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We have analyzed the chemical bonding and reactivity in the cubic molecule octahydridosilsesquioxane, Si8H8O12, and its counterpart Ge8H8O12 by means of ab initio quantum chemical methods and group theory. Density functional theory and MP2 methods combined with the basis sets 6-311+G(d) and 6-311++G(2d,p) were used for geometry optimization and vibrational frequency analysis. The geometries of Si8H8O12 and Ge8H8O12 are unstable under Oh symmetry and distort to the rare Th molecular symmetry. The energy gained from this pseudo-Jahn–Teller distortion ranges from 0.78 to 6.14 kcal mol−1 depending on methodological treatment. The Fukui functions and the molecular electrostatic potential were both used as DFT-based reactivity descriptors. Our study shows that Si8H8O12 and Ge8H8O12 are both hard amphoteric molecules. The cavity within each cage is acidic and able to encapsulate hard small bases such as F−. The exterior of the cages is basic and can form stable exohedral complexes with hard acids, as in the case of H+. The insertion of F− in Si8H8O12 and Ge8H8O12 cages gives the most stable endohedral complexes of the series studied, characterized by formation energies of −3.50 and −3.45 eV at CAM-B3LYP/6-311+G(d) and −3.61 and −3.68 eV at the MP2/6-311++G(d,p) level, respectively. The calculated formation energies of the exohedral and endohedral complexes align with the DFT reactivity descriptor analysis. [ABSTRACT FROM AUTHOR]

Two new structural motifs of the B24 clusters are constructed by use of the leapfrog transformation. The resulting leapfrog B24 has either a bowl shape with a square vacancy or a quasi‐planar 2D close‐packed triangular boron sheet. The neutral and ionic forms of the latter are found to be more stable than their homologous leapfrog bowl clusters, with the exception of the dicationic B24+2. While the leapfrog isomer is less stable than the tubular double ring in the neutral state, it becomes competitive in some ionic states. The nucleus independent chemical shift, electron localization function, ring current maps and the electronic structure of leapfrog B24 clusters reveal them to behave as aromatics. [ABSTRACT FROM AUTHOR]

Abstract: A furano sesquiterpenoid, known as siphonochilone (1), is commonly reported as the major compound in the roots and the rhizomes of Siphonochilus aethiopicus together with related oxidized sesquiterpenoids (2‐5). As part of investigating the UPLC QTOF MS ES+ chemical profiles of n‐hexane/dichloromethane (1:1) extracts from crushed fresh rhizomes, dried and powdered rhizomes and the dried powders held under storage at room temperature, we have recently realized that decomposition of 1 occurs during the processing of the rhizomes and the storage of the powders. This decomposition which involves autoxidation of the furan moiety leads to formation of the artefact sesquiterpenoid lactone (3) and potentially (4), which numerous papers misreport as naturally present in the plant. MP2/6‐31+G(d,p), B3LYP/6‐31+G(d,p) and B3LYP/6‐311+G(2d,p) calculations were performed on siphonochilone (1) and the sesquiterpenoid lactone artifacts (3) and (4) and results rationalized the observed autoxidation. [ABSTRACT FROM AUTHOR]

Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0, and Y+ (Y = Li, Na, K) and Z− (Z = F, Cl, Br) ions using M06-2X, B3LYP and ω B97XD functionals in conjunction with the 6–31 + + G(d,p), aug-cc-pVDZ(-X2C) and 6–311 + + G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation...O and cation-π interactions, while Z− anions generally establish anion...H–O contacts. Predicted binding energies at the M06-2X/6–311 + + G(d,p) level range between − 26.6 and − 70.2 kcal/mol for cationic complexes and − 20.4 and − 62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O...cation...O interactions where the cation is trapped between O37 and O38 atoms of TXA0. Anions do not behave uniformly towards TXA0: while the fluoride anion F− induces the deprotonation of TXA0, Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0...Y+ and TXA0...Z− complexes are mainly stabilized by electrostatic and inductive effects, whose combined contributions account for more than 60 percent of the total interaction energy. [ABSTRACT FROM AUTHOR]

A density functional theory (DFT) study is performedto determine the stability of the complexes formed between eitherthe N or O site of 3-methyl-4-pyrimidone and 1-methyl-2-pyrimidonemolecules and different ligands. The studied ligands are boron andalkali Lewis acids, namely, B(CH3)3, HB(CH3)2, H2B(CH3), BH3, H2BF, HBF2, BF3, Li+, Na+, and K+. The acids are divided into twogroups according to their hardness. The reactivity predictions, accordingto the molecular electrostatic potential (MEP) map and the naturalbond orbital (NBO) analysis, are in agreement with the calculatedrelative stabilities. Our findings reveal a strong regioselectivitywith borane and its derivatives preferring the nitrogen site in bothpyrimidone isomers, while a preference for oxygen is observed forthe alkali acids in the 3-methyl-4-pyrimidone molecule. The complexationof 1-methyl-2-pyrimidone with these hard alkali acids does not showany discrimination between the two sites due to the presence of acontinuous delocalized density region between the nitrogen and theoxygen atoms. The preference of boron Lewis acids toward the N siteis due to the stronger B–N bond as compared to the B–Obond. The influence of fluorine or methyl substitution on the boronatom is discussed through natural orbital analysis (NBO) concentratingon the overlap of the boron empty p-orbital with the F lone pairsand methyl hyperconjugation, respectively. The electrophilicity ofthe boron acids gives a good overall picture of the interaction capabilitieswith the Lewis base. [ABSTRACT FROM AUTHOR]

Abstract: A study of Ih to Th pseudo-Jahn–Teller (PJT) distortion in B80 is presented. Reduced matrix elements for vibronic coupling and resulting force constants were calculated in Ih to elucidate the origin of B80 symmetry breaking. Important orbital excitations involved are between inner orbitals 9hg, 5hg, and 6gu and virtual orbitals 8t2u and 8gg. Low-lying occupied orbitals interact more strongly than frontier molecular orbitals due to their density distribution on the capping atoms. The large energy gaps, associated with these excitations, attenuate the PJT effect. The force constant calculations for B80 point to a weak PJT energy stabilization of 304cm−1 at B3LYP/6-31G(d). [Copyright &y& Elsevier]

Density functional theory calculations at the B3LYP/SVP and B3LYP/6-31lG(d) levels were carried out for a series of XH3B80 complexes with X = {N, P, As, B, Al}. To probe the regioselectivity of B80, the electronic Fukui function, the molecular electrostatic potential (MEP), and the natural bond orbital (NBO) were determined. These indices were shown to provide reliable guides to predict the relative reactivities of the boron buckyball sites. Thermodynamic stabilities of the complexes formed by the reaction of B80 with nucleophiles (NH3, PH3, AsH3) and electrophiles (BH3, A1H3) are in good agreement with the prediction of regioselectivity indicated on the basis of Fukui and MEP indices. The qualitative results suggest the boron buckyball to be an amphoteric and hard molecule. It has two distinct reactive sites localized on caps and frame, which act as acids and bases, respectively. Most of the complexes are stable with formation energies comparable to that of the analogous complexes of the borane molecule, BH3BH3, BH3NH3, and BH3A1H3. The B-H-B bond characteristics of diborane are recovered in B80BH3. Exohedral complexes are more stable than endohedral complexes. The most stable complexes are those with NH3 on the caps and BH3 on the pentagonal ring of B80. [ABSTRACT FROM AUTHOR]

Abstract: We report the electronic structure of methyne boron buckyballs B68(CH)12, B72(CH)8 and B76(CH)4 obtained by substituting, respectively, 12, 8 and 4 boron cap atoms by methyne CH groups on the boron buckyball B80. DFT calculations and minimization techniques have been employed to characterize the structural and electronic properties of endo and exo isomers of these molecules in Th and T symmetry. A vibrational frequencies analysis predicts that only endo-B72(CH)8 and endo-B76(CH)4 correspond to a true minimum on the potential energy hypersurface with a cohesive energy similar to the boron buckyball. The stable substitutions are characterized by six rhombohedral B4 bonding motifs. [Copyright &y& Elsevier]

The ambident reactivity of small-sized XAHs (X=H, F, Cl, Br, CH3, and A=S, Se, Te) molecules towards the imidazole molecule (IMZ) has been investigated using wave function (MP2) and Density Functional Theory (B3LYP, B3LYP-D3). Molecular electrostatic potentials (MEPs) and frontier molecular orbitals of monomers are computed to rationalise the regioselectivity of IMZ towards XAHs. The chemical bonding of each complex is described in the framework of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) paradigms. The symmetry-adapted perturbation theory (SAPT) is employed to assess the physical nature of the interactions. Our findings suggest that XAHs mainly bind to IMZ through H-bonding and chalcogen-bonding interactions of weak to moderate strength, with binding energies ranging from −3.1 to −17.6 kcal/mol at the MP2/aug-cc-pVDZ(-PP) level. Topological QTAIM descriptors reveal all H-bonds between IMZ and XAHs to be purely noncovalent contacts, while chalcogen bonds of halogenated XAHs (X = F, Cl, Br) show a partial covalent character. SAPT2 calculations indicate that both H-bonded and chalcogen-bonded complexes are mainly stabilised by electrostatic interactions. Insights drawn from this study are expected to constitute the bedrock for further investigations about noncovalent interaction between middle to big-sized chalcogen-containing molecules and imidazole derivatives. [ABSTRACT FROM AUTHOR]

Abstract: A symmetry analysis of the valence shell in the boron buckyball B80 shows a perfect match with the symmetry of the valence shell in C60. The cap atoms participate in the bonding by 30 orbitals which transform as the σ-bonds along the 6–6 edges. Far reaching consequences for chemical and physical properties of B80, which until now only exists in silico, are expected. [Copyright &y& Elsevier]

Ring opening reaction of the formation of substituted MTIC acids at M062X/6-31G(d). Path-2 B-D-F: (B: TMZ-H, D: TMZ-Cl, F: TMZ-OH). Path-1 H-J-L: (H: TMZ-H, J: TMZ-CF3, L: TMZ-OH). • Pathway-1 and pathway-2 occur kinetically and thermodynamically. • Substitution tends to increase the energy barrier. • The lowest conformer of MTIC acid is proposed. • IHBs are disrupted in MTIC acids to form solute-solvent IHBs. MP2/6-311+G(d,p) was employed to study the mechanism of the initial step of ring opening of temozolomide (TMZ-H) and its substituted, TMZ-R (R = Cl, OH, CF3) analogues. The study reveals that the difference formation energies of substituted MTIC acids with respect to MTIC acid are ranging between 0.44 and 1.58 kcal/mol. The ring opening of TMZ-R along pathway-2 leads to the lowest conformer (D), whereas reactions along pathway-1 give rise to lower transition states. The barrier energies of TMZ-R are 1.60–3.75 kcal/mol larger than TMZ-H. The conformational analysis reveals that intramolecular hydrogen bonds do not have a stabilizing effect in water solvent. [ABSTRACT FROM AUTHOR]

Photodynamic antimicrobial activities of gallium and indium porphyrins as well as their quaternized derivatives have been investigated against S. aureus and E. coli biofilms, as well as on their planktonic (free floating) cells using a light emitting diode lamp at 415 nm. The studied photosensitizers show considerable ability to generate singlet oxygen and the quaternized molecules 2a and 3a are potential photodynamic antimicrobial chemotherapy (PACT) agents with log10 colony forming units >9 for E. coli and S. aureus planktonic cells. The quaternized derivatives are found to have higher ability to significantly suppress the biofilms of both S. aureus and E. coli in vitro. Therefore, this demonstrates that they are potentially suitable photosensitive agents for PACT use. The TD-B3LYP/LanL2DZ calculations were performed to evaluate the singlet excitation energies of quaternized and non-quaternized porphyrins in vacuo. Our study shows excellent agreement between time-dependent density-functional theory (TD-DFT) excited energies and experimental S1 > S0 excitation energies. The small deviation observed between the calculated and experimental spectra arises from the solvent effect. The excitation energies observed in these UV-visible spectra mostly originated from electron promotion between the highest occupied molecular orbital (HOMO) for the less intense band and the HOMO−1 for the most intense band of the ground states to the lower unoccupied molecular orbital (LUMO) of the excited states. [ABSTRACT FROM AUTHOR]

Density functional theory (B3LYP, B3LYP‐D3, wB97XD, M062X, and M06L) and ab initio methods (MP2 and CCSD(T)) in conjunction with 6‐31+G(d,p) and LanL2DZ were employed to investigate the interaction energies between [Co(NH3)5NO2]2+ linkage isomers and chloride and nitrate in both gas phase and solid state. The nature of the chemical bonding has been analyzed by means of the atoms in molecules, electron density shift, natural bond orbitals, symmetry adapted perturbation theory, and energy decomposition analysis. The electronic structures of the two lowest laying singlet states (So and S1) of [Co(NH3)5NO2](NO3)Cl isomers were also investigated using CASSCF(6,6) with LanL2DZ and 6‐31G(d) basis sets. Our results show that [Co(NH3)5NO2]2+ linkage isomers interact more strongly with chloride than nitrate. The structures of [Co(NH3)5NO2](NO3)Cl linkage isomers and their relative stabilities were examined in gas phase and in solid state and confirmed the nitro‐complex as the most stable following by a viable intermediate endo‐complex. Study of the nitro‐nitrito linkage isomerization in [Co(NH3)5NO2](NO3)Cl revealed that anions form strong electrostatic bonds with [Co(NH3)5NO2]2+ leading to decrease in an activation energy compared to the [Co(NH3)5ONO]2+ isomers. A concerted action of ionic interactions and hydrogen bonds are suspected of regulating the isomerization in solid state. Assessment of various DFT methods with respect to CCSD(T) suggests M062X suitable method for [Co(NH3)5NO2](NO3)Cl linkage‐isomerization study. Potential energy surface calculations at the CASSCF/6‐31G(d) level of theory shows that the conical intersection (S1/So) might play an important role in the photoisomerization of [Co(NH3)5NO2](NO3)Cl. [ABSTRACT FROM AUTHOR]

Context: Due to the expected decrease in the availability of conventional oils, numerous studies are currently underway to find complementary sources of energy. Among the explored avenue is that of biofuels. Ethyl valerate (ETV) and tripropionin (TPP) are two biofuels whose thermal decomposition has not received the attention it deserves. Herein, we have evaluated the bond dissociation enthalpies (BDHs) to predict how easy it is to break some bonds in these compounds, and subsequently contribute to revealing the initiation step in their combustion reactions. Our computations consistently predict C4-C5 and C1-C2 bonds in ETV and TPP as the weakest bonds, likely to break first and initiate the thermal decomposition of these two compounds, respectively. The conformational changes in ETV and TPP have only a small influence on the BDHs of 1 kcal/mol at M06-2X/6–311 + G(3df,2p). B3LYP and ωB97XD appear to be the most affordable methods for estimating BDHs at 6-31G(d,p) as they give good results for ETV (RMSD: 2.94 kcal/mol and 3.22 kcal/mol) and performed better than CBS-QB3 (RMSD: 3.64 kcal/mol). Using a larger basis set, the M06-2X (RMSD: 3.61 kcal/mol) and ωB97XD (RMSD: 3.51 kcal/mol) functionals are found to provide the most accurate predictions at 6–311 + G(3df,2p) as compared to G4MP2. Methods: BDHs of ETV and TPP are computed using density functional theory (DFT) and quantum chemistry composite methods at 6-31G(d,p) and 6–311 + G(3df,2p) levels. Because of its reliability and accuracy in thermochemical calculations, the G4MP2 theory is used as a reference to gauge the performance of DFT methods. All the calculations were carried out using the Gaussian 09 program. [ABSTRACT FROM AUTHOR]

Temozolomide was paired with guanine, 6-selenoguanine, and 6-thioguanine, as well as the SH tautomer of the latter. The potential energy surface of each heterodimer was searched for all minima, using Dispersion-Corrected Density Functional Theory and MP2 methods. Among the dozens of minima, three categories were observed. Stacked geometries place the aromatic systems of the two molecules parallel to one another, while the two systems are roughly perpendicular to one another in a second category. Also found are coplanar structures held together by H-bonds. Dispersion proves to be a dominating attractive force for the stacked structures, less so for perpendicular, and smallest for the coplanar dimers. Geometries and energetics are relatively insensitive to S and Se substitution, but tautomerization reverses relative stabilities of different geometries. [ABSTRACT FROM AUTHOR]