Investigation of water substitution at RuII complexes by conceptual density function theory approach.

In this paper, we investigated water exchange reactions and substitution of aqua RuII complexes of general formula [Ru(terpy)(N^N)(H2 O)]2+ (where N^N = ethylenediamine (en), 1,2-(aminomethyl)pyridine (ampy) and 2,2'-bipyridine (bipy)) by ammonia and thioformaldehyde. These reactions were studied in detail by applying conceptual density functional theory. This approach enabled us to gain further insight into the underlying reaction mechanism at the microscopic level (involving only direct participants of the reaction, without the influence of the solvent) and to put the concept of reaction mechanism on a quantitative basis. The course of the chemical reaction along the reaction coordinate ξ, is rationalized in terms of reaction energy, force, dipole moment, and reaction electronic flux (REF). The results yield and characterize the significant influence of an intermolecular hydrogen bond formed between the entering and the spectator ligand to the overall energy barrier of the reactions.

Effect of the Nucleophile's Nature on Chloroacetanilide Herbicides Cleavage Reaction Mechanism. A DFT Study.

In this study, the degradation mechanism of chloroacetanilide herbicides in the presence of four different nucleophiles, namely: Br-, I-, HS-, and S2O3-2, was theoretically evaluated using the dispersion-corrected hybrid functional wB97XD and the DGDZVP as a basis set. The comparison of computed activation energies with experimental data shows an excellent correlation (R2 = 0.98 for alachlor and 0.97 for propachlor). The results suggest that the best nucleophiles are those where a sulfur atom performs the nucleophilic attack, whereas the other species are less reactive. Furthermore, it was observed that the different R groups of chloroacetanilide herbicides have a negligible effect on the activation energy of the process. Further insights into the mechanism show that geometrical changes and electronic rearrangements contribute 60% and 40% of the activation energy, respectively. A deeper analysis of the reaction coordinate was conducted, employing the evolution chemical potential, hardness, and electrophilicity index, as well as the electronic flux. The charge analysis shows that the electron density of chlorine increases as the nucleophilic attack occurs. Finally, NBO analysis indicates that the nucleophilic substitution in chloroacetanilides is an asynchronous process with a late transition state for all models except for the case of the iodide attack, which occurs through an early transition state in the reaction.

Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux.

Quantum chemical calculations were used to study the mechanism of Diels-Alder reactions involving chiral anthracenes as dienes and a series of dienophiles. The reaction force analysis was employed to obtain a detailed scrutiny of the reaction mechanisms, it has been found that thermodynamics and kinetics of the reactions are quite consistent: the lower the activation energy, the lower the reaction energy, thus following the Bell-Evans-Polanyi principle. It has been found that activation energies are mostly due to structural rearrangements that in most cases represented more than 70% of the activation energy. Electronic activity mostly due to changes in σ and π bonding were revealed by the reaction electronic flux (REF), this property helps identify whether changes on σ or π bonding drive the reaction. Additionally, new global indexes describing the behavior of the electronic activity were introduced and then used to classify the reactions in terms of the spontaneity of their electronic activity. Local natural bond order electronic population analysis was used to check consistency with global REF through the characterization of specific changes in the electronic density that might be responsible for the activity already detected by the REF. Results show that reactions involving acetoxy lactones are driven by spontaneous electronic activity coming from bond forming/strengthening processes; in the case of maleic anhydrides and maleimides it appears that both spontaneous and non-spontaneous electronic activity are quite active in driving the reactions.

An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology.

In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). From the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions, the framework exploits the multideterminental structure of the hybrid TDDFT/CIS wave packet to compute fundamental one-electron quantities such as difference electronic densities, transient electronic flux densities, and transition dipole moments. The hybrid scheme is benchmarked against wave function data for the laser-driven state selective excitation in LiH. It is shown that all features of the electron dynamics are in good quantitative agreement with the higher-level method provided a judicious choice of functional is made. Broadband excitation of a medium-sized organic chromophore further demonstrates the scalability of the method. In addition, the time-dependent flux densities unravel the mechanistic details of the simulated charge migration process at a glance. © 2017 Wiley Periodicals, Inc.

An open-source framework for analyzing N-electron dynamics. I. Multideterminantal wave functions.

The aim of the present contribution is to provide a framework for analyzing and visualizing the correlated many-electron dynamics of molecular systems, where an explicitly time-dependent electronic wave packet is represented as a linear combination of N-electron wave functions. The central quantity of interest is the electronic flux density, which contains all information about the transient electronic density, the associated phase, and their temporal evolution. It is computed from the associated one-electron operator by reducing the multideterminantal, many-electron wave packet using the Slater-Condon rules. Here, we introduce a general tool for post-processing multideterminant configuration-interaction wave functions obtained at various levels of theory. It is tailored to extract directly the data from the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions. The procedure is implemented in the open-source Python program detCI@ORBKIT, which shares and builds on the modular design of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). The new procedure is applied to ultrafast charge migration processes in different molecular systems, demonstrating its broad applicability. Convergence of the N-electron dynamics with respect to the electronic structure theory level and basis set size is investigated. This provides an assessment of the robustness of qualitative and quantitative statements that can be made concerning dynamical features observed in charge migration simulations. © 2017 Wiley Periodicals, Inc.

ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water.

The partitioning of the reaction force based on the extended-transition-state natural orbital for chemical valence (ETS-NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered ("reactant perspective" and "product perspective"). The results show that the ETS-NOCV picture is fully consistent with REF and bond-order changes. In addition, proposed ETS-NOCV decomposition of the reaction force allows for the quantitative assessment of the influence of the observed bond-breaking and bond-formation processes, providing detailed information about the reaction-driving and reaction-retarding force components within the assumed partitioning scheme. © 2017 Wiley Periodicals, Inc.

Chemical potential and reaction electronic flux in symmetry controlled reactions.

In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc.

Imaging the Ultrafast Photoelectron Transfer Process in Alizarin-TiO2.

In this work, we adopt a quantum mechanical approach based on time-dependent density functional theory (TDDFT) to study the optical and electronic properties of alizarin supported on TiO2 nano-crystallites, as a prototypical dye-sensitized solar cell. To ensure proper alignment of the donor (alizarin) and acceptor (TiO2 nano-crystallite) levels, static optical excitation spectra are simulated using time-dependent density functional theory in response. The ultrafast photoelectron transfer from the dye to the cluster is simulated using an explicitly time-dependent, one-electron TDDFT ansatz. The model considers the δ-pulse excitation of a single active electron localized in the dye to the complete set of energetically accessible, delocalized molecular orbitals of the dye/nano-crystallite complex. A set of quantum mechanical tools derived from the transition electronic flux density is introduced to visualize and analyze the process in real time. The evolution of the created wave packet subject to absorbing boundary conditions at the borders of the cluster reveal that, while the electrons of the aromatic rings of alizarin are heavily involved in an ultrafast charge redistribution between the carbonyl groups of the dye molecule, they do not contribute positively to the electron injection and, overall, they delay the process.

Insights into the variations of kinetic and potential energies in a multi-bond reaction: the reaction electronic flux perspective.

CONTEXT: The debate over whether kinetic energy (KE) or potential energy (PE) are the fundamental energy components that contribute to forming covalent bonds has been enduring and stimulating over time. However, the supremacy of these energy components in reactions where multiple bonds are simultaneously formed or broken has yet to be explored. In this study, we use the reaction electronic flux (REF), an effective tool for investigating changes in driving electronic activity when bond formation or dissociation occurs in a chemical reaction, to examine the fluctuations in the KE and PE in a multi-bond reaction. To that end, the activation of CO 2 by low-valent group 14 catalysts through a concerted σ -bond metathesis mechanism is analyzed. The findings of this preliminary study suggest that the REF can be utilized as a tool to rationalize alterations in the KE and PE in a multi-bond reaction. Specifically, analyses across the reaction coordinate reveal that changes in the KE and PE precede activation in the REF, stimulating the electronic activity where bond formation or dissociation processes dominate. METHODS: The activation of CO 2 by the low-valent LEH catalysts (L = N,N'-bis(2,6-diisopropyl phenyl)- ß -diketiminate; E = Si, Ge, Sn, and Pb) was studied along the reaction coordinate at the M06-2X/6-31 G(d,p)-LANL2DZ(E) level of theory. The respective minimum energy path calculations were obtained using the intrinsic reaction coordinate (IRC) procedure. The reaction electronic flux (REF) was calculated through the computation of the electronic chemical potential using the frontier molecular orbital approximation. Mayer bond orders along the reaction coordinate have been determined using the NBO 3.1 program in Gaussian16. Most of the reaction coordinate quantities reported in this study (REF, KE, PE, among others) have been determined using the Kudi program and custom Python scripts.

Study of ß-Ga2O3 Ceramics Synthesized under Powerful Electron Beam.

The synthesis of ß-Ga2O3 ceramic was achieved using high-energy electron beams for the first time. The irradiation of gallium oxide powder in a copper crucible using a 1.4 MeV electron beam resulted in a monolithic ceramic structure, eliminating powder particles and imperfections. The synthesized ß-Ga2O3 ceramic exhibited a close-to-ideal composition of O/Ga in a 3:2 ratio. X-ray diffraction analysis confirmed a monoclinic structure (space group C2/m) that matched the reference diagram before and after annealing. Photoluminescence spectra revealed multiple luminescence peaks at blue (~2.7 eV) and UV (3.3, 3.4, 3.8 eV) wavelengths for the synthesized ceramic and commercial crystals. Raman spectroscopy confirmed the bonding modes in the synthesized ceramic. The electron beam-assisted method offers a rapid and cost-effective approach for ß-Ga2O3 ceramic production without requiring additional equipment or complex manipulations. This method holds promise for fabricating refractory ceramics with high melting points, both doped and undoped.

Insights into the activation process of CO2 through Dihydrogenation reaction.

Based on first principle calculation, activation of CO2 has been analyzed thoroughly by using different conceptual density functional theory based descriptors like reaction force, reaction force constant, reaction electronic flux, dual descriptor, etc. via dihydrogenation reaction of B3N3, H2 and CO2. The total reaction is a two-step reaction where initially B3N3H2 is formed from the reaction between B3N3 and H2 and in the second step HCOOH is form due to the reaction of CO2 by B3N3H2. It has been found that the di-hydrogen reaction for the CO2 activation is endothermic in nature, which can be changed to exothermic reaction by applying proper external electric field. Movement of H2 plays an important role in the CO2 activation process. The reaction force constant, Wiberg bond index and its derivative reveal that the reaction is slightly asynchronous and concerted in nature.

Hydrogenation and hydration of carbon dioxide: a detailed characterization of the reaction mechanisms based on the reaction force and reaction electronic flux analyses.

A computational DFT study of the reaction mechanism of hydrogenation and hydration of carbon dioxide is presented. It has been found that hydrogenation and hydration are endoenergetic reactions that are carried out in two steps, passing by a stable intermediate that is surrounded by energy barriers of 70 kcal/mol and 10 kcal/mol for hydrogenation and 50 kcal/mol and 10 kcal/mol for hydration. Using the reaction force analysis, we were able to characterize the physical nature of the activation barriers and found that activation energies are mostly due to structural rearrangements. An interesting difference in the reaction mechanisms disclosed by the reaction force and electronic flux analyses is that while in the hydrogenation reaction the mechanisms is conditioned by the H2 cleavage with a high energy barrier, in the hydration reaction the formation of a transient four member ring structure favoring an attractive local hydrogen bond interaction pushes the reaction toward the product with a considerably lower energy barrier.

Reaction electronic flux and its role in DNA intramolecular proton transfers.

Proton transfer reactions present a key step in many biological and chemical processes. Here, we focused on the electronic changes in the proton transfer reactions of the four DNA bases. In combination with the previous structural analysis the reaction electronic flux together with local descriptors as the Hirshfeld-I charges allow us to identify chemical events and rationalize the underlying reaction mechanism. Our results show that imine-enamine in adenine and citosyne, and keto-enol tautomerizations in thymine and guanine have different reaction mechanisms. The former involve net structural rearrangements driven by favoured electrostatic interactions between the proton and the acceptor atom whereas the keto-enol tautomerizations require electronic changes reflected in the reaction electronic flux and changes in the NBO bond orders which favour the proton transfer reaction.

Kudi: A free open-source python library for the analysis of properties along reaction paths.

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi.

How a Quantum Chemical Topology Analysis Enables Prediction of Electron Density Transfers in Chemical Reactions. The Degenerated Cope Rearrangement of Semibullvalene.

Recent works on the reaction mechanism for the degenerated Cope rearrangement (DCR) of semibullvalene (SBV) in the ground state prompted us to investigate this complex rearrangement in order to assign experimentally observed contrast features in the simulated electron distribution. We present a joint use of the electron localization function (ELF) and Thom's catastrophe theory (CT) as a powerful tool to analyze the electron density transfers along the DCR. The progress of the reaction is monitored by the structural stability domains of the topology of ELF, while the change between them is controlled by turning points derived from CT. The ELF topological analysis shows that the DCR of SBV corresponds to asynchronous electron density rearrangement taking place in three consecutive stages. We show how the pictures anticipated by drawing Lewis structures of the rearrangement correlate with the experimental data and time-dependent quantum description of the process.