Ab initio calculations on the thermodynamic properties of azaborospiropentanes

Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies, enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about −52 kJ per gram. Figure Optimized geometry for R-azatriborospiropentane (10) Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

TCNE-aniline charge transfer complex: ab initio and TDDFT investigations in gas phase

The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site is a C≡N and C=C bond center in the TCNE and, –NH₂ and π-electrons of aniline. The N atom of aniline is oriented toward the TCNE molecule. The charge transfer transition energy, estimated by calculating the ground-to-excited state transition electric dipole moments of the complex, agree well with the reported experimental value in chloroform medium. TCNE-aniline at ground state. TCNE-aniline at excited state     

A theoretical investigation of cytotoxic activity of celastroid triterpenoids

Quantum chemical calculations at the B3LYP/6-31G* level of theory have been carried out on 20 celastroid triterpenoids to obtain a set of molecular electronic properties and to correlate these with cytotoxic activities. The cytotoxic activities of these compounds can be roughly correlated with electronic effects related to nucleophilic addition to C(6) of the compounds: The energies of the frontier molecular orbitals (E _HOMO and E _LUMO), the HOMO-LUMO energy gap, the dipole moment, the charge on C(6), and the electrophilicity on C(6). Figure LUMO of Pristimerin.     

Development of realistic models for Double Metal Cyanide catalyst active sites

Realistic molecular models of one and two-centre catalytic active sites originating from the cleavage of a precursor material known to give rise to an active double metal cyanide catalyst are described. Via periodic density functional calculations the structure of the proposed catalytic sites are shown to be dependent on electrostatic and structural relaxation processes occurring at the surfaces of the precursor material. It is shown how these effects may be adequately captured by small molecular models of the active sites. The general methodology proposed should provide a computationally efficient basis for detailed future studies into catalytic reactions over double metal cyanide materials. Figure Reconstructed DMC [100]-surface: electrostatic potential mapped on charge density isosurface This work has been originally presented on the Modelling and Design of Molecular Materials conference in Wrocław, Poland.     

Ab initio analysis of the Cope rearrangement of germacrane sesquiterpenoids

The energetics of the Cope rearrangement of 17 germacrane sesquiterpenoids to their respective elemane forms have been calculated using both density functional theory (B3LYP/6-31G*) and post Hartee-Fock (MP2/6-31G**) ab initio methods. The calculations are in qualitative agreement with experimentally observed Cope rearrangements, but the two methods give slightly different results. MP2 calculations generally show more favorable elemene energies compared to the respective germacrenes (by around 3–4 kcal mol⁻¹) and smaller activation energies (by 2–3 kcal mol⁻¹). Additionally, neither method is accurate enough to consistently reproduce the germacrene/elemene equilibrium. Apparently, the generally small energy differences between the two forms in these sesquiterpenoids cannot be adequately reproduced at these levels of calculation. Figure The Cope rearrangement of the germacrane sesquiterpenoid bacchascandon to the elemane shyobunone     

Molecular electrostatic potentials in aromatic substituted 4-hydroxyquino-2-lones: Glycine/NMDA receptor antagonists

Hydroxyquinolone derivatives have proven to be useful for inhibition at the glycine binding site of N-methyl-D-aspartate (NMDA) receptor. In this work the electronic structure, molecular electrostatic potential (MESP) and vibrational characteristics of a set of C₃ substituted 4-hydroxyquino-2-lone (HQ) derivatives, which act as Glycine/NMDA receptor antagonists, have been investigated using the density functional calculations. In the optimized structures a substituent at the C₃ site of HQ tends to adopt a helical structure. MESP investigations reveal that the ligands showing better inhibition activity should possess electron-rich regions extending over the substituent and carbonyl group of HQ. A correlation of inhibitory activity to the molecular electrostatic potential topography at the carbonyl oxygen as well as to the molecular electron density topography turns out to be a significant output of the investigation. Figure Quantam chemical approach has been employed to understand the reactivity of a set of hydroxyquinolone derivatives known for their inhibition activity towards Glycine/NMDA receptor. Molecular electrostatic potential topography has been used as a tool to understand the reactivity pattern     

Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment

A pattern recognition algorithm for the alignment of drug-like molecules has been implemented. The method is based on the calculation of quantum mechanical derived local properties defined on a molecular surface. This approach has been shown to be very useful in attempting to derive generalized, non-atom based representations of molecular structure. The visualization of these surfaces is described together with details of the methodology developed for their use in molecular overlay and similarity calculations. In addition, this paper also introduces an additional local property, the local curvature (C _L), which can be used together with the quantum mechanical properties to describe the local shape. The method is exemplified using some problems representing common tasks encountered in molecular similarity. Figure Molecular surfaces for Lorazepam (left) and Diazepam (right)     

Ligation of Aza bases to the AgF<Subscript>2</Subscript> molecule: a theoretical study

We have analyzed the electronic structure and chemical bonding for molecular adducts of the Ag(II)F₂ molecule with various aza Lewis bases including ammonia, nitriles, secondary amines, and their derivatives exhibiting various degrees of fluorination. Density functional theory calculations indicate that a progressive shift occurs of the spin density from the Ag center towards the coordinating nitrogen atoms of aza ligands, as the ligation energy increases. Chemistry of Ag(II) might be extended with little effort beyond the known aza connections, to include nitriles, perfluorinated nitriles and perfluorinated amines. Figure Properties of a variety of novel adducts of the AgF₂ molecule with two aza bases (L), possible precursors of the AgF₂L₂ extended solids, were assessed by the DFT calculations Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. This work is dedicated to memory of Wojciech Ochmański, unforgettable person, good-hearted man, whose craftsmanship in work was second-to-none.     

The theoretical investigation of one of the derivatives of 1, 2-dithienylcyclopentene as a molecular switch

The structural and electronic properties of a three-state molecular switch—an active device in a nano-electronic circuit—were studied using the B3LYP/6-31G* method. Due to its chemical stability, high conductivity upon doping, and non-linear optical properties, polythiophene is among the most widely studied conjugated organic polymers, both experimentally and theoretically. The aim of the present work was to theoretically study a very complex case: a three-state switch synthesized and experimentally investigated by Nishida et al. (Org Lett 6:2523–2526, 2004). An initial set of test calculations showed B3LYP level of theory and 6-31G* basis set to be the most appropriate for our purpose, i.e., the study of the structure, charge and spin distributions, as well as electrical characteristics such as electric polarizability, HOMO-LUMO gap (HLG) and electric dipole moment, for one of the 1,2-dithienylcyclopentene derivatives. Also, natural bond orbital analyses were performed to calculate local charges and charge transfers in order to study the capability of the molecule as a molecular switch. The results reported here are of general significance, and demonstrate that it is possible to use certain structural and electrical properties to understand and design electro-photochromic compounds showing a switching function in cases where stable forms can be exchanged by light or electron transfer. Figure Model of a thiophene wire incorporating a redox active unit     

Alpha particle chemistry. On the formation of stable complexes between He2+ and other simple species: implications for atmospheric and interstellar chemistry

The possibility that stable complexes may be formed between alpha particles (He²⁺) and small molecules is investigated using QCISD quantum mechanical calculations. Implications for their presence in the terrestrial atmosphere and/or in interstellar space are discussed. Figure Optimized structure of a stable H₂OHe²⁺ complex     

An experimental and theoretical study of the enantioselective deprotonation of cyclohexene oxide with isopinocampheyl-based chiral lithium amides

The mechanism of the enantioselective deprotonation of cyclohexene oxide with isopinocampheyl-based chiral lithium amide was studied by quantum chemical calculations. The transition states of eight molecules were fully optimized at the ab initio HF/3-21G and density functional B3LYP/3-21G levels with Gaussian 98. The activation energies were calculated at the B3LYP/6-31+G(3df,2p)//B3LYP/3-21G level. We found the theoretical evaluation to be consistent with the experimental data. At the best case, an enantiomeric excess of up to 95% for (R)-2-scyclohexen-1-ol was achieved with (−)-N, N-diisopinocampheyl lithium amide. Enantioselective deprotonation of cyclohexene oxide Electronic Supplementary Material Supplementary material is available for this article at Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday.     

The structure of 5a,6–anhydrotetracycline and its Mg2+ complexes in aqueous solution

Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg²⁺ ion with 5a,6–anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate the experimental situation more closely. The results are analyzed by comparing the behavior of the title compound with that of tetracycline itself and possible causes for the stronger induction of the Tetracycline Receptor (TetR) by 5a,6–anhydrotetracycline than by tetracycline are considered. Energetically favored 3D -structure of the zwitteranionic 5a,6-anhydrotetracycline magnesium complex in solution Electronic Supplementary Material Supplementary material is available for this article at     

Characterization of a candidate multi-pole molecular switch using computational techniques

An organic molecule, designed in this study, is proposed as a candidate molecular switch and characterized using the B3LYP/6-31G* computational method. Structural and electronic properties of this molecular switch (M) and its singly charged (M⁺ and M⁻) species in their lowest and the first higher spin states are calculated and analyzed. Molecular volume and electronic spatial extent (ESE) of this nanoswitch undergo negligibly small changes (<2%) upon charging. Furthermore, the small difference between the calculated dipole moments of the M⁺ and M⁻ species shows that switching between negative and positive poles does not significantly affect the charge transfer performance of this molecular switch. Natural bond orbital (NBO) and spin density distributions are also calculated and analyzed. A preliminary study on the response of the proposed molecular switch to the external electric field approves its function as a multi-pole nanoswitch controlled by a bias voltage. Figure Electron transfer scheme and arrangement of the π-electrons in the turn-on state of the candidate multi-pole molecular switch.     

Aromaticity and electronic properties of Heterosuperbenzene (Heterohexabenzocoronene)

A global electrophilicity parameter and the aromaticity of some heterocyclic polyaromatic hydrocarbons were evaluated on the basis of DFT calculations. The substitution of carbon atoms by nitrogen atoms dramatically changes the global electrophilicity of the molecules, with the fully substituted molecule being the most electrophilic with a reactivity very close to that of fullerene. Figure Fully substituted heterohexabenzocoronene Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Three-dimensional structure of the catalytic domain of the yeast β-(1,3)-glucan transferase Gas1: a molecular modeling investigation

The three-dimensional (3D) structure of the catalytic domain of Gas1p, a protein belonging to the only family of β-(1,3)-glucan transferases so far identified in yeasts and some pathogenic fungi (family GH-72), has been predicted by combining results derived from threading methods, multiple sequence alignments and secondary-structure predictions. The 3D model has allowed the identification of several residues that are predicted to play a crucial role in structural integrity, substrate recognition and catalysis. In particular, the model of the catalytic domain can be useful for designing site-directed mutagenesis experiments and for developing inhibitors of Gas1p enzymatic activity. Figure Three-dimensional models of the Gas1p catalytic domain as predicted using as template 7A3H (PDB code) protein Electronic Supplementary Material Supplementary material is available for this article at     

Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies of various benzodiazepine analogues of γ-secretase inhibitors

A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as γ-secretase inhibitors using molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity. The MFA study was carried out using a training set of 54 compounds. The predictive ability of model developed was assessed using a test set of 13 compounds ( as high as 0.729). The analyzed MFA model has demonstrated a good fit, having r² value of 0.858 and cross validated coefficient, value as 0.790. The analysis of the best MFA model provided insight into possible modification of the molecules for better activity.   Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A computational approach to the synthesis of 1,3,5-thiadiazinane-2-thiones in aqueous medium: theoretical evidence for water-promoted heterocyclization

Based on experimental evidence and DFT studies, a probable cyclization route to 1,3,5-thiadiazinanes-2-thiones in aqueous medium is proposed. Experimental facts suggest the formation of a {[hydroxymethyl (substituted) carbamothioyl] sulfanyl}methanol intermediate via reaction of dithiocarbamate (DTC) and formaldehyde. Nucleophilic addition of glycine to this intermediate generates an adduct that undergoes intramolecular heterocyclization via an S_N2 reaction. Computational calculations predict an active role of water in the reaction mechanism that promotes intramolecular cyclization. Figure Energy profile of the proposed reaction mechanism for the synthesis of thiadiazinane-2-thione ring 11 in aqueous medium from a (hydroxymethylcarbamothioyl)sulfanylmethanol intermediate, 9     

Theoretical study of 1-(4-hexylcyclohexyl)-4-isothiocyanatobenzene: molecular properties and spectral characteristics

The mesogenic species 4-(4-hexylcyclohexyl) isothiocyanatobenzene (6CHBT) was studied with density functional theory and molecular mechanics in order to investigate the molecular properties, interactions between dimers and to interpret the IR spectrum. Two types of calculations were performed for model systems containing single and double molecules of 6CHBT. Calculations (involving conformation analysis) for isolated species indicated that the trans isomer, in the equatorial–equatorial conformation, is the most energetically stable. The 6CHBT molecule is polar, with a rather high (4.43 D) dipole moment with negatively charged isothiocyanato (NCS) ligand. The dimer–dimer interaction energies show that the head-to-head configuration (where van der Waals attraction forces play the major role) is the most energetically stable. Vibrational analysis provided detailed assignment of the experimental infra-red (IR) spectrum. Figure Most favorite 6CHBT head to head interaction - ESP mapped to electron density surface Dedication  This paper is dedicated to the memory of Dr. Wacław Witko, who introduced us to research on mesogenic systems.