Showing papers in "International Journal of Quantum Chemistry in 2021"

Topological indices and QSPR/QSAR analysis of some antiviral drugs being investigated for the treatment of COVID-19 patients.

Abstract: The spread of novel virus SARS-CoV-2, well known as COVID-19 has become a major health issue currently which has turned up to a pandemic worldwide. The treatment recommendations are variable. Lack of appropriate medication has worsened the disease. On the basis of prior research, scientists are testing drugs based on medical therapies for SARS and MERS. Many drugs which include lopinavir, ritonavir and thalidomide are listed in the new recommendations. A topological index is a type of molecular descriptor that simply defines numerical values associated with the molecular structure of a compound that is effectively used in modeling many physicochemical properties in numerous quantitative structure-property/activity relationship (QSPR/QSAR) studies. In this study, several degree-based and neighborhood degree sum-based topological indices for several antiviral drugs were investigated by using a M-polynomial and neighborhood M-polynomial methods. In addition, a QSPR was established between the various topological indices and various physicochemical properties of these antiviral drugs along with remdesivir, chloroquine, hydroxychloroquine and theaflavin was performed in order to assess the efficacy of the calculated topological indices. The obtained results reveal that topological indices under study have strong correlation with the physicochemical characteristics of the potential antiviral drugs. A biological activity (pIC50) of these compounds were also investigated by using multiple linear regressions (MLR) analysis.

Assessing conformer energies using electronic structure and machine learning methods

Abstract: We have performed a large-scale evaluation of current computational methods, including conventional small-molecule force fields, semiempirical, density functional, ab initio electronic structure methods, and current machine learning (ML) techniques to evaluate relative single-point energies. Using up to 10 local minima geometries across ~700 molecules, each optimized by B3LYP-D3BJ with single-point DLPNO-CCSD(T) triple-zeta energies, we consider over 6,500 single points to compare the correlation between different methods for both relative energies and ordered rankings of minima. We find promise from current ML methods and recommend methods at each tier of the accuracy-time tradeoff, particularly the recent GFN2 semiempirical method, the B97-3c density functional approximation, and RI-MP2 for accurate conformer energies. The ANI family of ML methods shows promise, particularly the ANI-1ccx variant trained in part on coupled-cluster energies. Multiple methods suggest continued improvements should be expected in both performance and accuracy.

Distance based and bond additive topological indices of certain repurposed antiviral drug compounds tested for treating COVID-19.

Abstract: The entire world is struggling to control the spread of coronavirus (COVID-19) as there are no proper drugs for treating the disease. Under clinical trials, some of the repurposed antiviral drugs have been applied to COVID-19 patients and reported the efficacy of the drugs with the diverse inferences. Molecular topology has been developed in recent years as an influential approach for drug design and discovery in which molecules that are structurally related show similar pharmacological properties. It permits a purely mathematical description of the molecular structure so that in the development of identification of new drugs can be found through adequate topological indices. In this paper, we study the structural properties of the several antiviral drugs such as chloroquine, hydroxychloroquine, lopinavir, ritonavir, remdesivir, theaflavin, nafamostat, camostat, umifenovir and bevacizumab by considering the distance and bond measures of chemical compounds. Our quantitative values of the topological indices are extremely useful in the recent development of designing new drugs for COVID-19.

Generalized unitary coupled cluster excitations for multireference molecular states optimized by the Variational Quantum Eigensolver

Abstract: The variational quantum eigensolver (VQE) algorithm, designed to calculate the energy of molecular ground states on near-term quantum computers, requires specification of symmetries that describe the system, e.g. spin state and number of electrons. This opens the possibility of using VQE to obtain excited states as the lowest energy solutions of a given set of symmetries. In this paper, the performances of various unitary coupled cluster (UCC) ansatze applied to VQE calculations on excited states are investigated, using quantum circuits designed to represent single reference and multireference wavefunctions to calculate energy curves with respect to variations in the molecular geometry. These ansatze include standard UCCSD, as well as modified versions of UCCGSD and k-UpCCGSD which are engineered to tackle excited states without undesired spin symmetry cross-over to lower states during VQE optimization. These studies are carried out on a range of systems including H$_2$, H$_3$, H$_4$, NH, and OH$^{+}$, CH$_2$, NH$^{+}_{2}$, covering examples of spin singlet, doublet and triplet molecular ground states with single and multireference excited states. In most cases, our calculations are in excellent agreement with results from full configuration interaction calculations on classical machines, thus showing that the VQE algorithm is capable of calculating the lowest excited state at a certain symmetry, including multireference closed and open shell states, by setting appropriate restrictions on the excitations considered in the cluster operator, and appropriate constraints in the qubit register encoding the starting mean field state.

Chemical insights into the electronic structure of Fe(II) porphyrin using FCIQMC, DMRG, and generalized active spaces

Abstract: Stochastic-CASSCF and DMRG procedures have been utilized to quantify the role of the electron correlation mechanisms that in a Fe-porphyrin model system are responsible for the differential stabilization of the triplet over the quintet state. Orbital entanglement diagrams and CI-coefficients of the wave function in a localised orbital basis allow for an effective interpretation of the role of charge-transfer configurations. A preliminary version of the Stochastic Generalized Active Space Self-Consistent Field method has been developed and is here introduced to further assess the pi-backdonation stabilizing effect.By the new method excitations between metal and ligand orbitals can selectively be removed from the complete CI expansion. It is demonstrated that these excitations are key to the differential stabilization of the triplet, effectively leading to a quantitative measure of the correlation enhanced pi-backdonation.

General cut method for computing Szeged‐like topological indices with applications to molecular graphs

Abstract: Szeged, PI and Mostar indices are some of the most investigated distance-based molecular descriptors. Recently, many different variations of these topological indices appeared in the literature and sometimes they are all together called Szeged-like topological indices. In this paper, we formally introduce the concept of a general Szeged-like topological index, which includes all mentioned indices and also infinitely many other topological indices that can be defined in a similar way. As the main result of the paper, we provide a cut method for computing a general Szeged-like topological index for any strength-weighted graph. This greatly generalizes various methods known for some of the mentioned indices and therefore rounds off such investigations. Moreover, we provide applications of our main result to benzenoid systems, phenylenes, and coronoid systems, which are well-known families of molecular graphs. In particular, closed-form formulas for some subfamilies of these graphs are deduced.

The expected values of Sombor indices in random hexagonal chains, phenylene chains and Sombor indices of some chemical graphs

Abstract: Hexagonal chains are a special class of catacondensed benzenoid system and phenylene chains are a class of polycyclic aromatic compounds. Recently, A family of Sombor indices was introduced by Gutman in the chemical graph theory. It had been examined that these indices may be successfully applied on modeling thermodynamic properties of compounds. In this paper, we study the expected values of the Sombor indices in random hexagonal chains, phenylene chains, and consider the Sombor indices of some chemical graphs such as graphene, coronoid systems and carbon nanocones.

Topological analysis of para‐line graph of Remdesivir used in the prevention of corona virus

Abstract: Topological indices are the molecular descriptors that characterize the formation of chemical compounds and they assist us to predict certain physical–chemical properties like molar refraction, molar volume, chromatographic behavior, boiling point, heat of vaporization and partition coefficient. The computation of the topological index of a drug design enable researchers to have a high quality conception of the physical science and bioorganic characteristics of drugs. Reverse degree based topological indices play important role for calculation of topological descriptor. Para‐line graphs are used to illustrate the molecular structure in another way and these illustrations are valuable in structural chemistry. In this article, we present some reverse degree based topological indices namely, the reverse general Randic index, the reverse atom bond connectivity index, the reverse geometric arithmetic index, the reverse forgotten index, the reverse Balaban index and different types of Zagreb indices for the para‐line graph of Remdesivir. The results attained can help in the design of new medicine for the prevention of corona virus. [ABSTRACT FROM AUTHOR] Copyright of International Journal of Quantum Chemistry is the property of John Wiley & Sons, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

High‐precision calculation of relativistic corrections for hydrogen‐like atoms with screened Coulomb potentials

Abstract: The first-order relativistic corrections to the non-relativistic energies of hydrogen-like atom embedded in plasma screening environments are calculated in the framework of direct perturbation theory by using the generalized pseudospectral method. The standard Debye-Huckel potential, exponential cosine screened Coulomb potential, and Hulthen potential are employed to model different screening conditions and their effects on the eigenenergies of hydrogen-like atoms are investigated. The relativistic corrections which include the relativistic mass correction, Darwin term, and the spin-orbit coupling term for both the ground and excited states are reported as functions of screening parameters. Comparison with previous theoretical predictions shows that both the relativistic mass correction and spin-orbit coupling obtained in this work are in good agreement with previous estimations, while significant discrepancy and even opposite trend is found for the Darwin term. The overall relativistic-corrected system energies predicted in this work, however, are in good agreement with the fully relativistic calculations available in the literature. We finally present the scaling law of the first-order relativistic corrections and discuss the validity of the direct perturbation theory with respect to both the nuclear charge and the screening parameter.