I would like to submit an erratum for the article with the title ‘Development of Kinetic Energy Density Functional Using Response Function Defined on the Energy Coordinate’ (Int. J. Quantum Chem. 2022;e26969, https://doi.org/10.1002/qua.26969). The corresponding author of the article is Hideaki Takahashi. The author found an error in producing the graph with the legend ‘OF-DFT’ in Fig. 8 in the article. The error in the graph is attributed to the fact that the atomic response function was spuriously multiplied by 2. We refer the editor to the main text of the erratum in more details. The graph was revised using the amended source code. Fortunately, it was found that the corrected graph was changed favorably as compared to the original one, showing better agreement with the reference calculation.
A set of new rasagiline derivatives is presented. They were designed to be antioxidant compounds with the potential to be used for treating neurodegenerative disorders. They are expected to be multifunctional molecules that can help reduce oxidative stress, which is thought to contribute to neurodegenerative disorders. The CADMA-Chem computational protocol was used to produce rasagiline derivatives and to evaluate their likeliness as oral drugs and antioxidants. Three of them were identified as the most promising ones. They are proposed to be better free radical scavengers than rasagiline. In addition, they are expected to keep the parent's molecule neuroprotective capability. Hopefully, the results presented here would promote further experimental and theoretical investigations on these compounds.
Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6-31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (ΔE, ΔH, and ΔG) of each reaction were calculated. A plot of the Gibbs energies of activation (ΔG‡) for C5 substituted Cyt and H2Cyt against the Hammett σ-constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher ΔG‡ and lower σ values compared to those of H2Cyt deamination reactions. C5 alkyl substituents (−H, −CH3, −CH2CH3, −CH2CH2CH3) increase ΔG‡ values for Cyt, while the same substituents decrease ΔG‡ values for H2Cyt which is likely due to steric effects. However, the Hammett σ-constants were found to decrease for both the Cyt and H2Cyt. Both ΔG‡ and σ values decrease for the substituents Cl and Br in the reaction Cyt, while ΔG‡ values increase and σ decrease in the reaction H2Cyt. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H2Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, ΔG‡ also increase for the C5 alkyl substituents (-H, −CH3, −CH2CH3, −CH2CH2CH3) in Cyt, while ΔG‡ decrease in H2Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO‒LUMO gap and activation energies.
Here we show that substituting the ten protons in the dianion of a bispentalene derivative (C18H102-) by six Si2+ dications produces a minimum energy structure with two planar tetracoordinate carbons (ptC). In Si6C18, the ptCs are embedded in the terminal C5 pentagonal rings and participate in a three-center, two-electron (3c-2e) Si-ptC-Si σ-bond. Our exploration of the potential energy surface identifies a triphenylene derivative as the putative global minimum. But robustness to Born-Oppenheimer molecular dynamics (BOMD) simulations at 900 and 1500 K supports bispentalene derivative kinetic stability. Chemical bonding analysis reveals ten delocalized π-bonds, which, according to Hückel’s 4n+2 π-electron rule, would classify it as an aromatic system. Magnetically induced current density analysis reveals the presence of intense local paratropic currents and a weakly global diatropic current, the latter agreeing with the possible global aromatic character of this specie.
The oxygen electroreduction mechanism on the V- and Nb-doped nitrogen-codoped (6,6)armchair carbon nanotube with incorporated MN4 fragment has been studied using the ωB97XD and PBE density functional theory approaches. The metal center in MN4 fragment and the adjacent NC=CN double bond (C2 site) of the support have been revealed as active centers. The metal active centers turned out to be irreversibly oxidized at the first step of ORR affording stable O*, 2O*, or O*HO* adsorbates depending on the applied electrode potential U, that makes them no longer active in ORR. Therefore, the C2 site comes at the forefront in ORR catalysis. Among the metal oxidized forms M(O)N4–, M(O)(O)N4– and M(O)(OH)N4–CNT, the C2 site of the latter turned out to be most active for 4e dissociative ORR. For both metals the last protonation/electron transfer step, HO* + H* = H2O, is the rate-limiting step. The alternative hydrogen peroxide formation is not only thermodynamically less favorable but also kinetically slower than the 4e dissociative ORR route on the C2 site of model M(O)(OH)N4–CNT catalyst.
The three lowest spin states (S=0,1,2) of twelve representative Na13+ isomers have been studied using both, KS-DFT via three hybrid density functionals, and benchmark multireference CASSCF and CASPT2 methods with a couple of Dunning’s correlation consistent basis sets. CASSCF(12,12) geometry optimizations were carried out. Since 12 electrons in 12 active orbitals span the chemically-significant complete valence space, the results of the present study provide benchmarks for Na13+. The CASPT2(12,12)/cc-pVTZ* lowest energy structures are three nearly degenerate singlets (S=0): an isomer formed from two pentagonal bipyramids fused together (PBPb), a capped centered-squared antiprism [CSAP-(1,3)] and an optimum tetrahedral OPTET(II) structure, the last two lying 0.88 and 1.63 kcal/mol above the first, respectively. The lowest triplet (S=1) and quintet (S=2) states lie 4.33 and 3.77 kcal/mol above the singlet global minimum, respectively. The latter is a deformed icosahedron while the former is a CSAP-(1,3). The flatness of the potential energy surface of this cluster suggests a rather strong dynamical character at finite temperature. Prediction of the lowest energy structures and electronic properties is crucially sensitive both to non-dynamical and dynamical electron correlation treatment. The CASPT2 vertical ionization energy is 3.66 eV, in excellent agreement with the $3.6 \pm 0.1$ eV experimental figure. All the isomers are found to have a strong multireference character, thus making Kohn-Sham density functional theory fundamentally inappropriate for these systems. Only large multiconfigurational complete active space self-consistent field (CASSCF) wavefunctions provide a reliable zeroth-order description; then the dynamic correlation effects must be properly taken into account for a truly accurate account of the structural and energetic features of alkali-metal clusters.
A technique is described to compute topological indices for supramolucular rosettes of tetraphenylethylene (TPE) and terpyridine (TPY) ligands with its applications on physicochemical and biological properties. This technique, we have applied to a self assembled TPE and TPY supramolucular graphs which is obtained in the form of rosette cycles. Also these type of rosettes graph finds significant applications in electrical sensors, light emitting diodes, bioimaging and photoelectric devices etc. As regarded to the next generation sensing applications with a typical induced aggregative emission behaviour, tetraphenylethylene can be utilised in constructing fluorescent probes. For this supramolucular systems we have done a work by computing some topological indices such as the variants of Zagreb index, Randić index, Sum Connectivity index, ABC index and Harmonic index.
Density functional calculations have been carried out to investigate the possibility of trapping of noble gas dimers by cyclocarbon dimer. Parallel-displaced conformation of the cyclocarbon dimer is found to be the minimum energy structure. Non-covalent interaction is found to hold the noble gas dimers. The lighter noble gases (He, Ne) posses repulsive interactions, the heavier one (Ar, Kr) are held by attractive interactions forming genuine bonds. Each of the noble gas atoms in turn forms non-covalent interaction with the cyclocarbon monomers. The bond dissociation energy of the noble gas dimers dramatically increases inside the cyclocarbon dimer. Energy decomposition analysis reveals that dispersion plays the major role towards the stabilization energy.
Non covalent biliproteins are found in a growing number of living organisms and even in viruses, such as SARS-CoV-2. Unlike the well described covalent biliproteins, such as the phytochromes, they present a vast structural and functional diversity, and often with limited experimental information. A very important tool (and sometimes the only one available) to study these systems is the UV-Vis spectrum, which is modulated both by conformational changes of the biliverdin chromophore and specific interactions with the apoprotein. In this work we present a theoretical study of the microscopic determinants of the UV-Vis spectrum of these compounds through the use of hybrid QM(TD-DFT)/MM techniques and molecular dynamics simulations. Comparing our results with existing experimental data, we prove that it is possible to predict spectroscopic properties, such as relative position and intensity ratio of main bands, with affordable methods, and to provide a microscopic explanation of them. This systematic information can be very useful for the study of described biliproteins or for those yet unknown.
Imidazole derivatives are the foundation of different types of drugs with a wide range of biological activities. In this study, the genetic algorithm multiple linear regression (GA- MLR), and backpropagation-artificial artificial neural network (BP-ANN) were applied to design QSPR models to predict the quantum chemical properties like the entropy(S) and enthalpy of formation(∆Hf) of imidazole derivatives. In order to draw molecular structure of 84 derivative compounds Gauss View 05 program was used. These structures were optimized at DFT-B3LYP / 6-311G* level with Gaussian09W. The Dragon software was used to calculate a set of different molecular descriptors, and the genetic algorithm procedure and backward stepwise regression were applied for the selection of descriptors. The resulting quantitative GA-MLR model of ∆Hf, showed that there is good linear correlation between the selected descriptors and ∆Hf of compounds. Also the results show that the BP-ANN model appeared to be superior to GA-MLR model for prediction of entropy. Different internal and external validation metrics were adopted to verify the predictive performance of QSPR models. The predictive powers of the models were found to be acceptable. Thus, these QSPR models may be useful for designing new series of imidazole derivatives and prediction of their properties.
We present ultra-fast quantum chemical methods for the calculation of infrared and ultraviolet-visible spectra designed to provide fingerprint information during autonomous and interactive explorations of molecular structures. Characteristic spectral signals can serve as diagnostic probes for the identification and characterization of molecular structures. These features often do not require ultimate accuracy with respect to peak position and intensity, which alleviates the accuracy--time dilemma in ultra-fast electronic structure methods. If approximate ultra-fast algorithms are supplemented with an uncertainty quantification scheme for the detection of potentially large prediction errors in signal position and intensity, an offline refinement will always be possible to confirm or discard the predictions of the ultra-fast approach. Here, we present ultra-fast electronic structure methods for such a protocol in order to obtain ground- and excited-state electronic energies, dipole moments, and their derivatives for real-time applications in vibrational spectroscopy and photophysics. As part of this endeavor, we devise an information-inheritance partial Hessian approach for vibrational spectroscopy, a tailored subspace diagonalization approach and a determinant-selection scheme for excited-state calculations.
Lithium-decorated (Li-decorated) C3N has been investigated as a potential material for high capacity reversible hydrogen storage. The energetic stability, dynamical stability and thermal stability were studied, indicating that C3N is energetically stable, imaginary frequencies are not found from the result of phonon spectrum calculation, and the free energy vibrates slightly around -64.63 eV during the 5000 fs period and no structure reconstruction. Electronic properties showed the band gaps are 0.39 eV and 1.12 eV, via PBE and HSE calculations, respectively. The four probable Li-adsorbed sites were calculated, indicating that the hollow site above the center of a hexagon ring HC site is the most likely site to absorb Li atom. Hydrogen molecules were added one by one to research the maximum hydrogen gravimetric density. Each Li atom can attach 10 hydrogen molecules within the range of physical adsorption processes (-0.1 ~ -0.4 eV/H2) and the hydrogen storage capacity can reach 8.81 wt%. Li-decorated C3N shows the greatest potential for on-board reversible solid-state hydrogen molecule storage application.
Sulfur hexafluoride decompositions have been studied to analyze their adsorption properties on pristine graphene (PG) and Mg-doped graphene (MgG). First of all, after calculating the formation energy of three Mg doping sites, the T doping site of Mg-doped graphene is the most stable one. Then, several characteristic structures with different orientations and positions of the gas molecules have been used to adsorb on PG and MgG, respectively. By calculating the adsorption energies and distance, the most stable adsorption structure of each gas molecule is obtained. In addition, charge transfer (Qt), the density of states (DOS) distribution, the energy of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were used to further analyze the conductivity change and chemical stability of each adsorption system. The results indicate that the adsorption interactions of H2S, SO2, SOF2 and SO2F2 on PG are weak. H2S adsorbed on MgG presented physical adsorption, while the adsorption behaviors of SO2, SOF2 and SO2F2 on MgG are chemisorption. And the adsorption strength was SO2F2 > SOF2 > SO2. In short, MgG shows better selectivity and higher sensitivity to SO2, SOF2 and SO2F2 than PG, demonstrating that the MgG material can be used as suitable gas sensing equipment based on SF6 decomposition products detection, which provides a meaningful guide of alkaline earth metal doped graphene in the detection of partial discharge and partial overheat in gas-insulated switchgears (GIS).
Singlet and triplet spin state energies for three-dimensionalHooke atoms, i .e. electrons in a quadratic confinement, with even number of electrons (2, 4, 6, 8, 10) is discussed using Full-CI and CASSCF type wavefunctions with a variety of basis sets and considering perturbative corrections up to second order. The effect of the screening of the electron-electron interaction is also discussed by using a Yukawa-type potential with different values of the Yukawa screening parameter (λee =0.2, 0.4, 0.6, 0.8, 1.0). Our results show that the singlet state is the ground state for 2 and 8 electron Hooke atoms, whereas the triplet is the ground spin state for 4, 6 and 10 electron systems. This suggests the following Auf bau structure 1s < 1p < 1d with singlet ground spin states for systems in which the generation of the triplet implies an inter-shell one electron promotion, and triplet ground states in cases when there is a partial filling of electrons of a given shell. It is also observed that the screening of electronelectron interactions has a sizable quantitative effect on the relative energies of both spin states, specially in the case of 2 and 8 electron systems, favouring the singlet state over the triplet. However, the screening of the electron-electron interaction does not provoke a change in the nature of the ground spin state of these systems. By analyzing the different components of the energy, we have gained a deeper understanding of the effects of the kinetic, confinement and electron-electron interaction components of the energy.
We have designed Ti3AlB2 and two new layered ordered double-transition metals MAX compound Ti2ZrAlB2 based on the structure of Ti3AlC2. By first-principles calculations with density functional theory, their structure, phase stability, elastic properties, electronic properties and thermal properties have been further investigated. Results show that they are all energetic, thermodynamically and mechanically stable. The bulk modulus, shear modulus, Young's modulus, Poisson's ratio and Debye temperature were computed to discuss their elastic and thermal properties. Results show that they are all good ductile materials with high melting points. Density of states and electron localization function of these three phases were presented to research the chemical bonds and explore the reason limiting their melting points.
In thiswork,we have computed and implemented one-body integrals concerning gaussian confinement potentials over gaussian basis functions. Then, we have set an equivalence between gaussian and Hooke atoms and we have observed that, according to singlet and triplet state energies, both systems are equivalent for large confinement depth for a series of even number of electrons n = 2, 4, 6, 8 and 10. Unlike with harmonic potentials, gaussian confinement potentials are dissociative for small enough depth parameter; this feature is crucial in order to model phenomena such as ionization. In this case, in addition to corresponding Taylor series expansions, the first diagonal and sub-diagonal Padé approximant were also obtained, useful to compute the upper and lower limits for the dissociation depth. Hence, this method introduces new advantages compared to others.
The rapid and successful strides in quantum chemistry in the past decades can be largely credited to a conspicuous synergy between theoretical and computational advancements. However, the architectural computer archetype that enabled such a progress is approaching a state of more stagnant development. One of the most promising technological avenues for the continuing progress of quantum chemistry is the emerging quantum computing paradigm. This revolutionary proposal comes with several challenges, which span a wide array of disciplines. In chemistry, it implies, among other things, a need to reformulate some of its long established cornerstones in order to adjust to the operational demands and constraints of quantum computers. Due to its relatively recent emergence, much of quantum computing may still seem fairly nebulous and largely unknown to most chemists. It is in this context that here we review and illustrate the basic aspects of quantum information and their relation to quantum computing insofar as enabling simulations of quantum chemistry. We consider some of the most relevant developments in light of these aspects and discuss the current landscape when of relevance to quantum chemical simulations in quantum computers.
A kinetic energy functional Ee was developed within the framework of the density-functional theory (DFT) based on the energy electron density for the purpose of realizing the orbital-free DFT. The functional includes the nonlocal term described with the linear-response function (LRF) of a reference system. As a notable feature of the present approach, the LRF is represented on the energy coordinate ε defined for each system of interest. In addition, an atomic system is taken as a reference system for the construction of the LRF, which shows a clear difference from the conventional approach based on the homogeneous electron gas. The explicit form of the functional Ee was formulated by means of the coupling-parameter integration scheme. The functional Ee was applied to the calculations of the kinetic energies of the pseudo atoms that mimics H, He, Ne, and Ar. Explicitly, the kinetic energy of each atom was computed using the functional Ee with respect to the variation of the valence charge Zv of each atom. In these calculations, the electron density n optimized by the Kohn-Sham DFT was adopted as an argument of the functional. It was found that the results are in excellent agreements with those given by the Kohn-Sham DFT. We also devised a method to perform the self-consistent field calculation utilizing the functional Ee The method was applied to the computation of the radial distribution functions of the electrons in the pseudo Ne and Ar atoms. It was demonstrated that the results reasonably agree with those yielded by the Kohn-Sham DFT.