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.
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.
Interactions of antimony-oxide clusters with trypanothione have been modelled to understand their inhibitory activity against leishmaniasis. Trypanothione is essential for the survival of leishmania parasites because it is responsible for maintaining their cellular thiol-disulfide redox regulation. Density functional theory (DFT) calculations show that the SbV oxide clusters form hydrogen bonds from the oxygens to the amine and carboxyl group of the trypanothione. The reaction between trypanothione and the SbV oxide cluster does not break the S-S bond of trypanothione, whereas the reaction with antimony-oxide clusters containing at least one SbIII atom leads to dissociation of the S-S bond of both the oxidized and the reduced form of trypanothione suggesting that antimony-oxide clusters with at least one SbIII atom may destroy trypanothione that is vital for the parasite metabolism.
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.
This work reports on a novel computational approach to the efficient evaluation of one-electron coupling coefficients as they are required during spin-adapted electronic structure calculations of the configuration interaction type. The presented approach relies on the equivalence of the representation matrix of excitation operators in the basis of configuration state functions and the representation matrix of permutation operators in the basis of genealogical spin eigenfunctions. After the details of this connection are established for every class of one-electron excitation operator, a recursive scheme to evaluate permutation operator representations originally introduced by Yamanouchi and Kotani is recapitulated. On the basis of this scheme we have developed an efficient algorithm that allows the evaluation of all nonredundant coupling coefficients for systems with 20 unpaired electrons and a total spin of S = 0 within only a few hours on a simple Desktop-PC. Furthermore, a full-CI implementation that utilizes the presented approach to one-electron coupling coefficients is shown to perform well in terms of computational timings for CASCI calculations with comparably large active spaces. More importantly, however, this work paves the way to spin-adapted and configuration driven selected configuration interaction calculations with many unpaired electrons.
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.
Polynomial graph invariants have been confirmed to have important applications in quantum chemistry and biological information. One of the famous polynomial graph invariants is the Tutte polynomial which gives multifarious interesting information about the graph structure. In this paper, we first give a simpler and more efficient method to get the Tutte polynomials of alternating polycyclic chains. Then we obtain the explicit expressions for the Tutte polynomials and the number of spanning trees of phenylene systems with given number of branching hexagons. Moreover, we determine the extremal values of the number of spanning trees among the phenylene systems with given one or two branching hexagons, and the corresponding extremal phenylene systems are characterized, respectively.
Through the comprehensive analysis of ab initio and experimental results of a large number of diatomic systems, the systematic deviation of ab initio method in vibrational energies prediction caused by physical/mathematical simplification is located. A joint ab initio and machine learning method based on information across molecules is proposed to deal with the problem. Starting from an ab initio model, and then systematically modifying it through machine learning, the vibrational energies prediction of many diatomic systems (SiC, HBr, NO, PC, N2, SiO, O2, ClF, etc.) have been improved, and significantly surpassed the more complex ab initio model. In addition to the improvement of accuracy, the new method also greatly reduces the computational expense, and is applicable for the systems without experimental data.
In order to study the properties of new energetic compounds formed by introducing nitroazoles into 2,4,6-trinitrobezene, the density, heat of formation and detonation properties of 36 nitro-1-(2,4,6-trinitrobenzene)-1H-azoles energetic compounds are studied by density functional theory, and their stability and melting point are predicted. The results show that most of target compounds have good detonation properties and stability. And it is found that nitro-1-(2,4,6-Trinitrophenyl)-1H-pyrrole compounds and nitro-1-(2,4,6-trinitropenyl)-1H-Imidazole compounds have good thermal stability, and their weakest bond is C-NO2 bond, the bond dissociation energy of the weakest bond is 222 kJ mol-1-238 kJ mol-1 and close to TNT (235 kJ mol-1). The weakest bond of the other compounds may be the C-NO2 bond or the N-N bond, and the strength of the N-N bond is related to the nitro group on azole ring.
Histidine (an imidazole-based amino acid) is a promising building block for short aromatic peptides containing a proton donor/acceptor moiety. Previous studies have shown that polyalanine helical peptides substituted at regular intervals with histidine residues exhibit both structural stability as well as high proton affinity and high conductivity. Here, we present first-principle calculations of non-aqueous histidine-containing 310-, and -helices and show that they are able to form hydrogen-bonded networks mimicking proton wires that have the ability to shuttle protons via the Grotthuss shuttling mechanism. The formation of these wires enhances the stability of the helices, and our structural characterizations confirm that the secondary structures are conserved despite distortions of the backbones. In all cases, the helices exhibit high proton affinity and proton transfer barriers on the order of 1~4 kcal/mol. Zero-point energy calculations suggest that for these systems, ground state vibrational energy can provide enough energy to cross the proton transport energy barrier. Additionally, ab initio molecular dynamics results suggests that the protons are transported unidirectionally through the wire at a rate of approximately 2 Å every 20 fs. These results demonstrate that efficient deprotonation-controlled proton wires can be formed using non-aqueous histidine-containing helical peptides.
Graphene quantum dots (GQDs) are known for their low toxicity, strong fluorescence, high surface area, large solubility and tunable band gaps. However, the change in their properties depends on the preparation processes of GQDs. Thus, certain types of preparation lead to certain defects, such as surface defect, edge defects, Stone-Wales defect. These structural defects are responsible for hindering GQDs to possess their regular shape that affects the morphological properties of GQDs. Thus, the optical and electrical properties get affected. The GQDs, which are synthesized via acidic methods are generally more vulnerable to defects compared to those synthesized using eco-friendly methods. Thereby, the aim of this review is to discuss the causes of structural defects. Moreover, it focuses on how they affect the properties of GQDs and to what extent they affect them. The processes of regulating defects have been elucidated so that more efficient applications can be designed using GQDs with controlled amounts of defects.
The effect of the presence of a deuterium (D) or tritium (T) isotope bonded to the alpha carbon of glycine is determined without the need to apply external forces e.g. electric fields or using normal mode analysis. Isotopic effects were accounted for using the mass-dependent diagonal Born-Oppenheimer energy correction (DBOC) at the CCSD level of theory. We calculated the stress tensor trajectories of the dominant C-N bond within next generation quantum theory of atoms in molecules (NG-QTAIM). S-character chirality was discovered using the stress tensor trajectories, instead of the Cahn–Ingold–Prelog (CIP) rules, for ordinary glycine. The S-character chirality was preserved after the substitution of the H on the alpha carbon for a D isotope but transformed to R-character chirality after replacement with the T isotope. This reversal of the chirality depending on the presence of a single D or T isotope bound to the alpha carbon adds to the debate on the nature of the extraterrestrial origins of chirality in simple amino acids. We demonstrate that NG-QTAIM is a promising tool for understanding isotopic induced electronic charge density changes, useful in analysis of infrared (IR) or circular dichroism (CD) spectra explaining changes in mode couplings and bands intensities or sign.
The noncovalent interactions between a redox-active molecule, phenyl-substituted dithiafulvene (Ph-DTF), and ten commonly encountered nitroaromatic compounds (NACs) were systematically investigated by means of density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations. Our modeling studies examined their 1:1 complexes in terms of equilibrium geometries, frontier molecular orbitals (FMOs), nature of noncovalent forces, intermolecular charge transfer (ICT), interaction energies and related energy decomposition analysis. The computational results indicate that Ph-DTF can form thermodynamically stable supramolecular complexes with trinitro-substituted benzenes (e.g., 2,4,6-trinisuchtrotoluene and picric acid), but its interactions with mono- and dinitrobenzenes do not exhibit such stability. The selective binding properties are further corroborated by AIMD simulations. Overall, this computational work establishes a comprehensive understanding of the nature of noncovalent interactions of Ph-DTF with various NACs, and the results can be used as theoretical guidance for the rational design of selective receptors and/or chemosensors for certain NACs that are of great concern in current industrial applications and environmental control.