has been carried out using a dual level of quantum chemical investigation to understand the mechanistic pathways and kinetics of the H-atom abstraction reaction. Firstly, geometry optimization and frequency calculations for all the species are performed using BHandHLYP/6-311++G(d,p) level of theory at 298 K, and energetic calculations are further refined using CCSD(T) method with the same basis set to explore all stationary points on potential energy profile. We have observed from the energy profile that H-atom abstraction from –OCH2 group of CH3CH2CH2OCH3 is the kinetically predominant pathway. The reported bond dissociation energy for the dominant path is found to be in good agreement with the experimentally determined value. Further, standard Gibbs free energies (ΔG°298) and standard enthalpies (ΔH°298) analyses also indicate that the H-atom abstraction from –OCH2 group of CH3CH2CH2OCH3 is thermodynamically more favourable than other abstraction channels. The rate coefficients are also reported using canonical transition state theory, which is found to be in good agreement with the experimental data. The atmospheric lifetime of title molecule is also calculated.

Datum: 27.03.2018

Theoretical spectroscopy of a NIR-absorbing benziphthalocyanine dye

### Abstract

Benziphthalocyanines are (Yanai et al. in Chem Phys Lett 393:51–57, 2004) phthalocyanines in which one isoindoline unit has been replaced by a phenyl ring. In this study, we focus on a macrocycle of this family recently synthesized by Uchiyama and co-workers (Toriumi et al. Angew Chem Int Ed 53:7814–7818, 2014), and composed of three indoline units (substituted with 2,6-diisopropylphenyl-oxy groups) and one resorcinol unit. We aim at characterizing the possible tautomers to evaluate whether this compound might exist as a mixture of several forms or not. To reach our goals, we use state-of-the-art ab initio theories, i.e., Time-Dependent Density Functional Theory coupled with a refined solvation model (the Polarizable Continuum Model) as well as post-Hartree Fock approaches. We first investigate the stability, the structure and the aromaticity of the possible tautomers before analyzing their spectroscopic signatures. Using an approach going beyond the vertical approximation, we compare experimental and theoretical 0–0 energies and band shapes. This study allows us to point out the dominant presence of the quinoidal form as well as to unravel the vibronic contributions responsible for the specific shape of the optical spectrum.

Datum: 24.03.2018

Direct inversion of the iterative subspace (DIIS) convergence accelerator for crystalline solids employing Gaussian basis sets

### Abstract

When dealing with crystalline solids, convergence of iterative procedures such as self-consistent field (SCF) or coupled–perturbed equations is often more difficult than in the case of molecular systems, specially when a local basis set of atom-centered Gaussians is adopted. Reasons are usually to be found in the close packing of atoms and peculiar chemical characters, such as metallic bond. In this work, a periodic implementation of the direct inversion of the iterative subspace (DIIS) method for crystalline solids is presented for SCF and electric field response up to second order. The error vectors are computed in reciprocal space and implemented for the energy, polarizability and up to second hyperpolarizability. The performance of different DIIS flavors is benchmarked on a representative set of 42 systems including metallic, ionic, molecular and covalent crystals, bulk crystals, surfaces and nanotubes, adopting all-electron basis sets as well as pseudopotentials. Interestingly, it is seen that the error vectors evaluated in the central (gamma) point of the Brillouin zone are sufficient in all cases for an optimal DIIS performance.

Datum: 23.03.2018

DFT calculations on subnanometric metal catalysts: a short review on new supported materials

### Abstract

Metal clusters have been used in catalysis for a long time, even in industrial production protocols, and a large number of theoretical and experimental studies aimed at characterizing their structure and reactivity, either when supported or not, are already present in the literature. Nevertheless, in the last years the advances made in the control of the synthesis and stabilization of subnanometric clusters promoted a renewed interest in the field. The shape and size of sub-nanometer clusters are crucial in determining their catalytic activity and selectivity. Moreover, if supported, subnanometric clusters could be highly influenced by the interactions with the support that could affect geometric and electronic properties of the catalyst. These effects also present in the case of metal nanoparticles assume an even more prominent role in the “subnano world.” DFT-based simulations are nowadays essential in elucidating and unraveling reaction mechanisms. The outstanding position of this corner of science will be highlighted through a selected number of examples present in the literature, concerning the growth and reactivity of subnanometric supported metal catalysts.

Datum: 23.03.2018

Low-energy stereodynamics in the ion–molecule reactions D + + D 2 /HD and H + + H 2 /HD: reagent vibrational excitation effect and mass factor effect

### Abstract

The low-energy chemical stereodynamics of these ion–molecule reactions D+ + D2 → D2 + D+, D+ + HD → DH + D+/D2 + H+, H+ + HD → H2 + D+/HD + H+ and H+ + H2 → H2 + H+ has been investigated by performing the quasi-classical trajectory calculations on the ground electronic state potential energy surface (11A′ PES). The polarization-dependent differential cross sections and the probability distributions of P(θr ) and P(ϕr ) have been calculated, compared and discussed within the center-of-mass frame and at the low collision energy of 100 meV. The calculation results indicate that the product scattering and the polarization of the product rotational angular momentum are sensitive to the reactant vibrational quantum number. Such sensitivity increases with the increasing value of mass factor. Moreover, the products from the reaction H+ + HD → HD + H+ show quite different scattering and polarization behaviors with reagent vibration excitation.

Datum: 15.03.2018

The acid strength of the HClO 4 / n (AlF 3 ) and HClO 4 / n (SbF 5 ) ( n  = 1–3) Lewis–Brønsted superacids containing the excess of the Lewis acid component

### Abstract

The acidic strength of selected Lewis–Brønsted superacids consisting of HClO4 Brønsted acid and containing the excess of either AlF3 or SbF5 Lewis acid component is evaluated on the basis of theoretical calculations employing ab initio methods. The Gibbs free energies of deprotonation processes for HClO4/n(AlF3) and HClO4/n(SbF5) (n = 1–3) are found to depend on the number (n) of AlF3 or SbF5 molecules (playing Lewis acid role) surrounding the HClO4 system. The successive attachment of either AlF3 or SbF5 molecules to HClO4 gradually increases the acidity strength of the resulting superacid which leads to the saturation achieved for 2–3 AlF3 molecules interacting with Brønsted acid. The preference of formation of the Lewis acid aggregates is observed during the analysis of the most stable HClO4/n(AlF3) and HClO4/n(SbF5) isomeric structures. The mixing ratios of HClO4 and either AlF3 or SbF5 compounds that should likely maximize their resulting acid strength are proposed and discussed.

Datum: 14.03.2018

Structural and energetic properties of tautomeric forms of phosphonyl thioamides

### Abstract

Stable tautomeric forms in a series of phosphonyl thioamides have been studied using DFT methods. The molecules studied in this contribution present a phosphonyl group in β-position of the C–S bond connected to the amine group. The three most stable tautomeric forms with double bonds on either C=N, C=S, or adjacent C=C have been described, and their relative energies together with the transition barriers have been evaluated. In such molecules a six-member ring can be formed by a hydrogen bond between the oxygen of the phosphonyl group and the H–N bond of the thioamide. The tautomeric form involving a C=N double bond is found less stable than the two other forms by more than 10 kcal/mol. The transition barriers between the various tautomers are calculated to be as large as 40 kcal/mol for the isolated molecules, but less than 30 kcal/mol in the presence of one water molecule. Similar results are obtained with various substituents on the phosphorus or on the nitrogen atom. Electronic vertical spectra have been calculated using the TD-DFT approach for the three stable tautomeric forms in a series of six substituted phosphonyl thioamides, and it is found that the signature of each tautomer is sufficiently specific to allow for their clear identification in a mixture using UV–Vis spectroscopy.

Datum: 13.03.2018

Theoretical perspectives on carbocation chemistry from energy decomposition analysis

### Abstract

Understanding carbocation formation is a central concern for all chemical sciences. The widely accepted explanation in terms of inductive/field and delocalization effects is based on quantities that are not straightforwardly computed in popular electronic structure methods. This work reports an alternative approach to the carbocation formation problem based on energy decomposition analysis, more specifically, CMOEDA. The order of stability for carbocations formation was successfully accounted in terms of the energy components. The focus of the analysis shifts from the product of the reaction, i.e., the carbocation itself, to the reactant neutral molecule. Notably, exchange repulsions are the largest energy contribution to increase carbocation stability in the order methyl, primary, secondary and tertiary. Polarization (orbital relaxation) plays a secondary role. Insertion of bulky groups increases the repulsion with the incipient anion (a hydride ion) and decreases the strength of the C–H bond. This pattern is confirmed for several other hydrocarbon cases. Additional systems like halomethanes, amino- and nitro-derivatives are also described.

Datum: 13.03.2018

Structure, fragmentation patterns, and electronic properties of small indium oxide clusters

### Abstract

A theoretical study of nanoparticles of indium oxide, one of the most relevant transparent conducting materials, is reported. By means of Density Functional Theory in the generalized gradient approximation, we investigated the atomic and electronic structures of the neutral and charged indium oxide clusters $$\text{In}_n\text{O}_m^{0/\pm }$$ with n = 1–6 and m = 1–8, as well as related properties like adiabatic ionization potentials and electron affinities. Based on total energy differences between the obtained global minimum configurations of parent clusters and possible fragments, we explored the respective fragmentation channels for cationic clusters and compared our results with those recently observed in Photodissociation measurements (Knight et al. in IJMS 304:29, 2011). The overall good agreement between theory and experiment provides compelling evidence of the calculated properties of these systems, whose knowledge is essential to take advantage of the nanoscale in future technological applications of these materials.

Datum: 10.03.2018

Adsorption of rare earth yttrium and ammonium ions on kaolinite surfaces: a DFT study

### Abstract

The ion-adsorbed rare earth is mainly concentrated in the in situ leaching process using NH4+ as the leaching agent. The adsorption mechanisms of Y3+ and NH4+ on kaolinite (001) and (00-1) surfaces were studied by density functional theory based on plane wave pseudopotential. The adsorption structures and energies, electrostatic potential, frontier orbital, Mulliken bond population and atomic charge, and electron density difference were calculated. The calculated results showed that the activity sites of kaolinite surfaces are located around the lying OH groups on (001) surface and above the center of the six-membered oxygen ring on (00-1) surface. Y3+ is adsorbed on kaolinite (001) surface primarily through covalent interaction while on kaolinite (00-1) surface primarily through Coulomb interaction. NH4+ is adsorbed on surface by electrostatic interaction and hydrogen bonding. The adsorption energy order on kaolinite (001) surface is Y3+ > NH4+ > H2O while NH4+ > Y3+ > H2O on kaolinite (00-1) surface. The presence of both the ligand water of cations and surface water can increase the Eads of NH4+/Y3+. The hydrated Y3+ can be still more strongly adsorbed on hydrated kaolinite surface than NH4+. When NH4+ is used as the leaching agent for ion-adsorption-type rare earth, it is necessary to increase the concentration of NH4+ to a certain value so that Y3+ could be effectively exchanged by NH4+.

Datum: 09.03.2018

Energy conversion process of substituted phthalocyanines with potential application to DSSC: a theoretical study

### Abstract

A series of zinc phthalocyanine dyes with different electron-donating substituents and four types of anchor groups (described in the paper as A1, A2, A3 and A4) that interact with a semiconductor (TiO2) cluster were studied employing DFT and TD-DFT methodologies with the B3LYP hybrid functional and its long-range corrected version (CAM-B3LYP). We analyzed the range visible and near UV regions; they are the most important regions for photon to current conversion, to obtain the microscopic information about the electronic transitions and its corresponding molecular orbitals (MOs) properties. The computations provided the character of transitions involved in the studied systems. The UV–Vis spectra of the isolated dyes were obtained and compared with the computed spectra of the dyes anchored to the (TiO2)15 cluster. Furthermore, we focus on four properties that can be optimized: $$\Delta G_{\text{inj}}^{0}$$ , LHE, $$\Delta G_{\text{rec}}^{0}$$ and τ. The results obtained in this work allow us to propose the A2 as adequate anchor when –N(CH3)2 is the substituent R. That is of potential interest for designing highly efficient dye-sensitized solar cells.

Datum: 09.03.2018

Modeling magnetic circular dichroism within the polarizable embedding approach

### Abstract

Magnetic circular dichroism (MCD) is defined as the differential absorption of left and right circularly polarized light in a sample subjected to an external magnetic field. In order to interpret the results of MCD measurements, theoretical predictions of key MCD parameters can be of utmost importance. From an experimental point of view, MCD spectra of molecules are often measured in an environment and most notably in a solution. Thus, it may be very important that the method used to predict the MCD parameters is able to correctly account for medium effects. In this paper, we investigate the quality of MCD calculations within the polarizable embedding approach, which represents a fully atomistic and polarizable representation of an environment surrounding a smaller region treated using quantum mechanics. Furthermore, we compare the performance of the polarizable embedding scheme to the use of the more conventional dielectric continuum approach. Results are presented for cytosine and hypoxanthine solvated in water.

Datum: 07.03.2018

Theoretical investigation on the effect of fluorine and carboxylate substitutions on the performance of benzodithiophene-diketopyrrolopyrrole-based polymer solar cells

### Abstract

Three donor–acceptor (D–A) polymers 24 were designed and investigated based on the reported polymer 1 with benzo[1,2-b:4,5-b′]dithiophene (BDT) as D fragment and diketopyrrolopyrrole (DPP) as A fragment. The fluorine substitutions on the BDT unit in molecule 2 have less influence on the lowest unoccupied molecular orbital (LUMO) compared with the carboxylate substitutions on the BDT unit in 3 and 4. The charge transfer rate (kinter-CT) of molecule 4 is the largest, which determines that molecule 4 has a priority in the interfacial process among these investigated molecules with the same acceptor PC61 BM. The designed molecules 24 show larger open-circuit voltages (Voc), relatively narrower bandgaps and higher value of kinter-CT/kinter-CR than 1. Moreover, the results demonstrate that fluorine and carboxylate substitutions on molecule 4 show a synergistic effect on the FMO energy levels and electron interfacial process, which is expected to help the further understanding of the design rules for polymer donor materials in polymer solar cells.

Datum: 07.03.2018

Coupled cluster evaluation of the second and third harmonic scattering responses of small molecules

### Abstract

The static and dynamic second harmonic ( $$\beta _{\mathrm{SHS}}$$ ) and third harmonic ( $$\gamma _{\mathrm{THS}}$$ ) scattering hyperpolarizabilities and depolarization ratios of water, carbon tetrachloride, chloroform, dichloromethane, chloromethane, and acetonitrile have been evaluated at the coupled cluster response theory level of approximation. Following two recent publications on their measurements, this is the first quantum chemical investigation on $$\gamma _{\mathrm{THS}}$$ and on its decomposition into its spherical tensor components. Substantial electron correlation and basis set effects are evidenced for $$\beta _{\mathrm{SHS}}$$ and $$\gamma _{\mathrm{THS}}$$ and for their depolarization ratios, and they depend on the nature of the molecule. Then, using the selected CCSD/d-aug-cc-pVDZ level, the chlorinated methane derivatives have been studied, showing that (i) the $$\gamma _{\mathrm{THS}}$$ response is dominated by its isotropic contribution, whereas (ii) for $$\beta _{\mathrm{SHS}}$$ the dipolar contribution increases from carbon tetrachloride to dichloromethane, chloroform, chloromethane, and acetonitrile. Comparisons with the experimental data obtained from measurements in liquid phase (i) show that the increase of $$\gamma _{\mathrm{THS}}$$ with the number for chlorine atoms is well reproduced by the calculations and (ii) suggest that the solvation effects are smaller for $$\gamma _{\mathrm{THS}}$$ than for $$\beta _{\mathrm{SHS}}$$ .

Datum: 07.03.2018

Category: Current Chemistry Research

Last update: 11.04.2018.