Relative Stability of Multiple Bonds between Germanium and Stibium. A Theoretical Study

Substituent effects on the potential energy surface of XGeSb (X=H, Li, Na, BeH, MgH, BH₂, AlH₂, CH₃, SiH₃, NH₂, PH₂, OH, SH, F, and Cl) were investigated by using B3LYP/Def2‐TZVP, B3PW91/Def2‐ TZVPP CCSD (T)//B3LYP/Def2‐TZVP methods. The isomers include structures with formal double (Ge=SbX) and triple (Xge=Sb) bonds to germanium‐stibium, so a direct comparison of these types of species is possible. Our model calculations indicate that electropositively substituted Ge=SbX species are thermodynamically and kinetically more stable than their isomeric Xge=Sb molecules. Moreover, the theoretical findings suggest that only the organic substitutions (such as CH₃) can make triply bonded Xge=Sb molecule more stable than the doubly bonded Ge=SbX species.     

Mismatch base pairing of the mutagen 8‐oxoguanine and its derivatives with adenine: A theoretical search for possible antimutagenic agents

Molecular geometries of 8‐oxoguanine (8OG), those of its substituted derivatives with the substitutions CH₂, CF₂, CO, CNH, O, and S in place of the N7H7 group, adenine (A), and the base pairs of 8OG and its substituted derivatives with adenine were optimized using the RHF/6‐31+G* and B3LYP/6‐31+G* methods in gas phase. All the molecules and their hydrogen‐bonded complexes were solvated in aqueous media employing the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory using the RHF/6‐31+G* and B3LYP/6‐31+G* methods. The optimized geometrical parameters of the 8OG‐A base pair at the RHF/6‐31+G* and B3LYP/6‐31+G* levels of theory agree satisfactorily with those of an oligonucleotide containing the base pair found from X‐ray crystallography. The pattern of hydrogen bonding in the CF₂‐ and O‐substituted 8OG‐A base pair is of Watson–Crick type and that in the unsubstituted and CH₂‐, CNH‐, and S‐substituted base pairs is of Hoogsteen type. In the CO‐substituted base pair, the hydrogen bonding pattern is of neither Watson–Crick nor Hoogsteen type. The CF₂‐substitution appears to introduce steric hindrance for stacking of DNA bases. On the basis of these results, it appears that among all the substituted 8OG molecules considered here, the O‐substituted derivative may be useful as an antimutagenic drug. It is, however, subject to experimental verification. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Design of donor–acceptor–donor (D–A–D) type small molecule donor materials with efficient photovoltaic parameters

Four Donor–Acceptor–Donor (D–A–D) type of donor molecules (M1‐M4) with triphenylamine (TPA) as donor moiety, thiophene as bridge, and thiazolothiazole as acceptor unit were designed and its photovoltaic parameters were equated with reference molecule “R.” DFT functional CAM‐B3LYP/6‐31G (d,p) was found best for geometry optimization and TD‐CAM‐B3LYP/6‐31G (d,p) was found suitable for excited state calculations. Among designed donor molecules, M4 manifests suitable lowest band gap of 4.73 eV, frontier molecular orbital energy levels as well as distinctive broad absorption of 455.3 nm due to the stronger electron withdrawing group. The electron‐withdrawing substituents contribute to red shifts of absorption spectra and better stabilities for designed molecules. The theoretically determined reorganization energies of designed donor molecules suggested excellent charge mobility property. The lower λ_e values in comparison with λ_h illustrated that these four donor materials would be ideal for electron transfer and M4 would be best amongst the investigated molecules with lowest λ_e of 0.0177. Furthermore, the calculated Voc of M4 is 2.04 V with respect to PC₆₀BM (phenyl‐C61‐butyric acid methyl ester). This study revealed that the designed donor materials are suitable and recommended for high performance organic solar cell devices.     

Can B3LYP be improved by optimization of the proportions of exchange and correlation functionals?

B3LYP is the most famous hybrid density functional theory model, which includes Hartree–Fock exchange, local exchange, gradient exchange correction, local correlation, and gradient correlation correction. Historically, the relative weight of each component in B3LYP, which is controlled by three empirical parameters (a₀, a_x, a_c), has not been optimized. In this work, we perform global optimization against accurate experimental reference, optimal empirical parameters, and the better version of B3LYP are obtained and denoted as OpB3LYP. The performance of OpB3LYP is widely tested over many species and chemical properties, the results show that the computational accuracy is significantly improved as compared to original B3LYP and the serious size dependence of B3LYP is remarkably overcome by the employment of OpB3LYP. The comparative assessment of OpB3LYP and other prevalent functionals indicates that OpB3LYP is a promising functional for large molecules. © 2015 Wiley Periodicals, Inc.     

Amide hydrogen bonding: control of the molecular and extended structures of two symmetrical pyridine‐2‐carboxamide derivatives

The crystal structures of two symmetrical pyridine‐2‐carboxamides, namely N,N′‐(propane‐1,3‐diyl)bis(pyridine‐2‐carboxamide), C₁₅H₁₆N₄O₂, (I), and N,N′‐(butane‐1,4‐diyl)bis(pyridine‐2‐carboxamide), C₁₆H₁₈N₄O₂, (II), exhibit extended hydrogen‐bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)...O hydrogen bonding favours the formation of one‐dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H...O hydrogen bonding links adjacent one‐dimensional chains to form a `porous' three‐dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) ų which combine into channels that run parallel to, and include, [001]. 4% of the unit‐cell volume of (I) is vacant. Compound (II) adopts a Z‐shaped conformation with inversion symmetry, and exhibits an extended structure comprising one‐dimensional hydrogen‐bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H...O hydrogen bonds. These hydrogen‐bonded chains interlock viaπ–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z‐shaped molecule thick and separated from the next sheet by the b‐axis dimension [7.2734 (4) Å].     

Enhanced optoelectronic properties with aromatic bridges: A computational study on N-methyl pyridinium and phenolate types of push-pull zwitterions

A series of zwitterions with varying bridges, connecting N-methyl pyridinium acceptor, with phenolate donor, are investigated using various methodologies like, HF, B3LYP, CAM-B3LYP and ωB97xD. In this systematic study effects of various mono aromatic rings as bridges, on the response properties like, the dipole moments (μ), polarizabilities (α), hyperpolarizabilities (β) and adiabatic absorptions were analyzed using CPHF and TDDFT (or TDHF) theories. Compared to many traditional bridges, as well as without a bridge, enhanced nonlinear optical (2ND order NLO) responses were observed for these aromatically bridged zwitterions (with benzene ring as bridge ~5.3 times and ~7.9 times enhanced hyperpolarizabilities were observed compared to either the ethylene bridge or without any bridge cases, respectively). Also, many significant differences and large enhancements in response properties were observed compared to our earlier works on non-zwitterionic system (~4.3 times enhanced hyperpolarizability—benzene as bridge case). For some bridge cases, 10- to 15-fold enhanced hyperpolarizabilities were observed compared to without any bridge case. This work reports a class of non-TICT chromophores, promoting bridge aromaticity control on structure–property correlation, as a suitable and efficient chromophore design strategy to create a wide range of function molecular chromophores. Also, unidirectional natures of response properties and large dipole moments can make these zwitterions suitable 1D-molecular materials for various contemporary technological applications, as poled polymer-based materials.     

A supramolecular ladder‐like network from trimesic acid and pyrazine N,N′‐dioxide

In the title complex, benzene‐1,3,5‐tricarboxylic acid–pyrazine N,N′‐dioxide (2/1), C₉H₆O₆·0.5C₄H₄N₂O₂, cocrystallized trimesic acid (TMA) and pyrazine N,N′‐dioxide (PNO) molecules form strong O—H...O hydrogen bonds, but also important weak C—H...O and dipole–dipole intermolecular interactions, to generate a densely packed three‐dimensional network. PNO molecules lie on inversion centres where they connect pairs of TMA sheets into distinct two‐dimensional hydrogen‐bonded layers perpendicular to the crystallographic ab diagonal.     

Theoretical study of molecular interaction between tirapazamine enzymatic catalysis metabolites and water

The weakly hydrogen‐bonded complexes, between tirapazamine enzymatic catalysis metabolites and water, have been investigated by density functional theory (DFT), using the B3LYP hybrid functional. The geometries of these complexes have been fully optimized at the B3LYP/6‐31G(d) and B3LYP/6‐311+G(d) levels. The stabilization energies and charge changes of some atoms have been calculated and analyzed. The results indicate that the catalysis metabolites and water can form stable hydrogen‐bonded complexes. Nine complexes are identified. It is important and necessary to add zero‐point vibrational energy (ZPVE) and basis set superposition error (BSSE) corrections for calculating stabilization energy. The results also reveal an important relationship between the relative stabilities of hydrogen‐bonded complexes and the final products of tirapazamine medication. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

1‐[5‐(4,5‐Dimethyl‐1,3,2‐dioxaborolan‐2‐yl)thiophen‐2‐yl]ethanone and 4‐(4,4,5,5‐tetramethyl‐1,3,2‐dioxaborolan‐2‐yl)benzaldehyde

In both title compounds, C₁₀H₁₃BO₃S, (I), and C₁₃H₁₇BO₃, (II), the molecules adopt nearly planar conformations. The crystal packing of (I) consists of a supramolecular two‐dimensional network with a herringbone‐like topology formed by self assembly of centrosymmetric pairs of molecules linked via dipole–dipole interactions. The crystal structure of (II) consists of a supramolecular two‐dimensional network built up from centrosymmetric pairs of molecules viaπ–π interactions. These pairs of molecules are self‐organized in an offset fashion related by a symmetry centre, generating supramolecular ribbons running along the [101] direction. Neighbouring ribbons are stacked via complementary van der Waals and hydrophobic methyl–methyl interactions.     

Density functional studies on hydrogen‐bonded clusters of hydrogen halides and the interaction on halide anions

Density functional theory (DFT) calculations have been performed to study the structures and stability of X^?·(HX)_n=2–5 clusters where X = F, Cl, Br at B3LYP/6‐311++G** level of theory. The presence of halide ions in these clusters disintegrates the hydrogen halide clusters. All the hydrogen halides are then hydrogen bonded to the centrally placed halide ions, thereby forming multiple hydrogen bonds. The interaction energies have been corrected for the basis set superposition error (BSSE) using Boy's counterpoise correction method. Evidence for the destruction of hydrogen bonds in hydrogen halide clusters due to the presence of halide ions is further obtained from topological analysis and natural bond orbital analysis. The chemical hardness and chemical potential have been calculated for all the anion clusters. The above analysis reveals that hydrogen bonding in these systems is not an essentially electrostatic interaction. The nature of the stabilization interactions operative in these multiple hydrogen‐bonded clusters has been explained in terms of many‐body contribution to interaction energies. From these studies, an attempt has been made to understand the nature of the molecular properties resulting from different electronegativities of the halogens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Lanthanide induced shifts as a conformational probe for o,o,o′,o′-tetrasubstituted diphenyls

The ¹H NMR spectra of several symmetrical diphenyls, having two unlike substituents on the ortho positions of each aromatic ring, were determined in the presence of Eu(fod)₃ and of Pr(fod)₃. The lanthanide induced shifts were used to establish the more probable conformation of the molecules, as deduced from computer calculations assuming pseudocontact interactions. It was found that the two like groups are in opposite conformation and that the inter-ring angles are in the order of 15–35°.     

Complexes of 4‐substituted phenolates with HF and HCN: Energy decomposition and electronic structure analyses of hydrogen bonding

We have computationally studied para‐X‐substituted phenols and phenolates (X = NO, NO₂, CHO, COMe, COOH, CONH₂, Cl, F, H, Me, OMe, and OH) and their hydrogen‐bonded complexes with B^? and HB (B = F and CN), respectively, at B3LYP/6‐311++G** and BLYP‐D/QZ4P levels of theory. Our purpose is to explore the structures and stabilities of these complexes. Moreover, to understand the emerging trends, we have analyzed the bonding mechanisms using the natural bond orbital scheme as well as Kohn–Sham molecular orbital (MO) theory in combination with quantitative energy decomposition analyses [energy decomposition analysis (EDA), extended transition state‐natural orbitals for chemical valence (ETS‐NOCV)]. These quantitative analyses allow for the construction of a simple physical model that explains all computational observations. © 2012 Wiley Periodicals, Inc.     

Excited state properties,fluorescence energies,and lifetimes of a poly(fluorene‐phenylene), based on TD‐DFT investigation

The structural and electronic properties of fluorene‐phenylene copolymer (FP)_n, n = 1–4 were studied by means of quantum chemical calculations based on density functional theory (DFT) and time dependent density functional theory (TD‐DFT) using B3LYP functional. Geometry optimizations of these oligomers were performed for the ground state and the lowest singlet excited state. It was found that (FP)_n is nonplanar in its ground state while the electronic excitations lead to planarity in its S₁ state. Absorption and fluorescence energies were calculated using TD‐B3LYP/SVP and TD‐B3LYP/SVP+ methods. Vertical excitation energies and fluorescence energies were obtained by extrapolating these values to infinite chain length, resulting in extrapolated values for vertical excitation energy of 2.89 and 2.87 eV, respectively. The S₁ ← S₀ electronic excitation is characterized as a highest occupied molecular orbital to lowest unoccupied molecular orbital transition and is distinguishing in terms of oscillator strength. Fluorescence energies of (FP)_n calculated from TD‐B3LYP/SVP and TD‐B3LYP/SVP+ methods are 2.27 and 2.26 eV, respectively. Radiative lifetimes are predicted to be 0.55 and 0.51 ns for TD‐B3LYP/SVP and TD‐B3LYP/SVP+ calculations, respectively. These fundamental information are valuable data in designing and making of promising materials for LED materials. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Density functional theory study on hydrogen‐bonded complexes of adenine with polyformamide molecules

The structures of hydrogen‐bonded complexes A–F_n (n = 2–7) of adenine with polyformamide molecules have been fully optimized at B3LYP/6‐31G(d) basis set level. All the formamide molecules prefer to be N? H proton donor rather than C? H proton donor and are favorably bound to the five‐numbered moiety of adenine. A displacement of formamide molecules to one side of adenine mean plane has happened with an increasing number of formamide molecules. An obvious effect of hydrogen‐bonding cooperativity can be seen during the complex process. The most interesting geometrical change of adenine upon the complex is the shortening of the bond C4? N6 resulting from the strengthening of the conjugation between the π system of the adenine ring and the lone pair of the nitrogen atom. An existence of weak N? H···π bonding interaction between the π system of adenine and N? H bond of F7 is found and further conformed by an natural bond orbital analysis specially carried out on A–F₇. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Hydrogen bonding interaction between 1,4‐dioxane and water

This work reports an interaction of 1,4‐dioxane with one, two, and three water molecules using the density functional theory method at B3LYP/6‐311++G* level. Different conformers were studied and the most stable conformer of 1,4‐dioxane‐(water)_n (n = 1–3) complex has total energies ?384.1964038, ?460.6570694, and ?537.1032381 hartrees with one, two, and three water molecules, respectively. Corresponding binding energy (BE) for these three most stable structures is 6.23, 16.73, and 18.11 kcal/mol. The hydrogen bonding results in red shift in O? O stretching and C? C stretching modes of 1,4‐dioxane for the most stable conformer of 1,4‐dioxane with one, two, and three water molecules whereas there was a blue shift in C? O symmetric stretching and C? O asymmetric stretching modes of 1,4‐dioxane. The hydrogen bonding results in large red shift in bending mode of water and large blue shift in symmetric stretching and asymmetric stretching mode of water. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Density functional theoretical study of pKa of RCOOH (RH,CH3, and C2H5) using the combination of the extended clusters‐continuum model

The accurate pK_a determinations for three carboxylic acids have been investigated using the combination of the extended clusters‐continuum model at B3LYP/6‐31+g(d,p) and B3LYP/6‐311++g(d,p) levels. To take into account of the effect of the water combined with carboxylic acids in different positions, eleven molecular clusters were considered. Among these clusters, the one involving the carboxylic acid wrapped up with water molecules and saturated with hydrogen bonds (four hydrogen bonds around ? COOH) leads to the best B3LYP pK_a results compared to the experimental data. For those clusters saturated with hydrogen bonds, when n = 3 (the number of water molecules), the average absolute errors between the calculated pK_a results and experimental data of these three carboxylic acids were 0.19 (0.23) and 0.12 (0.22) pK_a at B3LYP/6‐31+g(d,p)//PCM (IEFPCM) and B3LYP/6‐311++g(d,p)//PCM (IEFPCM) levels, respectively; when n = 4, they are 0.53 (1.23) and 1.09 (1.03) pK_a, respectively. On the basis of the above results, the molecular cluster saturated with four hydrogen bonds formed by three waters and one carboxylic acid molecule was the chief existence in the carboxylic acid solution. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A theoretical study on electronic structure and structure–activity properties of novel drug precursor 6‐acylbenzothiazolon derivatives

In this work, electronic properties and structure–activity relationship (SAR) parameters of 20 novel drug precursor 6‐acylbenzothiazolon derivatives with analgesic activity have been investigated theoretically by performing Austin Model‐1 (AM1) and DFT‐B3LYP/6‐31G (d) calculations with the aim to correlate the properties of each substance—particularly electronic properties and SAR parameters—with the biological interactions that are linked to their pharmacological effects. Their molecular properties were related to the biological activity of these drug precursor molecules. The relationship between octanol–water partition coefficient (log P) and each of the SAR parameters [E_LUMO–HOMO, molecular volume (V_m), ionization potential (IP), electron affinity, electronegativity (χ), chemical hardness (η), chemical softness (S), electrophilic index (ω), and molar refractivity] present linear correlation except for IP and χ. This result suggests that there are future prospects for designing or developing new drugs based on the correlation between the theoretically calculated parameters. According to AM1 calculation, the values of heat of formation of 6‐acylbenzothiazolon derivatives are negative (exothermic), which shows that these molecules are thermodynamically stable. E_LUMO–HOMO energy levels of the studied molecules are 4–5 eV, which also indicate that they are kinetically unstable. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hybrid-DFT Study and NBO Analysis of the Stereoelectronic Interaction Effects (Associated with the Anomeric Effects) on the Conformational Properties of 2,3,5,6-Tetrahalo-1,4-dioxanes and Their Analogs Containing S and Se Atoms

NBO analysis and hybrid density functional theory–based method (B3LYP/6-311+G**) was used to study the anomeric effects (AE), dipole–dipole interactions, and steric repulsion effects on the conformational properties of 2,3,5,6-tetrahalo-1,4-dioxane [halo = F (1), Cl (2), Br (3)], 2,3,5,6-tetrahalo-1,4-dithiane [halo = F (4), Cl (5), Br (6)], and 2,3,5,6-etrahalo-1,4-diselenane [halo = F (7), Cl (8), Br (9)]. B3LYP/6-311+G** results revealed a strong axial preference in compounds 1–3. Gibbs free energy difference (G _eq–G _ax) values (e.g., ΔG _eq-ax) between the axial and equatorial conformations of compound 1 to compound 3 are 8.19, 3.86, and 3.13 kcal mol^?1, respectively, as calculated by the B3LYP/6-311+G** level of theory. On the other hand, the NBO analysis of donor–acceptor (bond–antibond) interactions revealed that the AE for compounds 1–3 are ?12.26, ?16.46, and ?18.11 kcal mol^?1, respectively. Contrary to the increase of the AE values from compound 1 to compound 3, the increase of the steric repulsions (e.g., 1,3-syn-axial repulsions) could fairly explain the decrease of the axial conformation stability in compounds 1–3 compared to their equatorial conformations. Further, the correlations between the AE, structural parameters, and conformational behavior of compounds 4–9 have been investigated.     

2‐tert‐Butylamino‐4‐chloro‐6‐ethylamino‐1,3,5‐triazine: a structure with Z′ = 4 containing two different molecular conformations and two independent chains of hydrogen‐bonded R22(8) rings

The title compound (trivial name terbutylazine), C₉H₁₆ClN₅, (I), crystallizes with Z′ = 4 in the space group Pca2₁, and equal numbers of molecules adopt two different conformations for the ethylamine groups. The four independent molecules form two approximately enantiomorphic pairs. Eight independent N—H...N hydrogen bonds link the molecules into two independent chains of R₂²(8) rings, in which the arrangement of the alkylamine substituents in the independent molecules precludes any further crystallographic symmetry. The significance of this study lies in its finding of two distinct molecular conformations within the structure and two distinct ways in which the molecules are organized into hydrogen‐bonded chains, and in its comparison of the hydrogen‐bonded structure of (I) with those of analogous 1,3,5‐triazines and pyrimidines.