Reactivity of thymine peroxy radical in DNA and its fate under hypoxia or oxygen-less conditions are studied at the M06-2X/6-31+G(d,p) level. The spaciously most accessible H2’ can be abstracted by C6-peroxy radical in an intranucleotidyl manner with the estimated barriers of 18.8 ~ 21.1 kcal/mol. The calculations show that C6-peroxy radical has a highly more reactivity towards C(sp3)-H abstraction reactions than its relative C6-yl, which is a counter-intuitive case. The formed hydroperoxide with the C6-OaObH2’ constituent can fast transfer ObH2’ group to C2’ radical in an intranucleotidyl manner with a low barrier (ca. 13.2 kcal/mol) and very strong heat release. The results show that the formed hydroperoxide product is unstable so that it could be quickly transformed into other species and thus is very hard to be experimentally observed. Afterwards, H2’ can be again abstracted by C6-oxyl radical to result in formation of thymine glycol which is the main products. The parallel C5-C6 bond scission reaction leads to formation of the precursor for 5-hydroxy-5-methylhydantion. The two competitive reactions have very low barriers. Based on our present calculations, the new radical reaction paths to formation of the DNA oxidation products are suggested under hypoxia or oxygen-less conditions, which is different from the previously suggested paths under high oxygen concentration surroundings.
With the aim of describing bound and continuum states for diatomic molecules, we develop and implement a spectral method that makes use of Generalized Sturmian Functions (GSF) in prolate spheroidal coordinates. In order to master all computational issues, we apply here the method to one-electron molecular ions and compare it with benchmark data for both ground and excited states. We actually propose two different computational schemes to solve the two coupled differential equations. The first one is an iterative 1d procedure in which one solves alternately the angular and the radial equations, the latter yielding the state energy. The second, named direct $2d$ method, consists in representing the Hamiltonian matrix in a two–dimensional GSF basis set, and its further diagonalization. Both spectral schemes are timewise computationally efficient since the basis elements are such that no derivatives have to be calculated numerically. Moreover, very accurate results are obtained with minimal basis sets. This is related on one side to the use of the natural coordinate system and, on the other, to the intrinsic good property of all GSF basis elements that are constructed as to obey appropriate physical boundary conditions. The present implementation for bound states paves the way for the study of continuum states involved in ionization of one or two-electron diatomic targets.
In this study, we performed density functional theory calculations using the B3LYP, M052X, M062X, and APFD functionals to investigate substituent effects on the mechanism of 1,3-dipolar cycloaddition, a classical and effective method for the synthesis of heterocyclic compounds. The results showed that changing the substituents on the chloroxime compounds affects the energy level of the highest occupied molecular orbital and consequently, the progress of the reaction. Finally, it provided an effective idea for this kind of reaction in the design of organic synthesis and the necessary theoretical basis for revealing the course of this reaction.
The pattern of cyclic conjugation was thoroughly studied in the series of N- and P-acenaphthylene derivatives using several different aromaticity indices: the energy effect (ef), multicenter delocalization index (MCI), harmonic oscillator model of aromaticity (HOMA) index and nucleus independent chemical shifts (NICS). The Kekulé-structure-based reasoning predicts that there would be no cyclic conjugation in the “empty” five-membered heteroatom-containing rings in the studied molecules. It was found that, according to the ef, MCI and HOMA values, the extent of cyclic conjugation in the pentagonal rings is strongly influenced by the number and mutual arrangement of the hexagonal rings. In addition, it was revealed that in some of the examined molecules the intensity of cyclic conjugation in the “empty” pentagons is even stronger than that of some hexagonal rings within the same molecule. The obtained results refute what one would expect based on ”chemical intuition”, which is usually strongly rooted to the Kekulé structures.
The performance of a series of density functionals has been tested for the insertions of ethylene, methyl acrylate (MA), and vinyl bromide (VB) catalyzed by α-diimine palladium complexes. Sixty-seven density functionals are screened, and the results are compared with available experimental data. Eleven hybrid functionals (M06, BHandH, mPW1PW91, HSEh1PBE, mPW3PBE, LC-ωPBE, mPW1PBE, PBE0, M06-HF, M06-2X, M05-2X) showed better performance in the insertions of both ethylene and MA, and could be therefore suitable for ethylene-MA copolymerization. Meanwhile, three GGA (PW91PW91, HCTH, HCTH407), two meta-GGA (TPSSTPSS, tHCTH), and ten hybrid functionals (M06, BHandH, TPSSh, B971, B98, B1B95, PBE0, M06-2X, tHCTHhyb, M05-2X) perform well in the ethylene-VB copolymerization. Besides, nine D3 or D3BJ augmented functionals are found to be suitable for both copolymerization systems. The D2 dispersion correction overestimated insertion energy barriers of these monomers and is unsuitable for such copolymerization. In addition, the double-zeta basis set is found to be sufficient for solvation single-point calculation of these systems.
Osmium analogue to ruthenium anticancer drug NAMI-A; (ImH)[trans-OsCl4(DMSO)(Im)] (Im=imidazole, DMSO=dimethyl sulfoxide) (Os-NAMI-A) shows a three-fold higher activity in colon carcinoma. Hydrolysis mechanism of Os-NAMI-A has been investigated using density functional theory (DFT) in combination with CPCM solvation model. Calculated activation free energy values for the first chloro ligand hydrolysis in the gaseous and aqueous medium are found to be ΔGg=31.79 and ΔGaq=28.72 kcal/mol, respectively. While, activation free energy for the second cis chloro ligand hydrolysis calculated in the gas and solvent phases are observed to be significantly lower (ΔGg=29.12 and ΔGaq=22.61 kcal/mol), suggesting enhanced feasibility of second hydrolysis. However, hydrolysis of DMSO ligand in the formation of cis-[OsCl2(H2O)3(Im)]+ (P-3cis) is found to be thermodynamically preferred in aqueous medium (19.49 kcal/mol) with rate constant value of 3.20×10-2 s-1. In addition, molecular docking simulation reveals that cis-diaquated Os-NAMI-A (P-2cis) interacts with DNA (PDB ID: 1pgc) more effectively having binding energy -5.63 kcal/mol. Therefore, results of this investigation may lead us to understand the solution behaviour of osmium azole complexes as well as their mode of interaction with biomolecules which in return helps in potential anticancer drug designing.
A special class of conjugated hydrocarbons known as phenylenes, which is composed of a special arrangement of six- and four-membered rings. In particular, any two six-membered rings (hexagons) are not adjacent, and every four-membered ring(square) is adjacent to a pair of nonadjacent hexagons. If each hexagon of phenylene is adjacent only to two squares, then the obtained chain is called the phenylene chain. The main object of this paper is to determine the expected values of the sum-connectivity, harmonic, and symmetric division indices of this class of conjugated hydrocarbons. The comparisons between the expected values of these indices with respect to the random phenylene chains have been determined explicitly. The graphical illustrations have been given in terms of the differences between the expected values of these indices.
The present study reports nonlinear optical properties such as first and second hyper polarizabilities (β and γ) of Y-shaped polymer (P1) and substituted polymers. The basic Y-shaped polymer (R=R1=H) named as P1. Upon substitution of one OCH3 group in ortho position of Oxygen becomes polymer P2 (R1=H, R=OCH3) and two OCH3 group as P3 (R1=R=OCH3). We have also reported structural parameters, vibrational and electronic absorption spectra of polymer and substituted using quantum chemical methods. The geometrical parameters such as dipole moment, bond length and angles are reported at B3LYP/6-311++g** level of theory. In addition, the vibrational, electronic absorption spectra and NLO properties are also reported at the same level of theory. There is significant change in dipole moment and energy observed whereas symmetry, bond length and angles are resembling in Y-shaped and substituted polymer. The vibrational spectra of Y-shaped polymer (P1) having the intense peak is C-H stretching mode observed at 1258 cm-1. These Theoretical vibrational modes are well matching with available experimental determinations. The method dependent and the along the X, Y and Z-direction hyperpolarizabilites also reported. This study confirms the polymer P1 and P2 showing first and second hyperpolarizability response whereas P3 do not show. The electronic absorption spectra for polymer and substituted polymers are also reported at the same level of theory using (TDDFT) approach. The wavelength of electronic transition, oscillator strength and HOMO-LUMO gap also reported.
Electrochemical ammonia synthesis is being actively studied as a low temperature, low pressure alternative to the Haber-Bosch process. This work studied iridium as the electrochemical catalyst, following a previous study of adsorption characteristics on platinum. The characteristics studied include bond energies, bond lengths, spin densities, and free and adsorbed vibrational frequencies for the molecules N2, N, NH, NH2, and NH3. Overall, these descriptive characteristics explore the use of dispersion-corrected Density Functional Theory methods that can model N2 adsorption – the key reactant for electrochemical ammonia synthesis via transition metal catalysis. Specifically, three methods were tested: hybrid B3LYP, a dispersion-corrected form B3LYP-D3, and semi-empirical B97-D3. The latter semi-empirical method was explored to increase the accuracy obtained in vibrational analysis as well as reduce computational time. Two lattice surfaces, (111) and (100), were compared. The adsorption energies are stronger on (100) and follow the trend EB3LYP > EB3LYP-D3 > EB97-D3 on both surfaces.
The current study investigates the correlation between biological activity and physicochemical properties of a few specific estradiol isomers. Theoretical studies on the physicochemical properties of estradiol isomers were performed using different quantum mechanical methods. The computational methods used in this study include the Density Functional Theory (DFT) method, the Hartree-Fock (HF) method and Semi-empirical (AM1) method. Some physicochemical properties such as dipole moment, molecular weight, the energy of the highest occupied molecular orbital (E HOMO), the energy of the lowest unoccupied molecular orbital (E LUMO), polarizability, the octanol-water partition coefficient (Log P), polar surface area (PSA) the number of hydrogen bond donors (HBDs) and the number of hydrogen bond acceptors (HBAs), the surface area, volume of the molecule, and ovality are calculated for the isomers. However, only dipole moment values are suitable to identify a correlation of experimental biological activity of estradiol isomers. To the best of our knowledge, this is the first report on the relationships between dipole moment and biological activities of estradiol isomers. It is observed that the active compound has a significantly higher dipole moment value compared to the inactive compound. We have also analyzed the geometrical and graphical models of these isomers and related compounds to evaluate the differences in the molecular charge distributions.
Atomically precise metallic clusters behaving as superatoms, are relevant building blocks towards new materials under the bottom-up approach. Here we discussed the plausible formation of the Cu10Ru cluster as a superatomic specie accounted its 1S2 1P6 1D10 shell order, with the aim of identification of particular clusters with enhanced stability. By stochastic structure search on Cu10Ru clusters, we found six low-lying cluster isomers with ΔE values from 0.0 to 4.7 kcal∙mol above the ground state denoting an endohedral motif with the Ru dopant inside the Cu10 cage, as the favored structures. By using molecular dynamics simulations we found a clear trend of encapsulation of the Ru atom at low temperatures, quantified by the Cu-Ru bonding distances during the annealing procedure. The 17-ve counterpart, Cu9Ru shows a large electron affinity, owing to the trend to achieve a electronic shell closing as a new superhalogen species. These results are useful for further rationalization and design of novel superatoms expanding the libraries of endohedral clusters.
Quantum-chemical “descriptors”, including atomic partial charges, orbitals, and electrostatic potentials are powerful tools for understanding chemical reactivity. Localized defects in graphene are a particular challenge for these tools, especially to model the adsorption processes and to predict the interactions of transition metals with these defects. Such defects often have little charge polarization and a combination of localized and delocalized states. Our orbital overlap distance D(r) measures the “size” of occupied orbital lobes about point r, distinguishing the hybridization state and compact vs. diffuse character of local electronic structure. Here we apply the overlap distance to graphene defects. We find that the overlap distance clearly distinguishes differential reactivities of different atoms at intrinsic defects. Combining the overlap distance and electrostatic potential provides a rich picture of extrinsic defect reactivity, including semiquantitative predictions of transition metal binding.
In this theoretical study, we investigate the electronic potential energy curves, spectroscopic parameters, vibrational energy levels and transition dipole moments for the diatomic dications BeRb2+, BeCs2+ and SrRb2+. We consider an ab initio approach based on the use of non-empirical pseudopotentials and parameterized l dependent polarization potentials. Results show that 1-22Σ+ for BeRb2+, 1-52Σ+ for BeCs2+ and 1-32Σ+ for SrRb2+ are repulsive. While the 32Σ+ for BeRb2+, 42Σ+ for BeCs2+ and 42Σ+ for SrRb2+ are metastable states. These states can accommodate some vibrational energy levels. Interesting avoided crossings between some 2+ states are localized and examined. Until now no experimental and theoretical studies have been made for each system. Consequently, we discuss our results by comparing with some data of similar systems. Besides, the transition dipole moments of the ground state to a few excited states are computed and presented. The information associated with the electronic structures, spectroscopic parameters as well as the transition properties that provide in this paper is anticipated to serve as guidelines for further experimental and theoretical researches for each diatomic dication considered in this work.
The atomic structure, spin states of the interface based on iron-porphyrin and armchair graphene nanoribbon (FeP/AGNR) and potential energy surface of FeP atop of AGNR migration is investigated via DFT theory. The multiplicity of Fe ion in iron porphyrin for all possible types of coordination is determined as a triplet. It is estimated that FeP would place atop AGNR at the position where two Fe-N bonds are located above the C-C bond, another two are located above C atoms. The barrier of migration of iron porphyrin complex atop of graphene armchair nanoribbon is found to be smaller the temperature factor, making the heterostructure to be in temperature equilibrium between different types of coordination of the iron porphyrin atop of graphene nanoribbon
Unique superhalogen properties of Pt(CN)n complexes (n = 1–6) containing cyanide (CN) pseudohalogen moieties bound with platinum (Pt) atom have been investigated under the quantum chemical formalism. The study involves theoretical calculations for both neutral and anionic forms of Pt(CN)n using density functional theory (DFT) with the hybrid functional B3LYP. In order to improve the accuracy of calculations, 6–311+G(d) basis set was implemented for CN moieties, whereas, SDD basis set supplemented with Stuttgart/Dresden relativistic effective core potential was used for Pt atom. HOMO–LUMO energy band gaps, vibrational frequencies and dissociation energies of Pt(CN)n complexes have been calculated to investigate their relative stability as well as reactivity. Additionally, superhalogen properties and salt forming capability of Pt(CN)n complexes have also been analyzed. Focus of analysis is on the delocalization of charges over attached CN ligands in successive members of the Pt(CN)n species. Reliable low–cost investigations on superacidity properties of associated protonated species have also been carried out keeping their industrial applications in mind.
We have recently developed a computational methodology to separate the effects of size, composition, symmetry and fluxionality in explaining the experimental photoelectron spectra of mixed-metal clusters. This methodology was successfully applied first in explaining the observed differences between the spectra of Al13- and Al12Ni- and more recently to explain the measured spectra of AlnMo-, n=3-5,7 clusters. The combination of our approach and new synthesis techniques can be used to prepare cluster based materials with tunable properties. In this work we use the methodology to predict the spectrum of Al6Mo-. This system was chosen because its neutral counterpart is a perfect octahedron and it is distorted to a D3d symmetry and was not observed in the recent experiments. This high symmetry cluster bridges the less symmetric Al5Mo- and Al7Mo-structures. The measured spectra of Al5Mo- has well defined peaks, while that of Al7Mo-does not. This can be explained by the fluxionality of Al7Mo-, as at least 6 different structures lie within the range that can be reached by thermal effects. We predict that Al6Mo- has well defined peaks, but some broadening is expected as there are two low-lying isomers, one of D3d and the second of D3h symmetry that are only 0.052 eV apart.
Etherification mechanism of 4,5-dihydroxy-1,3-bis (hydroxymethyl) imidazolidin-2-one (DMDHEU) with the primary alcohols and the –OH hydroxyl groups of cellulose chain (n=1-2) in acidic condition were investigated by using density functional theory (DFT) method and a two-layer ONIOM approach. Geometry and energy of reactants, products, intermediate complexes, carbocation intermediate, and transition states were optimized at B3LYP/6-311g(d,p) level and ONIOM (B3LYP/6-311g(d,p):PM3MM) level. Computational results indicate that the etherification adheres to unimolecular nucleophilic substitution (SN1) mechanism; the reactant and product can form the activated complexes with H+ ions in which H+ ions are occupied by the O-atom of C=O group in the reactant complex and the product complex. Potential energy surface (PES) of the reaction has the triple-well shape. Effect of substituent R in primary alcohol R-CH2OH (R = H, CH3, CH2CH3, CH2OCH3, CH2F) and cellulose chain on the reactivity is significant. The energy barrier of H+ ions releasing step is much higher than those of the activation steps. The calculational data is in the good agreement with the experimental data in the literature.
The polyphenyl chains with $n$ hexagons are the special graphs of unbranched polycyclic aromatic hydrocarbons. The objective of this study is to find the expected values of the multiplicative version of the atomic-bond connectivity index and geometric-arithmetic index of this class of special hydrocarbons. The average values of these two indices with respect to the set of all polyphenyl chains have been determined. Finally, the comparisons between the expected values of the aforementioned indices in the random polyphenyl and spiro chains, have been outlined.