Computational insights into octyl-D-xyloside isomers towards understanding the liquid crystalline structure: physico-chemical features

We applied density functional theory to study octyl-D-xyloside isomers in order to explain the features responsible for the liquid crystal mesophases. Compared to a glucoside, the xylose headgroup has a proton instead of the hydroxymethyl group on C5. Thus, a xyloside has a reduced headgroup volume that renders it less hydrophilic. Our results have shown that the xylose headgroup may adopt stable pyranose and furanose conformations, which may lead to different effective headgroup hydrophilicities. These features are probably responsible for forming two non-equivalent inverse micelles, which are self-assembled into a cubic discontinuous phase with a space group of Fd3m commonly found for xylosides. While different factors are responsible for controlling the relative stability of each isomer, the role of intramolecular hydrogen bonding was highlighted for the investigated single molecule. The polarisable continuum model was used to take into account the solvent effect in order to understand the molecular behaviour in very polar systems. Results from calculations carried out in gas phase were used for comparative purposes. The molecular electrostatic potential calculations for these xylolipids demonstrate sugar amphoterism, which is implicated in the heterogeneity nature of lipid self-assembly.     

Computational insights into the effects of reagent structure and bases on nucleophilic monofluoromethylation of aldehydes

Although fluorobis(phenylsulfonyl)methane(FBSM) and its cyclic analog 2-fluoro-1,3-benzodithiole-1,1,3,3-tetraoxide(FBDT) possess similar physicochemical properties, Shibata et al. found that FBSM failed to undergo nucleophilic monofluoromethylation of aldehydes regardless of the reaction conditions attempted(using various organic and inorganic bases). However, it was later discovered by Hu et al. that the nucleophilic monofluoromethylation could be accomplished by employing lithium hexamethyldi...     

Computational insight into the electronic structure and absorption spectra of lithium complexes of N-confused tetraphenylporphyrin

The present work is a theoretical investigation on lithium complexes of N-confused tetraphenylporphyrins (aka inverted) employing density functional theory (DFT) and time-dependent DFT, using the B3LYP, CAM-B3LYP, and M06-2X functionals in conjunction with the 6-31G(d,p) basis set. The purpose of the present study is to calculate the electronic structure and the bonding of the complexes to explain the unusual coordination environment in which Li is found experimentally and how the Li binding affects the Q and the Soret bands. The calculations show that, unlike a typical tetrahedral Li(+) cation, this Li forms a typical bond with one N and interacts with the remaining two N atoms, and it is located in the right place to form an agostic-like interaction with the internal C atom. The reaction energy, the enthalpy for the formation of the lithium complexes of N-confused porphyrins, and the effect of solvation are also calculated. The insertion of Li into N-confused porphyrin, in the presence of tetrahydrofuran, is exothermic with a reaction energy calculated to be as high as -72.4 kcal/mol using the lithium bis(trimethylsilyl)amide reagent. Finally, there is agreement in the general shape among the vis-UV spectra determined with different functionals and the experimentally available ones. The calculated geometries are in agreement with crystallographic data, where available.     

Computational insights into the acceptor chemistry of phosphenium cations

Phosphines are traditionally considered as Lewis bases or ligands in transition metal and main group complexes. Despite their electron-rich (lone pair-bearing) nature, an extensive coordination chemistry for Lewis acidic phosphorus centers is being developed; such chemistry provides a new synthetic approach for phosphorus-element bond formation, leading to new types of structures and modes of bonding. Complexes of Ph2P+ with a variety of donor elements (P, N, C) give experimentally short donor-acceptor bond lengths, when compared to other cationic phosphorus Lewis acid complexes. We have calculated that the energy of the lowest unoccupied molecular orbital (LUMO) in Ph2P+ is lower than that of (Me2N)2P+, which partially explains the greater exothermicity of reactions of donors with the diaryl acceptor. Furthermore, the energies required to distort the diphenylphosphenium cation from its ground-state geometry are significantly smaller than those of the diamido cations and, thus, enhance the exothermicity of donor coordination. These computational data, in conjunction with evidence from experimental solid-state structures, indicate that Ph2P+ is a significantly better Lewis acid relative to the more common diaminophosphenium analogues (R2N)2P+ and are used to elucidate the nature of the bonding in donor-phosphenium complexes.     

Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases

In this work, selectivity mechanism of APP-IP inhibitor (β-amyloid precursor protein-derived inhibitory peptide) over matrix metalloproteinases (MMPs including MMP-2, MMP-7, MMP-9 and MMP-14) was investigated by molecular modeling methods. Among MMPs, MMP-2 is the most favorable one for APP-IP interacting based on our calculations. The predicted binding affinities can give a good explanation of the activity difference of inhibitor APP-IP. In Comparison with MMP-2/APP-IP complex, the side chain of Tyr214^MMP-7 makes the binding pocket so shallow that the whole side chain of Tyr3^APP-IP can not be fully embraced, thus unfavorable for the N-terminal of APP-IP binding to MMP-7. The poor selectivity of APP-IP toward MMP-9 is mainly related with the decrease of interaction between the APP-IP C-terminal and MMP-9 due to the bulky side chains of Pro193 and Gln199, which is in agreement with experiment. The mutations at residues P193A and Q199G of MMP-9 alternate the binding pattern of the C-terminal of APP-IP by forming two new hydrogen bonds and hydrophobic interactions with MMP-9. The mutants favor the binding affinity of MMP-9 largely. For MMP-14/APP-IP, the large steric effect of Phe204^MMP-14 and the weak contributions of the polar residues Asn231^MMP-14 and Thr190^MMP-14 could explain why MMP-14 is non-selective for APP-IP interacting. Here, the molecular modeling methods were successfully employed to explore the selective inhibitor of MMPs, and our work gives valuable information for future rational design of selective peptide inhibitors toward individual MMP.     

Computational study of the substitution effect on the mechanism for phospha-Wittig reaction

The phospha-Wittig reaction HP=PH₃ + O=CHX → HP=CHX + O=PH₃ (X = H, F, Cl, Me, OMe, NMe₂, CMe₃) was examined using the density functional theory calculations. All of the structures were completely optimized at the B3LYP/6-311++G** level of theory. The reactivities of various O=CHX were examined by estimating their activation energies. The main finding of this work is that the configuration mixing model can successfully predict the relative ordering of the activation energy and reaction enthalpies of the phospha-Wittig reaction. It was demonstrated that O=CHX with more electro-releasing substituents will possess a smaller singlet–triplet splitting. This will facilitate the phospha-Wittig reaction and will result in a larger exothermicity.     

New insights into the structure of polyelectrolyte complexes

The formation of polyelectrolyte complexes (PECs) from oppositely charged linear polyelectrolytes (PELs) was studied using static light scattering at various salt concentrations. The PELs used were poly(allylamine hydro chloride) (PAH) and the two polyanions poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). Physical characteristics such as the radii of gyration, molecular weights, and water contents of the PECs were determined at various molar mixing ratios. Despite relatively small differences in chemical structure between PAA and PMAA, fairly large differences were detected in these physical characteristics. Generally, PECs comprising PMAA were larger and contained more water. Moreover, by using cryogenic transmission electron microscopy, transmission microscopy and atomic force microscopy, shape and structure of the prepared PECs were investigated both in solution and after drying. The PECs were found to be spherical in solution and the shape was retained after freeze-drying. PECs adsorbed on silica surfaces and dried in air at room-temperature still showed a three-dimensional structure. However, the relatively low aspect ratios indicated that the PECs collapsed significantly due to interactions with the silica during adsorption and drying. At intermediate ionic strengths (1-10 mM), stagnation point adsorption reflectometry (SPAR) showed that the adsorption of low charged cationic PAH-PAA PECs on silica surfaces increased if the pH value was increased from pH 5.5 to 7.5.     

Computational insights into the molecular mechanisms for chromium passivation of stainless-steel surfaces

First principles DFT calculations are used to gain insights into the molecular mechanism of Cr passivation of FeCr alloy surfaces. The systems studied represent early stages of oxidation of FeCr alloys when the oxide layers extend just a few atomic layers into the bulk. A Monte-Carlo atom-swapping algorithm was developed to efficiently explore possible atomic positions and identify the most promising structures that yield overall energy lowering. Analysis of the resulting low energy structures show that the surface oxide layer is rich in chromium while there is a reduction in chromium in the metallic phase near the alloy-oxide interface. Furthermore, there is an increased concentration of Fe near the oxide-air surface. Analysis of the molecular structure of the oxide layers found that oxidized Cr was predominantly in the Cr₂O₃ phase, while oxidized Fe was present as both FeO and Fe₂O₃. We propose that the oxidative variability of Fe facilitates O diffusion in the iron-rich phases because of the range of geometries available for accommodating the O atom. In contrast, O diffusion is less facile in Cr, which has little variability in oxidation state.     

Mechanistic insights into the Bazarov synthesis of urea from NH3 and CO2 using electronic structure calculation methods

The mechanism of the noncatalyzed and reagent-catalyzed Bazarov synthesis of urea has extensively been investigated in the gas phase by means of density functional (B3LYP/6-31G(d,p)) and high quality ab initio (CBS-QB3) computational techniques. It was found that the first step of urea formation from NH3(g) and CO2(g) corresponds to a simple addition reaction leading to the carbamic acid intermediate, a process being slightly endothermic. Among the three possible reaction mechanisms considered, the addition-elimination-addition (AEA) and the double addition-elimination (DAE) mechanisms are almost equally favored, while the concerted (C) one was predicted kinetically forbidden. The second step involves the formation of loose adducts between NH3 and carbamic acid corresponding to an ammonium carbamate intermediate, which subsequently dehydrates to urea. The formation of "ammonium carbamate" corresponds to an almost thermoneutral process, whereas its dehydration, which is the rate-determining step, is highly endothermic. The Bazarov synthesis of urea is strongly assisted by the active participation of extra NH3 or H2O molecules (autocatalysis). For all reaction pathways studied the entire geometric and energetic profiles were computed and thoroughly analyzed. The reaction scheme described herein can be related with the formation of both isocyanic acid, H-N=C=O, and carbamic acid, H2N-COOH, as key intermediates in the initial formation of organic molecules, such as urea, under prebiotic conditions.     

Influence of Cl substitution on the electronic structure and catalytic activity of ceria

Cl-containing cerium dioxide(Ce O2) catalysts have been found to exhibit unique catalytic activities. In the present work, using density functional theory calculations with the inclusion of on-site Coulomb correction, we systematically studied the effect of Cl on the physicochemical properties of Ce O2 surfaces by substituting one subsurface O with Cl. The calculated results show that substituting an O atom with a Cl atom results in structural distortion and the reduction of one surface Ce4+ cation to Ce3+. The protruding Ce3+ cation greatly improves the adsorption energy of O2 to produce an active O2- species, and maintains the catalytic oxidation cycle of CO on Ce O2(110). These results may help us obtain a better understanding of Cl-ceria interacting systems and provide some guidance for the design of effective Ce O2-based catalysts.     

Computational study of the electronic structure of substituted phenylcarbene in the gas phase

Gas-phase calculations for ortho-, meta-, and para-substituted phenylcarbenes demonstrate that aromatic ring substituents can have a large effect on the singlet-triplet splitting in these molecules. For example, p-aminophenylcarbene is predicted to have a singlet-triplet splitting (DeltaE(ST)) of 0.7 kcal/mol, which is 4.7 kcal/mol smaller than that of the parent phenylcarbene. However, when the mesomeric effect of pi-donation is removed, as in the meta-substituted molecules, this affect is greatly attenuated. m-Amino substitution lowers the DeltaE(ST) to 5.2 kcal/mol, a change of only 0.2 kcal/mol from the parent phenylcarbene. The sensitivity of phenylcarbene to substitution is judged by the slope of the line correlating the singlet-triplet gaps to linear free energy (LFE) parameters. In this study, the best linear correlation for DeltaE(ST) in the para-substituted phenycarbenes is observed when plotted against sigma(p)(+). The resultant slope (rho) is 5.0. The origin of this effect is preferential interaction of aryl substituents with the singlet rather than the triplet species as demonstrated by electron density analyses.     

Electrophilic substitution and electronic structure of indolo[2,3-b]quinoxaline

The nitration and bromination of 6-methylindolo[2,3-b]quinoxaline take place in the 9 position. The reactivity indexes were calculated within the framework of the Hückel MO and CNDO (complete neglect of differential overlap) methods. Only the -charge distribution is in satisfactory agreement with the experimental data on electrophilic substitution in the investigated compound.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 6, pp. 840–842, June, 1984.     

Hydroxyl radicals in ice: insights into local structure and dynamics

The hydroxyl radical and its reactivity within ice environments are crucial to many important atmospheric reactions. The associated molecular mechanisms are largely unknown due to challenges posed by direct experimental measurements and computational studies of this transient species. Here we report insights into the local structure and behaviour of the hydroxyl radical in bulk ice through an extensive study utilizing Car-Parrinello molecular dynamics simulations. Interstitial and in-lattice hydroxyl radicals in hexagonal ice were investigated at primarily 190 K. Our findings, utilizing both HCTH/120 and BLYP functionals, show that OH* can exhibit greater mobility than other ice defects (the trapping energy estimated to be only 0.09 eV). We observe the formation of a two-center three-electron hemibond structure between the hydroxyl radical and an in-lattice water molecule; while controversial, such a structure in ice may be amenable to experimental detection due to its relative stability. Our results show that interstitial water molecules can strongly influence the mobility of the hydroxyl radical in bulk ice through the displacement of the radical to an interstitial location. We also demonstrate that the H-transfer reaction from an interstitial water to the radical is a rare event in ice. Together, these results predict that the radical can be a reactive species in bulk ice, as both interstitial and in-lattice OH* can be available for reactions with other species. These microscopic insights should contribute to our understanding of the reactivity of OH* in ice and its implications to atmospheric reactions.     

Spectroscopic and computational studies of nitrile hydratase: insights into geometric and electronic structure and the mechanism of amide synthesis

Nitrile hydratases (NHases) are mononuclear nonheme enzymes that catalyze the hydration of nitriles to amides. NHase is unusual in that it utilizes a low-spin (LS) Fe^III center and a unique ligand set comprised of two deprotonated backbone amides, cysteine-based sulfenic acid (RSO(H)) and sulfinic acid (RSO₂^–), and an unmodified cysteine trans to an exogenous ligand site. Electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and low-temperature absorption (LT-Abs) spectroscopies are used to determine the geometric and electronic structures of butyrate-bound (NHaseBA) and active (NHaseAq) NHase. These data calibrate DFT models, which are then extended to explore the mechanism of nitrile hydration by NHase. In particular, the nitrile is activated by coordination to the LS Fe^III and the sulfenate group is found to be deprotonated and a significantly better nucleophile than water that can attack the coordinated nitrile to form a cyclic species. Attack at the sulfenate S atom of the cyclic species is favorable and leads to a lower kinetic barrier than attack by water on coordinated, uncyclized nitrile, while attack at the C of the cyclic species is unfavorable. The roles of the unique ligand set and low-spin nature of the NHase active site in function are also explored. It is found that the oxidized thiolate ligands are crucial to maintaining the LS state, which is important in the binding and activation of nitrile susbtrates. The dominant role of the backbone amidate ligands appears to be as a chelate in keeping the sulfenate properly oriented for nucleophilic attack on the coordinated substrate.     

Computational convergence of electronic structure calculations of transition metal ligand complexes

Calculations of binding energies and optimum geometries of compounds of the series M(H₂O)⁺ with M = Sc to Zn have been carried out and compared with gas-phase experimental data and with the Rosi and Bauschlicher MCPF calculations. Hartree–Fock calculations and correlated calculations at MP2, MP4, and QCISD(T) levels were used to test the dependence of the results upon the level of correlation. A test of basis set dependence was also carried out, using parallel calculations on four basis sets ranging in size from a small DZ set to a TZ contraction. Correlation levels above MP2 and elaboration of the metal d-function basis set to (4d/3d) size or greater were both necessary for convergence with the most uniformly reliable results obtained from QCISD(T) calculations on a basis set with a (6d/4d) contraction for the d-function space. However, MP2 or higher-level calculations with a contracted four or five d function set [(5d/3d) or (4d/3d)] are capable of yielding results on binding energies and geometries close to the current gas-phase experimental uncertainty on electrostatically bound transition metal complexes. © 1993 John Wiley & Sons, Inc.     

Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase

ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.     

The influence of terminal push-pull substitution on the electronic structure and optical properties of pentacenes

The synthesis of 2,3-R(2)-9,10-(OMe)(2)-substituted pentacenes (R=OMe, F, Br, CN; 1-4) from 2,3-R(2)-9,10-dimethoxy-6,13-dihydro-6,13-ethanopentacene-15,16-diones (α-diketone-bridged precursors) by photochemically induced bis-decarbonylation (Strating-Zwanenburg reaction) is described. Under matrix-isolation conditions (solid Ar, 10 K) the S(1) transitions of 1 and 2 undergo hypsochromic and those of 3 and 4 bathochromic shifts compared to parent pentacene. The S(1) transition wavelengths correlate well with the difference of substituent parameters σ(p). A computational analysis of the excited states at the CAM-B3LYP/6-311+G** level of theory provides an assignment of the electronic transitions. Photolysis in solution at room temperature yields red [R=OMe (1)], blue [R=Br (3), F (2)], and green [R=CN (4)] pentacenes. The compounds are oxygen-sensitive and have low solubility, but their formation can be monitored by UV/Vis and, in the case of R=CN, also by (1)H NMR spectroscopy. The S(1) transition in 4 does not show the typical pentacene fine structure in the electronic absorption spectrum. Photogeneration in the presence of oxygen leads to a number of photoproducts that could be identified by monitoring the reaction by (1)H NMR spectroscopy for R=OMe.