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Protein folds recognized by an intelligent predictor based-on evolutionary and structural information

Tue, 10/27/2015 - 04:54

Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks incorporated in an adaptive heterogeneous particle swarm optimizer. The main contribution of NiRecor is that it is a data-driven and highly-performing predictor without manually tuning control parameters for different data sets. In biological science, since evolutionary- and structure-based information of amino acid sequences is greatly important in determination of tertiary structure of a protein, accordingly, in NiRecor we employ two different feature sets, which involve position specific scoring matrix and secondary structure prediction matrix, to predict the structural classes of protein folds. The experimental results demonstrate the proposed method is powerful in predicting protein folds with higher precisions by improvements of 1.1 ∼7.8 percentages on three benchmark datasets by comparing with several existing predictors. © 2015 Wiley Periodicals, Inc.

As an outstanding issue in protein science, protein-fold recognition is highly important for determining the tertiary structure of a protein from its primary sequence. How to correctly recognize the protein folds from sequences? Accordingly, a swarm-optimized predictor—a data-driven predicting method—is proposed to solve this scientific problem. Without manually tuning parameters, it avoids laborious work on finding an appropriate predictor for the problem and exhibits a good performance, even on different protein datasets.

Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra

Tue, 10/27/2015 - 04:53

The restricted active-space (RAS) approach can accurately simulate metal L-edge X-ray absorption spectra of first-row transition metal complexes without the use of any fitting parameters. These characteristics provide a unique capability to identify unknown chemical species and to analyze their electronic structure. To find the best balance between cost and accuracy, the sensitivity of the simulated spectra with respect to the method variables has been tested for two models, [FeCl6]3– and [Fe(CN)6]3–. For these systems, the reference calculations give deviations, when compared with experiment, of ≤1 eV in peak positions, ≤30% for the relative intensity of major peaks, and ≤50% for minor peaks. When compared with these deviations, the simulated spectra are sensitive to the number of final states, the inclusion of dynamical correlation, and the ionization potential electron affinity shift, in addition to the selection of the active space. The spectra are less sensitive to the quality of the basis set and even a double-ζ basis gives reasonable results. The inclusion of dynamical correlation through second-order perturbation theory can be done efficiently using the state-specific formalism without correlating the core orbitals. Although these observations are not directly transferable to other systems, they can, together with a cost analysis, aid in the design of RAS models and help to extend the use of this powerful approach to a wider range of transition metal systems. © 2015 Wiley Periodicals, Inc.

With an appropriate choice of active space, basis set, and computational procedure, the restricted active space approach can be used to simulate metal L-edge X-ray absorption spectra with reasonable accuracy and computational cost. The sensitivity of the simulated results with respect to geometrical changes opens up for analysis of dynamical processes.

Ion strength limit of computed excess functions based on the linearized Poisson–Boltzmann equation

Fri, 10/23/2015 - 02:35

The linearized Poisson–Boltzmann (L-PB) equation is examined for its κ-range of validity (κ, Debye reciprocal length). This is done for the Debye–Hückel (DH) theory, i.e., using a single ion size, and for the SiS treatment (D. Fraenkel, Mol. Phys. 2010, 108, 1435), which extends the DH theory to the case of ion-size dissimilarity (therefore dubbed DH–SiS). The linearization of the PB equation has been claimed responsible for the DH theory's failure to fit with experiment at > 0.1 m; but DH–SiS fits with data of the mean ionic activity coefficient, γ± (molal), against m, even at m > 1 (κ > 0.33 Å−1). The SiS expressions combine the overall extra-electrostatic potential energy of the smaller ion, as central ion—Ψa>b(κ), with that of the larger ion, as central ion—Ψb>a(κ); a and b are, respectively, the counterion and co-ion distances of closest approach. Ψa>b and Ψb>a are derived from the L-PB equation, which appears to conflict with their being effective up to moderate electrolyte concentrations (≈1 m). However, the L-PB equation can be valid up to κ ≥ 1.3 Å−1 if one abandons the 1/κ criterion for its effectiveness and, instead, use, as criterion, the mean-field electrostatic interaction potential of the central ion with its ion cloud, at a radial distance dividing the cloud charge into two equal parts. The DH theory's failure is, thus, not because of using the L-PB equation; the lethal approximation is assigning a single size to the positive and negative ions. © 2015 Wiley Periodicals, Inc.

A new criterion for the goodness of the linearization of the Poisson–Boltzmann (PB) equation in electrolyte theories—replacing the traditional one (i.e., the “thickness of the ion cloud,” 1/κ)—is the average value of the potential energy of electrostatic ionic interaction, Φave, at radial distance r from the origin, dividing the ion cloud into two parts of equal charge; based on the value of this “Φ1/2” at “r1/2”, the linearized PB equation is shown effective for aqueous electrolyte solutions at 25°C up to at least κ = 1.3 Å−1.

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform

Fri, 10/23/2015 - 02:34

The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc.

The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling molecular dynamics simulations using the AMOEBA polarizable force field on GPU platform. Two examples show that the implementation in the work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way

DSPMP: Discriminating secretory proteins of malaria parasite by hybridizing different descriptors of Chou's pseudo amino acid patterns

Tue, 10/20/2015 - 09:47

Identification of the proteins secreted by the malaria parasite is important for developing effective drugs and vaccines against infection. Therefore, we developed an improved predictor called “DSPMP” (Discriminating Secretory Proteins of Malaria Parasite) to identify the secretory proteins of the malaria parasite by integrating several vector features using support vector machine-based methods. DSPMP achieved an overall predictive accuracy of 98.61%, which is superior to that of the existing predictors in this field. We show that our method is capable of identifying the secretory proteins of the malaria parasite and found that the amino acid composition for buried and exposed sequences, denoted by AAC(b/e), was the most important feature for constructing the predictor. This article not only introduces a novel method for detecting the important features of sample proteins related to the malaria parasite but also provides a useful tool for tackling general protein-related problems. The DSPMP webserver is freely available at http://202.207.14.87:8032/fuwu/DSPMP/index.asp. © 2015 Wiley Periodicals, Inc.

The identification of proteins secreted by the malaria parasite is important for developing effective drugs and vaccines against this infection. The amino acid composition for buried and exposed sequences (AAC(b/e)) is the most important feature for improving predictive accuracy. The differentiation scores of AAC(b/e) were markedly different between secretory and non-secretory proteins.

Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence

Tue, 10/20/2015 - 09:46

Ions are engaged in multiple biological processes in cells. By binding to the macromolecules or being mobile in the solvent, they maintain the integrity of the structure of macromolecules; participate in their enzymatic activity; or screen electrostatic interactions. While experimental methods are not always able to assign the exact location of ions, computational methods are in demand. Although the majority of computational methods are successful in predicting the position of ions buried inside macromolecules, they are less effective in deciphering positions of surface bound ions. Here, we propose the new BION algorithm (http://compbio.clemson.edu/bion_server_ph/) that predicts the location of the surface bound ions. It is more efficient and accurate compared to the previous version since it uses more advanced clustering algorithm in combination with pairing rules. In addition, the BION webserver allows specifying the pH and the salt concentration in predicting ions positions. © 2015 Wiley Periodicals, Inc.

Ions are important component of all living cells. Upon binding to macromolecules, they support their unique fold and participate in enzymatic activities. Here, we introduce the new algorithm, implemented in BION webserver (http://compbio.clemson.edu/bion_server_ph/) that predicts the location of ions on the surface of proteins based on electrostatic and geometrical properties of both ions and proteins. The advanced clustering procedure in combination with pairing rules improves both the efficiency and the accuracy of the method.

Simulated tempering based on global balance or detailed balance conditions: Suwa–Todo, heat bath, and Metropolis algorithms

Thu, 10/15/2015 - 05:36

Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa–Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa–Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa–Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa–Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa–Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa–Todo algorithm when compared with the Metropolis algorithm. © 2015 Wiley Periodicals, Inc.

The autocorrelation of the potential energy depends on algorithms that are used when the transition probability of simulated tempering is calculated. The reduction of the autocorrelation time is important for efficient sampling. The Suwa–Todo algorithm shows better sampling efficiency than the Metropolis algorithm, which is usually used in Monte Carlo simulations.

A CASSCF/CASPT2 insight into excited-state intramolecular proton transfer of four imidazole derivatives

Tue, 10/13/2015 - 06:00

Excited-state intramolecular proton transfer (ESIPT) of four imidazole derivatives, 2-(2′-hydroxyphenyl)imidazole (HPI), 2-(2′-hydroxyphenyl)benzimidazole (HPBI), 2-(2′-hydroxyphenyl)-1H-phenanthro[9,10-d]imidazole (HPPI) and 2-(2′-hydroxyphenyl)-1-phenyl-1H-phenanthro[9,10-d]imidazole (HPPPI), were studied by the sophisticated CASSCF/CASPT2 methodology. The state-averaged SA-CASSCF method was used to optimize their geometry structures of S0 and S1 electronic states, and the CASPT2 calculations were used for the calibration of all the single-point energies, including the absorption and emission spectra. A reasonable agreement is found between the theoretical predictions and the available experimental spectral data. The forward ESIPT barriers of four target compounds gradually decrease with the increase of molecular size. On the basis of the present calculations, it is a plausible speculation that the larger the size, the faster is the ESIPT rate, and eventually, HPPPI molecule can undergo a completely barrierless ESIPT to the more stable S1 keto form. Additionally, taking HPI as a representative example, the radiationless decays connecting the S0 and S1/S0 conical intersection structures were also studied by constructing a linearly interpolated internal coordinate (LIIC) reaction path. The qualitative analysis shows that the LIIC barrier of HPI in the keto form is remarkably lower than that of its enol-form, indicating that the former has a big advantage over the latter in the nonradiative process. © 2015 Wiley Periodicals, Inc.

Ab initio CASSCF and CASPT2 methods have been used to explore the excited-state intramolecular proton transfer (ESIPT) reactions of four imidazole-based compounds. The forward ESIPT barriers of the four compounds gradually decrease with the increase of molecular size. Presumably, the larger the size, the faster is the ESIPT rate, and eventually, 2-(2′-hydroxyphenyl)-1-phenyl-1H-phenanthro[9,10-d]imidazole molecule can undergo a completely barrierless ESIPT to the more stable S1 keto form.

DOX: A new computational protocol for accurate prediction of the protein–ligand binding structures

Tue, 10/13/2015 - 05:59

Molecular docking techniques have now been widely used to predict the protein–ligand binding modes, especially when the structures of crystal complexes are not available. Most docking algorithms are able to effectively generate and rank a large number of probable binding poses. However, it is hard for them to accurately evaluate these poses and identify the most accurate binding structure. In this study, we first examined the performance of some docking programs, based on a testing set made of 15 crystal complexes with drug statins for the human 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR). We found that most of the top ranking HMGR–statin binding poses, predicted by the docking programs, were energetically unstable as revealed by the high theoretical-level calculations, which were usually accompanied by the large deviations from the geometric parameters of the corresponding crystal binding structures. Subsequently, we proposed a new computational protocol, DOX, based on the joint use of molecular Docking, ONIOM, and eXtended ONIOM (XO) methods to predict the accurate binding structures for the protein–ligand complexes of interest. Our testing results demonstrate that the DOX protocol can efficiently predict accurate geometries for all 15 HMGR-statin crystal complexes without exception. This study suggests a promising computational route, as an effective alternative to the experimental one, toward predicting the accurate binding structures, which is the prerequisite for all the deep understandings of the properties, functions, and mechanisms of the protein–ligand complexes. © 2015 Wiley Periodicals, Inc.

The detailed knowledge of the protein–ligand binding structures is always important for the deep understanding of protein-ligand interactions. The new computational protocol DOX, which takes the advantage of molecular Docking method's efficiency and QM methods' (ONIOM and eXtended ONIOM) accuracy, can be used to predict the accurate binding structures for the protein–ligand complexes of interest, as an effective alternative to the costly experimental methods.

Assessment of the extended Koopmans' theorem for the chemical reactivity: Accurate computations of chemical potentials, chemical hardnesses, and electrophilicity indices

Tue, 10/13/2015 - 05:59

The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials and electron affinities from any level of theory. Although it is widely applied to ionization potentials, the EKT approach has not been applied to evaluation of the chemical reactivity. We present the first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω). We assess the performance of the EKT approaches for post-Hartree–Fock methods, such as Møller–Plesset perturbation theory, the coupled-electron pair theory, and their orbital-optimized counterparts for the evaluation of the chemical reactivity. Especially, results of the orbital-optimized coupled-electron pair theory method (with the aug-cc-pVQZ basis set) for predictions of the chemical reactivity are very promising; the corresponding mean absolute errors are 0.16, 0.28, and 0.09 eV for μ, η, and ω, respectively. © 2015 Wiley Periodicals, Inc.

The first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω) is presented.

Glucose transformation to 5-hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study

Sat, 10/10/2015 - 07:25

Isomerization and transformation of glucose and fructose to 5-hydroxymethylfurfural (HMF) in both ionic liquids (ILs) and water has been studied by the reference interaction site model self-consistent field spatial electron density distribution (RISM-SCF-SEDD) method coupled with ab initio electronic structure theory, namely coupled cluster single, double, and perturbative triple excitation (CCSD(T)). Glucose isomerization to fructose has been investigated via cyclic and open chain mechanisms. In water, the calculations support the cyclic mechanism of glucose isomerization; with the predicted activation free energy is 23.8 kcal mol−1 at experimental condition. Conversely, open ring mechanism is more favorable in ILs with the energy barrier is 32.4 kcal mol−1. Moreover, the transformation of fructose into HMF via cyclic mechanism is reasonable; the calculated activation barriers are 16.0 and 21.5 kcal mol−1 in aqueous and ILs solutions, respectively. The solvent effects of ILs could be explained by the decomposition of free energies and radial distribution functions of solute-solvent that are produced by RISM-SCF-SEDD. © 2015 Wiley Periodicals, Inc.

A combination of quantum mechanics and statistical mechanics, called reference interaction site model self-consistent field spatial electron density distribution, is used to investigate the transformation reaction of glucose to 5-hydroxymethylfurfural in aqueous and ionic liquids (ILs). The cyclic mechanism is more favorable in the aqueous solutions. Conversely, open chain mechanism is preferable in ILs.

Schleyer hyperconjugative aromaticity and Diels–Alder reactivity of 5-substituted cyclopentadienes

Wed, 10/07/2015 - 08:27

Schleyer's discovery of hyperconjugative aromaticity and antiaromaticity in 5-substituted cyclopentadienes further expanded our understanding of the pervasive influence of aromaticity. Acceptors induce antiaromatic character by Schleyer's negative hyperconjugative aromaticity, and donors have the opposite effect. We computationally explored the Diels–Alder reactivity of 5-substituted cyclopentadienes with ethylene and maleic anhydride. The predicted billionfold difference in the computed gas phase rate constants at room temperature for the Diels–Alder reactions of 5-substituted cyclopentadienes with ethylene or maleic anhydride results from differences in the transition state distortion energies, which are directly related to the hyperconjugative aromaticity of these molecules. © 2015 Wiley Periodicals, Inc.

Quantum chemical calculations are used to investigate the effect of substituents at the 5-position of cyclopentadiene on the stabilities and the activation energies (Ea) for the Diels–Alder reactions. Acceptors induce antiaromatic character by Schleyer's negative hyperconjugative aromaticity; donors have the opposite effect. The interaction energies (red) are nearly constant, and the differences in Ea arise mainly through changes in the distortion energies of the diene (blue) and dienophile (green). (Values reported in kcal/mol.)

Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table

Wed, 10/07/2015 - 08:27

A comprehensive theoretical treatment is presented for the electronic excitation spectra of ca. 50 different mono-, di-, and tetrasubstituted naphthalenediimides (NDI) using time-dependent density functional theory (TDDFT) at ZORA-CAM-B3LYP/TZ2P//ZORA-BP86/TZ2P with COSMO for simulating the effect of dichloromethane (DCM) solution. The substituents XHn are from groups 14–17 and rows 2–5 of the periodic table. The lowest dipole-allowed singlet excitation (S0–S1) of the monosubstituted NDIs can be tuned from 3.39 eV for F to 2.42 eV for TeH, while the S0–S2 transition is less sensitive to substitution with energies ranging between 3.67 eV for CH3 and 3.44 eV for SbH2. In the case of NDIs with group-15 and −16 substituents, the optical transitions strongly depend on the extent to which XHn is planar or pyramidal as well as on the possible formation of intramolecular hydrogen bonds. The accumulative effect of double and quadruple substitution leads in general to increasing bathochromic shifts, but the increased steric hindrance in tetrasubstituted NDIs can lead to deformations that diminish the effectiveness of the substituents. Detailed analyses of the Kohn–Sham orbital electronic structure in monosubstituted NDIs reveal the mesomeric destabilization of the HOMO as the primary cause of the bathochromic shift of the S0–S1 transition. © 2015 Wiley Periodicals, Inc.

It is shown through TDDFT explorations that naphthalenediimide's (NDI's) strong S0–S1 transition offers excellent opportunities for tuning its absorption frequency through substituents. Kohn–Sham MO analyses reveal that the S0–S1 gap can be reduced by pushing the overall HOMO up in energy using a more electropositive substituent. The S0–S1 transition can be pushed beyond the “700 nm barrier” which is crucial for developing antenna molecules absorbing near-infrared photons in the solar spectrum.

Low-energy structures of benzene clusters with a novel accurate potential surface

Wed, 09/30/2015 - 08:31

The benzene-benzene (Bz-Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz-Bz analytical potential energy surface which is fine-tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz-Bz interaction is modeled, an analytical function for the energy of the clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest-energy structures of clusters (for ), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low-lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low-lying isomers of and clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low-energy isomers of the n = 13 and 19 magic-number clusters is performed. The two lowest-energy isomers show S6 and C3 symmetry, respectively, which is compatible with the experimental results available in the literature. The structures reported here are all non-symmetric, showing two central Bz molecules surrounded by 12 nearest-neighbor monomers in the case of the five lowest-energy structures. © 2015 Wiley Periodicals, Inc.

This paper reports a detailed global optimization study on benzene clusters modeled with a new potential energy surface, which has been fine-tuned on accurate ab initio data. The low-energy structures obtained in this computational work are compatible with the available experimental results.

Isomerization and fragmentation pathways of 1,2-azaborine

Tue, 09/29/2015 - 10:30

The generation of 1,2-azaborine (4), the BN-analogue of ortho-benzyne, was recently achieved by elimination of tert-butyldimethylchlorosilane under the conditions of flash vacuum pyrolysis. The present investigation identifies by computational means pathways for the thermal isomerization and fragmentation of 1,2-azaborine. The computations were performed using single reference (hybrid/density functional, second order Møller-Plesset perturbation, and coupled cluster theories) as well as multiconfiguration methods (complete active space SCF based second order perturbation theory, multireference configuration interaction, and multiconfiguration coupled electron pair approximation) with basis sets up to polarized triple-ζ quality. The 1,2-azaborine is, despite the distortion of its molecular structure, the most stable C4H4BN isomer investigated. The formation of BN-endiyne isomers is highly unfavorable as the identified pathways involve barriers close to 80 kcal mol−1. The concerted fragmentation to ethyne and 2-aza-3-bora-butadiyne even has a barrier close to 120 kcal mol−1. The fragmentation of BN-enediynes has energetic requirements similar to enediynes. © 2015 Wiley Periodicals, Inc.

Very recently, the isolation of 1,2-azaborine was achieved in a cryogenic matrix. The possible isomerization, ring opening, and fragmentation pathways of 1,2-azaborine are investigated computationally and compared with available experimental and theoretical results for the all-carbon system.

Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges

Thu, 09/24/2015 - 00:45

A polarizable quantum mechanics (QM)/ molecular mechanics (MM) approach recently developed for Hartree–Fock (HF) and Kohn–Sham (KS) methods has been extended to energies and analytical gradients for MP2, double hybrid functionals, and TD-DFT models, thus allowing the computation of equilibrium structures for excited electronic states together with more accurate results for ground electronic states. After a detailed presentation of the theoretical background and of some implementation details, a number of test cases are analyzed to show that the polarizable embedding model based on fluctuating charges (FQ) is remarkably more accurate than the corresponding electronic embedding based on a fixed charge (FX) description. In particular, a set of electronegativities and hardnesses has been optimized for interactions between QM and FQ regions together with new repulsion–dispersion parameters. After validation of both the numerical implementation and of the new parameters, absorption electronic spectra have been computed for representative model systems including vibronic effects. The results show remarkable agreement with full QM computations and significant improvement with respect to the corresponding FX results. The last part of the article provides some hints about computation of solvatochromic effects on absorption spectra in aqueous solution as a function of the number of FQ water molecules and on the use of FX external shells to improve the convergence of the results. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Development of code and methodologies for excited state properties with polarizable QM/MM methods.

Computational design of organometallic oligomers featuring 1,3-metal-carbon bonding and planar tetracoordinate carbon atoms

Thu, 09/24/2015 - 00:44

Density functional theory computations (B3LYP) have been used to explore the chemistry of titanium–aromatic carbon “edge complexes” with 1,3-metal-carbon (1,3-MC) bonding between Ti and planar tetracoordinate Cβ. The titanium-coordinated, end-capping chlorides are replaced with OH or SH groups to afford two series of difunctional monomers that can undergo condensation to form oxide- and sulfide-bridged oligomers. The sulfide-linked oligomers have less molecular strain and are more exergonic than the corresponding oxide-linked oligomers. The HOMO–LUMO gap of the oligomers varies with their composition and decreases with growing oligomer chain. This theoretical study is intended to enrich 1,3-MC bonding and planar tetracoordinate carbon chemistry and provide interesting ideas to experimentalists. Organometallic complexes with the TiE2 (E = OH and SH) decoration on the edge of aromatic hydrocarbons have been computationally designed, which feature 1,3-metal-carbon (1,3-MC) bonding between titanium and planar tetracoordinate β-carbon. Condensation of these difunctional monomers by eliminating small molecules (H2O and H2S) produce chain-like oligomers. The HOMO–LUMO gaps of the oligomers decreases with growing oligomer chain, a trend that suggests possible semiconductor properties for oligomers with longer chains. © 2015 Wiley Periodicals, Inc.

Organometallic complexes with the TiE2 (E=OH and SH) decoration on the edge of aromatic hydrocarbons have been computationally designed, which feature 1,3-metal-carbon (1,3-MC) bonding between titanium and planar tetracoordinate β-carbon. Condensation of these di-functional monomers by eliminating small molecules (H2O and H2S) produce chain-like oligomers. The HOMO-LUMO gaps of the oligomers decreases with growing oligomer chain, a trend that suggests possible semi-conductor properties for oligomers with longer chains.

Cyclization of an α, β-Unsaturated hydrazone catalyzed by a BINOL-phosphoric acid: Pericyclic or not?

Wed, 09/16/2015 - 03:51

Density functional theory is used to study the mechanism of the title reaction, one of the first catalytic asymmetric 6π-electrocyclizations observed experimentally. The benzylideneacetone-derived phenyl hydrazone is chosen as model substrate for the cyclization reaction, both in the protonated (A) and unprotonated (B) form, while the isoelectronic carbon analogue, 1,5-diphenylpentadienyl anion (C), serves as a reference for comparisons. The barrier to cyclization is computed to be more than 15 kcal/mol lower in A compared with B, in line with the observed acid catalysis. The relevant transition states to cyclization are characterized for A and C using orbital inspection, natural bond orbital analysis, nucleus independent chemical shifts, and stereochemical indicators. The cyclization of C is confirmed to be pericyclic, while that of A can be described as pseudopericyclic ring closure involving an intramolecular nucleophilic addition. © 2015 Wiley Periodicals, Inc.

Density functional theory is used to answer the question whether the cyclization of the unsaturated hydrazone proceeds in a pericyclic or pseudopericyclic manner. As reference for a 6π-electrocyclization, the isoelectronic pentadienyl anion is taken into account as well.

d-AO spherical aromaticity in Ce6O8

Tue, 08/18/2015 - 10:37

After the first introduction of π aromaticity in chemistry to explain the bonding, structure, and reactivity of benzene and its derivatives, this concept was further applied to many other compounds featuring other types of aromaticity (i.e., σ, δ). Thus far, there have been no reports on d-AO-based spherical σ aromaticity. Here, we predict a highly stable bare Ce6O8 cluster of a spherical shape using evolutionary algorithm USPEX and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that bare Ce6O8 cluster exhibits d-AO spherical σ aromaticity, thus explaining its exotic geometry and stability. Ce6O8 complex plays an important role in many reactions and is known to exist in many forms, such as in NH4[Ce6(μ3O)5(μ3OH)3(μ2-C6H5COO)9(NO3)3(DMF)3]*DMF*H2O compound, which is prepared under room temperature, and acts as an oxidizing agent. © 2015 Wiley Periodicals, Inc.

A highly stable bare Ce6O8 cluster of a spherical shape is predicted using evolutionary algorithm and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that the bare Ce6O8 cluster exhibits a unique 6c2e chemical bonding, thus, explaining its exotic geometry and stability.