Has the trimethylene radical cation been observed?: An Ab initio molecular orbital study

Ab initio calculations have been performed on the cyclopropane radical cation and the trimethylene radical cation. The former radical cation has been claimed to undergo irreversible ring opening to the latter in CFCl₂CF₂Cl matrices at 80 K. However, the computational results reported here show that the energy of the cyclopropane radical cation is much lower than that of the (0,0) trimethylene radical cation, thus casting doubt on the possibility of irreversible ring opening of the former to the latter. It is suggested that the ring-opened species that is observed in the matrix by EPR has a nucleophile strongly coordinated to the carbocationic center.     

He 2++ molecular ion in a strong time-dependent magnetic field: a current-density functional study

The He molecular ion exposed to a strong ultrashort time‐dependent (TD) magnetic field of the order of 10⁹ G is investigated through a quantum fluid dynamics (QFD) and current‐density functional theory (CDFT) based approach using vector exchange‐correlation (XC) potential and energy density functional that depend not only on the electronic charge‐density but also on the current density. The TD‐QFD‐CDFT computations are performed in a parallel internuclear‐axis and magnetic field‐axis configuration at the field‐free equilibrium internuclear separation R = 1.3 au with the field‐strength varying between 0 and 10¹¹ G. The TD behavior of the exchange‐ and correlation energy of the He is analyzed and compared with that obtained using a [B‐TD‐QFD‐density functional theory (DFT)] approach based on the conventional TD‐DFT under similar computational constraints but using only scalar XC potential and energy density functional dependent on the electronic charge‐density alone. The CDFT based approach yields TD exchange‐ and correlation energy and TD electronic charge‐density significantly different from that obtained using the conventional TD‐DFT based approach, particularly, at typical magnetic field strengths and during a typical time period of the TD field. This peculiar behavior of the CDFT‐based approach is traced to the TD current‐density dependent vector XC potential, which can induce nonadiabatic effects causing retardation of the oscillating electronic charge density. Such dissipative electron dynamics of the He molecular ion is elucidated by treating electronic charge density as an electron‐“fluid” in the terminology of QFD. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Is a molecular orbital measurable by means of tomographic imaging?

Interpretation of experiments involving use of vacuum ultraviolet radiation to effect ionization of N₂ in terms of measurements of a molecular orbital is erroneous.     

Effect of intermolecular O-H ⋯ O hydrogen bonding on the molecular structure of phenol: An ab initio molecular orbital study

The effect of intermolecular O-H O hydrogen bonding on the molecular structure of phenol has been studied by SCF ab initio MO calculations at the HF/6-31G * level. The systems investigated are eight phenol-water complexes and the dimer and trimer of phenol. Optimized geometries show that hydrogen bond formation causes a consistent pattern of changes in the structure of the molecule. When phenol acts as a proton donor, the expected increase ofr (O-H) is accompanied by a slight decrease ofr(C-O) and of the internal ring angles at theipso andpara positions, and by an increase ofr(C _ipso © _ortho ). These changes suggest that the relative contribution of polar canonical forms to the electronic structure of the molecule increases upon hydrogen bond formation, since this enhances the strength of the interaction. The opposite changes occur when phenol acts as a proton acceptor, except forr(O-H), which is the same as in the free molecule. If phenol acts as a proton donorand as a proton acceptor, the two hydrogen bonds become stronger due to a synergic effect. In this case, however, the structural deformation of the molecule is less pronounced than in the previous cases, due to the opposite effect of the two hydrogen bonds. The available experimental evidence on gas-crystal structural differences for phenol is critically reviewed, also in the light of the present results on gas-phase complexes.     

Poly(oxyethylene)–cation interactions in aqueous solution: a molecular dynamics study

We have performed molecular dynamics simulations of a poly(oxyethylene) (POE) chain with 15 ethylene oxide units in an aqueous solution in the presence of potassium cations for 1 ns. The effect of the potassium ions on the POE aqueous solution characteristics are examined for the energetics, the hydration, the chain conformation and dynamics, and the solvent structure in comparison to those in the absence of cations. The POE's helical conformation is considerably distorted by complex formations with K⁺, and a significant perturbation of the POE hydration by K⁺ is observed. The competition between the K⁺–water and the K⁺–POE associations is found to be heavily shifted toward the latter. Furthermore, the POE–water pair interaction energy drastically decreases upon addition of K⁺. The observations, along with the decreased chain flexibility, point to the salting-out of POE salt aqueous solutions.     

Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study

We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree–Fock (HF)/6‐31G*, HF/6‐31G**, second‐order Møller–Plesset perturbation (MP2)/6‐31G*, and MP2/6‐31G** levels for three Src homology 3 (SH3) domains and five proline‐recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline‐rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline‐rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Catalytic effect of molecular iodine in Diels–Alder reaction: a density functional theory study

We explore here the feasibility of employing molecular iodine as Lewis acid catalyst for Diels–Alder (DA) reaction using conceptual density functional theory (DFT) based reactivity indices and transition state analysis at the DFT (B3LYP)/6-31G(d) level of theory. Catalytic effect of iodine is probed using reactivity indices considering six different substituents for the diene at the 2-position and five different substituents at the 1-position of the olefinic dienophile. Comparison of HOMO diene–LUMO dienophile gap between the catalyzed and uncatalyzed processes confirms catalytic effect of iodine in DA reaction. Mechanistic details of both the uncatalyzed and the iodine catalyzed processes is achieved through transition state analysis for four possible stereoisomeric reactive channels with respect to isoprene–acrolein model reaction. A significant cutback in activation barrier is observed in presence of iodine. Influence of iodine on regioselectivity of the reaction and asynchronicity of bond formation is analyzed using local version of the HSAB principle and philicity index.     

Activating multistep charge-transfer processes in fullerene-subphthalocyanine-ferrocene molecular hybrids as a function of π-π orbital overlap

We have synthesized two different fullerene-subphthalocyanine-ferrocene conjugates. The molecules were designed so that the ferrocene unit is linked at the subphthalocyanine axial position through a phenoxy spacer while the C(60) is rigidly held close to the concave face of the macrocycle via a 3-fold C(3)-symmetrical anchoring. The Bingel trisaddition reaction leading to the final products proceeded with very high regioselectivities and full diastereoselectivity. The only difference between both systems is the length of the triple tether employed, which finely regulates the regioselectivity of the trisaddition reaction and the distance between the subphthalocyanine and the C(60) complementary π-π surfaces. Thus, when the tether is connected to the subphthalocyanine through a direct C-C bond, a short π-π distance of 3.25-3.30 ? was calculated. In contrast, when it is connected through a slightly longer C-O-C bond, the distance increases to 3.5-3.6 ?. This π-π distance has a strong influence on the ground-state electronic interactions between the subphthalocyanine and the C(60), as determined from electronic absorption and cyclic voltammetry measurements. In addition, fluorescence and time-resolved transient absorption experiments demonstrated that different mechanisms operate in the two systems after photoexcitation. Despite the similar HOMO-LUMO gaps, only when the two complementary π-π surfaces of the subphthalocyanine and the C(60) are held at a close distance, therefore showing a high degree of orbital overlap, is a multistep electron transfer process triggered, ultimately leading to the long-lived, spatially separated C(60) radical anion and ferrocenium radical cation pair. A full account of the synthesis, characterization, and studies of the ground- and excited-state electronic interactions occurring in these conjugates, as well as in their reference C(60)-subphthalocyanine and subphthalocyanine-ferrocene dyads, is presented in this article.     

How effective is internal excitation in promoting the HCl + 1,3-butadiene addition reaction?

Excitation of the C-H overtones of 1,3-butadiene in the presence of HCl to an energy ≈ 16 kcal mol⁻¹ in excess of the activation energy causes the formation of no detectable addition products. This indicates that the rate constant for the formation of 1-chloro-2-butene is at least slower than 2.1× 10⁻¹⁴ cm³ molecule⁻¹ s⁻¹.     

Role of CH�C�� interaction energy in self-assembled gear-shaped amphiphile molecules: correlated ab initio molecular orbital and density functional theory study

Ab initio molecular orbital and density functional theory calculations with inclusion of dispersion interaction effect are employed to reveal the characteristic features of intermolecular interactions for the molecular capsule (1 ₆) consisting of six gear-shaped amphiphile molecules (1) discovered by Hiraoka et al. (J Am Chem Soc 130:14368?C14369, 2008). The contributions of CH?C?? and ?ШC?? type dispersion energies are found to be indispensable for the formation of hexameric capsule 1 ₆ by the analysis of decomposed interaction energies between fragmented-model species in the 1 molecule. We have also calculated the hexameric capsule (2 ₆) from demethylated 1 molecule (2). Such subtle structural difference induces the different characters of intermolecular interactions, in which the stabilization energy of hexameric 2 ₆ capsule is about 40?kcal/mol smaller than that of the original 1 ₆ capsule, due to the lack of three methyl groups for the CH?C?? interactions in 2 molecules.     

Introduction of unsaturated pendant groups to polyethylene by γ-ray irradiation under a 1,3-butadiene atmosphere

Ultra-high-molecular-weight polyethylene (Mˉ _v: 5 × 10⁶, 100-times elongated film) was irradiated with γ-rays under a 1,3-butadiene atmosphere at room temperature. Electron paramagnetic resonance (EPR) measurements indicated that the radicals formed on the polyethylene substrate during the irradiation were short-lived. EPR, Fourier transform IR spectroscopy, solid-state NMR, and differential scanning calorimetry of the as-irradiated materials indicated that butadiene molecules were covalently bound to the polyethylene chains as pendant groups bearing trans-vinylene and vinyl functions in a ratio of 3:1. Some crosslinks among the pendants, or between pendants and the main chains were produced. The number of unsaturated pendants introduced (including bridges) per carbon atom of the polyethylene main chain was dependent on the irradiation dose and the butadiene pressure, and was 0.096 butadiene units for 10 kGy irradiation under a 304 kPa butadiene atmosphere. The unsaturated pendants or bridges on the polyethylene chain thus introduced may be good targets to functionalize polyethylene by covalent modification. Received: 22 February 1999 Accepted in revised form: 30 June 1999     

How much carbon dioxide can be stored in the structure H clathrate hydrates?: a molecular dynamics study

The stability of structure H (sH) carbon dioxide clathrate hydrates at three temperature-pressure conditions are determined by molecular dynamics simulations on a 3x3x3 sH unit cell replica. Simulations are performed at 100 K at ambient pressure, 273 K at 100 bars and also 300 K and 5.0 kbars. The small and medium cages of the sH unit cell are occupied by a single carbon dioxide guest and large cage guest occupancies of 1-5 are considered. Radial distribution functions are given for guests in the large cages and unit cell volumes and configurational energies are studied as a function of large cage CO(2) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at three temperature/pressure conditions stated above. At the low temperature, large cage occupancy of 5 is the most stable while at the higher temperature, the occupancy of 3 is the most favored. Calculations are also performed to show that the CO(2) sH clathrate is more stable than the methane clathrate analog. Implications on CO(2) sequestration by clathrate formation are discussed.     

Host–guest complexation of a nitroheterocyclic compound with cyclodextrins: a spectrofluorimetric and molecular modeling study

Nitroheterocyclic compounds (NC) were candidate drugs proposed for Chagas disease chemotherapy. In this study, we investigated the complexation of hydroxymethylnitrofurazone (NFOH), a potential antichagasic compound, with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD), Hydroxypropyl-β-cyclodextrin (HP-β-CD), Dimethyl-β-cyclodextrin (DM-β-CD) and γ-cyclodextrin (γ-CD) by fluorescence spectroscopy and molecular modeling studies. Hildebrand–Benesi equation was used to calculate the formation constants of NFOH with cyclodextrins based on the fluorescence differences in the CDs solution. The complexing capacity of NFOH with different CDs was compared through the results of association constant according to the following order: DM-β-CD > β-CD > α-CD > HP-β-CD > γ-CD. Molecular modeling studies give support for the experimental assignments, in favor of the formation of an inclusion complex between cyclodextrins with NFOH. This is an important study to investigate the effects of different kinds of cyclodextrins on the inclusion complex formation with NFOH and to better characterize a potential formulations to be used as therapeutic options for the oral treatment of Chagas disease.     

Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region

For a quantitative understanding of molecular structure, interaction and dynamics, accurate modelling of the energetics of both near-equilibrium and less optimal contacts is important. In this work, we explore the potential energy surfaces of representative ion-π complexes. We examine the performance of a semi-empirical QM/MM approach and the corresponding QM/MMpol model, where inducible point dipoles are additionally employed in the MM region. The predicted potential energy surfaces of cation-benzene complexes are improved by inclusion of explicit MM polarisation of the π-molecule. For cation-formamide complexes, inducible dipoles appreciably improve energetic estimates at geometries forming non-optimal interactions. Energetic component analysis suggests that the implicit MM polarisation of the fixed charge QM/MM model mirrors the behaviour of the QM/MMpol dipole model for the energetics of near-equilibrium conformations. However, for complexes at less optimal orientations, the QM/MM model exhibits higher errors than the QM/MMpol approach, being unable to capture orientation-dependent variations in polarisation energy.     

Hyperbranched modification of unsaturated side chains of polyethylene introduced by γ-ray irradiation under a 1,3-butadiene atmosphere

 Amino and other functional groups were introduced to a polyethylene substrate starting from the unsaturated pendant and bridge groups (collectively called side chains) of polyethylene, which had been prepared by γ-ray irradiation under an atmosphere of 1,3-butadiene of the polyethylene substrate (the drawn film of ultra-high- molecular-weight polyethylene, Mˉv: 5 × 10⁶). 2-Aminoethylamino groups were introduced to the side chains through treatment either with bromine or with peracetic acid vapor followed by immersion in ethylenediamine. Introduction of amino groups were confirmed by Fourier transform IR spectrometry, ninhydrin test, and acid–base titration. Starting from 2-aminoethylaminated polyethylene, modification cycles to grow a dendrimer on the film were applied; these consisted of 2-methoxycarbonylethylation and 2-aminoethylamidation. This technique resulted in hyperbranched modification of the polymer. The product is a kind of dendrimer grown on the surface of polyethylene film with amplified amino ends and has anion-exchange capacity and absorbs acid dye. Its application in practical uses is discussed. Received: 31 March 2000 Accepted: 2 January 2001     

Concentration dependence of the methane structure in silicalite-1: a molecular dynamics study using the Møller-Plesset-based potential

M?ller-Plesset perturbation-based potentials have been used in molecular dynamics simulations to examine methane diffusion in silicalite-1. The simulation box contains 2 unit cells of silicalite-1 and varying loading numbers (n(ld)) from 1, 2, 3, to 4 methane molecules per intersection, corresponding to 8, 16, 24, and 32 molecules per simulation box, respectively. Consistent with the previous study, a preferential diffusing path for methane is close to the channel axes. The structure of the methane molecules in the silicalite-1 pore was exhibited in terms of the methane-methane radial distribution function (RDF) in which the first peak appears at 6.4 A for n(ld) < or = 2, becomes a broad maximum at n(ld) = 3, and splits into two sharp peaks centered at 6.4 and 8.6 A at n(ld) = 4. This fact can be clearly described by an intensification of the methane density in the straight and zigzag channels but a decrease in the intersection when the loading increases. These features of the observed RDFs are in contrast with the previous report using a molecular dynamics force-field potential in which the RDFs for all concentrations show first maxima at approximately 4 A. The analysis of the relative residence times of methane at different sites inside the silicalite suggests that the zigzag channel is the most favored location. The computed self-diffusion coefficients as well as the heat of adsorptions are in reasonable agreement with the available values.     

Hydrogen bonding in ε-caprolactam dimer: a quantum-chemical study

The equilibrium geometries, vibrational frequencies, and IR band intensities were calculated for the monomer and hydrogen-bonded cyclic dimer of -caprolactam (1) by the density functional B3LYP/6-311++G(d,p) method and compared with the experimental data. The gas phase IR spectrum of monomer of 1 was first measured. The calculated hydrogen bonding enthalpy H/2 in the hydrogen-bonded dimer in the gas phase (–5.93 kcal/mol) is consistent with the published data. The computed scaled (scaling factor 0.97) vibrational frequencies of the monomer and dimer are in good agreement with the experimental data. The geometry of the -caprolactam monomer remains nearly unchanged in its dimer except for the N-H, C-O, and C-N bond lengths that respectively change from 1.012, 1.230, and 1.369 in the former to 1.029, 1.246, and 1.350 in the latter. The frequencies, eigenvectors, and IR intensities of the amide modes of the monomer and dimer differ dramatically. The calculated NH and CO frequency shifts due to hydrogen bonding are in good agreement with the experimental data, but theoretical intensification of the NH IR band is much greater than that observed experimentally (by nearly 69 times vs. 11 times, respectively). The calculated N...O intermolecular distance in the structure of -caprolactam dimer equals the experimental value (2.89 ). The influence of the basis set employed on the results of calculations is discussed.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1818–1825, September, 2004.     

Interaction of manzamine A with glycogen synthase kinase 3β: a molecular dynamics study

The search for the possible binding site of manzamine A to glycogen synthase kinase 3β(GSK-3β) was performed by molecular docking followed by molecular dynamics simulation and calculations of the Gibbs free energy of inhibitor—kinase binding. The cavity between the glycine-rich loop, the loop C, and the activation loop is the most likely site of interaction.