Mechanistic study of palladium-catalyzed telomerization of 1,3-butadiene with methanol

The Pd-catalyzed telomerization in the presence of phosphine and carbene ligands has been computed. It is shown that the C–C coupling of the less stable complex A with one trans- and one cis-butadiene in syn orientation forms the most stable intermediate B and is favorable both kinetically and thermodynamically. Protonation of B leads to equilibrium of the two most stable isomers of intermediate C. The overall regioselectivity is favored thermodynamically.      

Theoretical study of spin-spin coupling across the hydrogen (O-H⋯N) bond in adenosine derivatives

The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes. The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2′,3′-O-isopropylideneadenosine between the -CH₂OH (at 5″ proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the ^4h J _NH coupling across the H″-C-O-H···N hydrogen bond in adenosine derivatives in various solvent models. Figure Coupling constants in 8-bromo-2′,3′-O-isopropylideneadenosine Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

DFT investigation of the 1-octene metathesis reaction mechanism with the Phobcat precatalyst

The productive self-metathesis reaction of 1-octene in the presence of the Phobcat precatalyst [RuCl₂(Phoban-Cy)₂(=CHPh)] using density functional theory was investigated and compared to the Grubbs 1 precatalyst [RuCl₂(PCy₃)₂(=CHPh)]. At the GGA-PW91/DNP level, the geometry optimization of all the participating species and the PES scans of the various activation and catalytic cycles in the dissociative mechanism were performed. The formation of the catalytically active heptylidene species is kinetically and thermodynamically favored, while the formation of trans-tetradecene is thermodynamically favored.      

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 molecular-dynamics simulation study of diffusion of a single model carbonic chain on a graphite (001) surface

Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid–liquid interface. Furthermore, we have studied the relation between the mean-square gyration radius and N. Figure Log–log plot of the self-diffusion coefficient D versus the chain length N. The error bars are the standard deviation measured in three repeated simulations     

The molecular structure of a curl-shaped retinal isomer

Computational studies of retinal protonated Schiff base (PSB) isomers show that a twisted curl-shaped conformation of the retinyl chain is a new low-lying minimum on the ground-state potential energy surface. The curl-shaped isomer has a twisted structure in the vicinity of the C₁₁=C₁₂ double bond where the 11-cis retinal PSB isomerizes in the rhodopsin photoreaction. The twisted configuration is a trapped structure between the 11-cis and all-trans isomers. Rotation around the C₁₀–C₁₁ single bond towards the 11-cis structure is prevented by steric interactions of the two methyl groups on the retinyl chain and by the torsion barrier of the C₁₀–C₁₁ bond in the other direction. Calculations of spectroscopic properties of the 11-cis, all-trans, and curl-shaped isomers provide useful data for future identification of the new retinal PSB isomer. Circular dichroism (CD) spectroscopy might be used to distinguish between the retinal PSB isomers. The potential energy surface for the orientation of the β-ionone ring of the 11-cis retinal PSB reveals three minima depending on the torsion angle of the β-ionone ring. Two of the minima correspond to 6-s-cis configurations and one has the β-ionone ring in 6-s-trans position. The calculated CD spectra for the two 6-s-cis configurations differ significantly indicating that the sign of the β-ionone ring torsion angle could be determined using CD spectroscopy. Calculations of the CD spectra suggest that a flip of the β-ionone ring might occur during the first 1 ps of the photoreaction. Rhodopsin has a negative torsion angle for the β-ionone ring, whereas the change in the sign of the first peak in the experimental CD spectrum for bathorhodopsin could suggest that it has a positive torsion angle for the β-ionone ring. Calculated nuclear magnetic resonance (NMR) shielding constants and infrared (IR) spectra are also reported for the retinal PSB isomers. Figure The figure shows the optimized molecular structure of the curl-shaped retinal isomer. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Boron nitride cages from B12N12 to B36N36: square–hexagon alternants vs boron nitride tubes

The structures and stabilities of square–hexagon alternant boron nitrides (B _x N _x , x=12–36) vs their tube isomers containing octagons, decagons and dodecagons have been computed at the B3LYP density functional level of theory with the correlation-consistent cc-pVDZ basis set of Dunning. It is found that octagonal B₂₀N₂₀ and B₂₄N₂₄ tube structures are more stable than their square–hexagon alternants by 18.6 and 2.4 kcal mol⁻¹, respectively, while the square–hexagon alternants of other cages are more stable. Trends in stability as a function of cluster size are discussed.Figure The octagonal B₂₀N₂₀ and B₂₄N₂₄ tube structures are more stable than their square-hexagon alternant cagesDedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

Why are dimethyl sulfoxide and dimethyl sulfone such good solvents?

We have carried out B3PW91 and MP2-FC computational studies of dimethyl sulfoxide, (CH₃)₂SO, and dimethyl sulfone, (CH₃)₂SO₂. The objective was to establish quantitatively the basis for their high polarities and boiling points, and their strong solvent powers for a variety of solutes. Natural bond order analyses show that the sulfur–oxygen linkages are not double bonds, as widely believed, but rather are coordinate covalent single S⁺→O⁻ bonds. The calculated electrostatic potentials on the molecular surfaces reveal several strongly positive and negative sites (the former including σ-holes on the sulfurs) through which a variety of simultaneous intermolecular electrostatic interactions can occur. A series of examples is given. In terms of these features the striking properties of dimethyl sulfoxide and dimethyl sulfone, their large dipole moments and dielectric constants, their high boiling points and why they are such good solvents, can readily be understood. Figure Dimers of dimethyl sulfoxide (DMSO; left) and dimethyl sulfone (DMSO2; right) showing O S—O -hole bonding and C H—O hydrogen bonding. Sulfur atoms are yellow, oxygens are red, carbons are gray and hydrogens are white     

Theoretical study of [ XN5 ]− (X=O, S, Se, Te) systems

A series of [XN₅]⁻ (X=O, S, Se, Te) compounds has been examined with ab initio and Density Functional Theory (DFT) methods. The five-membered nitrogen ring series of structures are global minima and may exist or be characterized due to their significant dissociation barriers (29.7–32.7 kcal mol⁻¹). Nucleus-independent chemical shifts (NICS) criteria and the presence of (4n+2) π-electrons confirmed that the five-membered nitrogen ring in their structures exhibits characteristics of aromaticity. Thus, the strong stability of the five-membered nitrogen ring structures may be attributed partially to their aromaticity.      

The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (P<Superscript>III</Superscript>)

Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus–carbon bond cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (P^III). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that decomposition to P^III derivatives proceeds via an elimination reaction. Figure The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (P^III)     

A theoretical study on unusual intermolecular T-shaped X–H...π interactions between the singlet state HB=BH and HF, HCl, HCN or H2C2

The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid hydrogen of HF, HCl, HCN and H₂C₂ using MP2 and B3LYP methods at 6-311++G(2df,2p) and aug-cc-pVTZ levels. The binding energies follow the order of HB=BH...HF>HB=BH...HCl>HB=BH...HCN>HB=BH...H₂C₂. The hydrogen-bonded interactions in HB=BH...HX are found to be stronger than those in H₂C=CH₂...HX and OCB≡BCO...HX. The analyses of natural bond orbital (NBO) and the electron density shifts reveal that the nature of the T-shaped X–H...π hydrogen-bonded interaction is that much of the lost density from the π-orbital of B=B bond is shifted toward the hydrogen atom of the proton donor, leading to the electron density accumulation and the formation of the hydrogen bond. The atoms in molecules (AIM) theory have also been applied to characterize bond critical points and confirm that the B=B double bond can be a potential proton acceptor. The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid hydrogen of HF, HCl, HCN and H₂C₂     

Theoretical study of the hydrogen-bonded complexes serotonin–water/hydrogen peroxide

Eight H-bonded complexes between serotonin (5-hydroxy-tryptamine) and water/hydrogen peroxide were studied at the B3LYP and HF levels of theory, using the 6-31+G(d) basis set. A thermodynamic analysis was performed in order to find the most stable complex. The calculated bonding parameters showed that the most stable H-bonded complex is formed between serotonin and hydrogen peroxide by means of the intermolecular H-bond –H₂N...H–OOH. Fig. a Theoretical study of the hydrogen-bonded supersystems serotonin-water/hydrogen peroxide     

Mesoscopic simulation studies on micellar phases of Pluronic P103 solution

The microphase separation dynamics of the triblock copolymer surfactant P103 [(ethylene oxide)₁₇(propylene oxide)₆₀(ethylene oxide)₁₇] was investigated by a dynamic variant of mean-field density functional theory. Different self-assembled aggregates, spherical micelles, micellar clusters and disk-like micelles, are explored in the solution. The spherical micelle above critical micelle concentration (CMC) is a dense core consisting mainly of PPO and a hydrated PEO swollen corona, and is in good agreement with the experimental results concerning their structures. At a concentration of 10–15%, micellar clusters with a larger PPO core form as a result of coalescence among spherical micelles. At concentrations above 16% by volume, a series of disk-like micelles come into being. The order parameters show that spherical micelles are easily formed, while the micellar clusters or disk-like micelles need a longer time to reach steady equilibrium. The results show that mesoscopic simulation can augment experimental results on amphiphilic polymers, and provide some mesoscopic information at the mesoscale level. Figure Coalescence of Micelles with time evolution for 15% vol system. □ represents spherical micelle that coalesce. (a) 180 μs, (b) 190 μs, (c)225 μs, and (d) 250 μs     

Halogen bonding: the σ-hole

Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the σ-hole, on the outermost portion of the halogen’s surface, centered on the R–X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF₃X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the configuration, where the z-axis is along the R–X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the σ-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the σ-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a σ-hole is observed for the Cl in CF₃Cl, but not in CH₃Cl. Figure Schematic representation of the atomic charge generation. The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian. The semiempirical MEP is then scaled to DFT or ab initio level and atomic charges are generated from it by the restrained electrostatic potential (RESP) fit method.     

Density functional computations of enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes

The enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes was studied by means of the density functional theory (DFT). All the structures were optimized completely at the B3LYP/6-31G(d,p) level. To obtain more exact energies, single-point energy calculations at B3LYP/6-31+G(d,p) level were carried out on the B3LYP/6-31G(d,p) geometries. As shown, this enantioselective alkynylation was endothermic. The chirality-determining step for the alkynylation was the formation of the catalyst–ethanol complexes and the transition states for this step involved a six-membered ring. The dominant products predicted theoretically were of (R)-chirality, in good agreement with experiment.      

Blue shifts <Emphasis Type="Italic">vs</Emphasis> red shifts in σ-hole bonding

σ-Hole bonding is a noncovalent interaction between a region of positive electrostatic potential on the outer surface of a Group V, VI, or VII covalently-bonded atom (a σ-hole) and a region of negative potential on another molecule, e.g., a lone pair of a Lewis base. We have investigated computationally the occurrence of increased vibration frequencies (blue shifts) and bond shortening vs decreased frequencies (red shifts) and bond lengthening for the covalent bonds to the atoms having the σ-holes (the σ-hole donors). Both are possible, depending upon the properties of the donor and the acceptor. Our results are consistent with models that were developed earlier by Hermansson and by Qian and Krimm in relation to blue vs red shifting in hydrogen bond formation. These models invoke the derivatives of the permanent and the induced dipole moments of the donor molecule. Figure Computed electrostatic potential on the molecular surface of Cl-NO₂. Color ranges, in kcal mol⁻¹, are: red, greater than 25; yellow, between 10 and 25; green, between 0 and 10; blue, between −4 and 0; purple, more negative than −4. The chlorine is facing the viewer, to the right. Note the yellow region of positive potential on the outer side of the chlorine, along the extension of the N–Cl bond. The blue region shows the sides of the chlorine to have negative potentials. The calculations were at the B3PW91/6–31G(d,p) level.     

The tri–μ–hydrido–bis[(η5–C5Me5)aluminum(III)] theoretical study, the assets of sandwiched M2H3 (M of 13th group elements) stability

The stability of the tri–μ–hydrido–bis[(η⁵–C₅Me₅)aluminum], Cp*₂Al₂H₃, 1 is studied at B3LYP/6–311+G(d,p), CCSD(T)//B3LYP/6–311+G(d,p) and MP4//B3LYP/6–311+G(d,p) levels. The coordination between Al₂H₃ entity and both C₅(CH₃)₅ groups is ensured by strong electrostatic and orbital interactions. The orbital analysis of the interacting fragments shows that Al₂H₃ acceptor, which keeps its tribridged structure, implies the vacant ( \texta₁￠ ) \left( {{\text{a}}_1^\prime } \right) and five antibonding (a₂^￠￠ a_2^{\prime \prime } , e′ and e″) molecular orbitals to interact with two orbitals mixtures, b₁ and e" of the donors (C₅Me₅). When we take into account the solvent effect, the computation shows that 1 seems to be stable in condensed phase with a tribridged bond between the Al atoms [Cp*Al(μ-H)₃AlCp*], whereas in the gas phase, the monobridged Cp*AlH(μ-H)AlHCp* 4 is slightly favored (4 kcal mol⁻¹). We propose that 1 could be prepared thanks to Cp*Al (2) and Cp*AlH₂ (3) reaction in acidic medium. The experimental treatment of this type of metallocenes would contribute to the development of the organometallic chemistry of 13th group elements.      

σ-hole bonding between like atoms; a fallacy of atomic charges

Covalently bonded atoms, at least in Groups V–VII, may have regions of both positive and negative electrostatic potentials on their surfaces. The positive regions tend to be along the extensions of the bonds to these atoms; the origin of this can be explained in terms of the σ-hole concept. It is thus possible for such an atom in one molecule to interact electrostatically with its counterpart in a second, identical molecule, forming a highly directional noncovalent bond. Several examples are presented and discussed. Such “like-like” interactions could not be understood in terms of atomic charges assigned by any of the usual procedures, which view a bonded atom as being entirely positive or negative. Figure Calculated electrostatic potential on the surface of SCl₂. The sulfur is in the foreground, the chlorines are at the back. Color ranges (kcal mol⁻¹): purple negative, blue between 0 and 8, green between 8 and 15, yellow between 15 and 20, red more positive than 20. Note that the sulfur has regions of both positive (red) and negative (purple) electrostatic potential