Synthesis and Conformation of 3,6‐Connected Cyclohexadiene Chains

3,6‐Connected cyclohexadienes as precursors for polyphenylenes are synthesized and characterized by mass spectrometry and NMR spectroscopy. Pure fractions of trimers, hexamers, and nonamers are collected after separation of the product mixture by recycling GPC. The anticipated formation of rigid linear structures, due to the trans‐configuration of the monomeric units, is supported by density functional theory and experimentally confirmed by dynamic light scattering from dilute solution at low scattering angles. The obtained translational diffusion coefficients are represented by rigid rod‐like or prolate ellipsoid‐like molecular shapes. The measurements of diffusion coefficients reveal a length‐dependent ratio of 1:2:3 between the three oligomers, which directly correlates to the expected length extension from trimer to nonamer.

     

SG-0: a small standard grid for DFT quadrature on large systems

We report the development of a new standard quadrature grid for DFT calculations. Standard Grid 0 (SG-0) is designed to be approximately half as large as, and to provide approximately half the accuracy of, the established SG-1 grid. It is based on MultiExp and Lebedev quadrature for radial and angular coordinates, respectively. We find that SG-0 is typically 50% faster than SG-1 for energy, gradient, and hessian calculations for the exchange-correlation energy. This leads to a 35-38% speedup in the total gradient and hessian computations, and we particularly recommend its use for preliminary calculations on moderately large biochemical systems. It has been implemented as the default grid for DFT calculations in the Q-Chem 3.0 package.     

Directing the Self‐Assembly of Semiconducting Copolymers: The Consequences of Grafting Linear or Hyperbranched Polyether Side Chains

The synthesis and self‐assembly of novel semiconducting rod–coil type graft block copolymers based on poly(para‐phenylene vinylene) (PPV) copolymers is presented, focusing on the ordering effect of linear versus hyperbranched side chains. Using an additional reactive ester block, highly polar, linear poly(ethylene glycol), and hyperbranched polyglycerol side chains are attached in a grafting‐to approach. Remarkably, the resulting novel semiconducting graft copolymers with polyether side chains show different solubility and side‐chain directed self‐assembly behavior in various solvents, e.g., cylindrical or spherical superstructures in the size range of 10 to 120 nm, as shown by TEM. By adjusting the molecular weight and the topology of the polyether segments, self‐assembly into defined superstructures can be achieved, which is important for the efficient charge transport in potential electronic applications.

     

DFT study on cooperativity in the interactions of hydrazoic acid clusters

Density functional theory at the B3LYP level with the 6‐311G** basis set is performed to calculate the systems consisting of up to four hydrazoic acid molecules. The dimers are found to exhibit cyclic and chain structures with N … H contacts at ca. 2.1–2.7 Å. However, there are only cyclic structures with N … H contacts at ca. 2.0–2.3 Å and 2.0–2.1 Å in the trimer and tetramer, respectively. Hydrogen bond distances in the trimer and tetramer are shorter than those in the cyclic dimer as a result of the stronger interaction between molecules. The contribution of cooperative effect to the interaction energy is significant. After the correction of the basis set superposition error and zero‐point energy, the binding energies are ?10.69, ?29.34, and ?54.26 kJ·mol^?1 for the most stable dimer, trimer, and tetramer, respectively. The calculated IR shifts for N? H stretching mode increase with the size of the cluster growths, reaching more than 200 cm^?1 in the tetramer. For the most stable clusters, the transition from the monomer to dimer, dimer to trimer, and trimer to tetramer involve changes of ?14.40, ?25.68, and ?31.88 kJ·mol^?1 for the enthalpies at 298.15 K and 1atm, respectively. We also perform Mulliken populations analysis and find the Mulliken populations on intermolecular N … H increasing in the sequence of the dimer, trimer, and tetramer. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 279–286, 2003     

Toward the discovery of new soft quasicrystals: From a numerical study viewpoint

This is a progress review of an emerging research front: soft quasicrystals including liquid crystalline dendrons, nanoparticles, mesoporous silica, colloids, ABC star and linear terpolymers, and even water and silicon. As an aid to readers, we explain the basics of quasicrystals developed in solid‐state physics: orders in quasicrystals, higher dimensional crystallography, approximants, phason randomness, and the origin of quasicrystal formation. Then we review some numerical studies from early to recent ones. Our main purpose is to elucidate how to construct quasicrystalline structures: The introduction of additional components or a new length‐scale is the key to discover new quasicrystals. As a case study, we describe our recent studies on ABC star terpolymer systems and present the results of simulations of dodecagonal polymeric quasicrystals. In the case of dodecagonal quasicrystals, one easily finds that the key is to search square‐triangle tiling structures with changing components. Application to photonic quasicrystals is reviewed as well. Our hope is that this review will contribute furthering quasicrystal chemistry. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Synthesis of soluble poly(para‐phenylene) with a long polymer chain: Characteristics of regioregular poly(1,4‐phenylene)

Soluble poly(para‐phenylene) having a long polymer chain (more than six repeat units) was synthesized with a tert‐butyl end‐group (t‐PPP) and was found to have improved solubility and excellent optical properties. Poly(1,3‐cyclohexadiene) (PCHD) consisting of only 1,4‐cyclohexadiene (1,4‐CHD) units was synthesized with a tert‐butyl end‐group (t‐PCHD), and completely dehydrogenated to obtain t‐PPP. This end‐group effectively prevented the crystallization of t‐PPP, and polymers containing up to 16 repeat units were soluble in tetrahydrofuran. Soluble t‐PPP obtained had an ability to form a tough thin film prepared by spin‐coating method. Optical analyses of t‐PPP provided strong evidence for a linear polymer chain structure. A block copolymer of t‐PPP and a soluble polyphenylene (PPH) was then synthesized, and the excellent optical properties were retained by this block copolymer along with its solubility. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5223–5231, 2008     

1-Cyclohepta-2,4,6-trienyl-selanes--a 77Se NMR study: indirect nuclear 77Se--13C spin-spin coupling constants and application of density functional theory (DFT) calculations

1-Cyclohepta-2,4,6-trienyl-selanes Se(C(7)H(7))(2) (2c), R--Se--C(7)H(7) with R = Bu, (t)Bu, Ph, 4-F--C(6)H(4) (12a,b,c,d) were prepared by the reaction of the corresponding silanes, Si(SeMe(3))(2) and R--Se--SiMe(3), respectively, with tropylium bromide C(7)H(7)Br. In spite of the low stability of the selanes even in dilute solutions and at low temperature, they could be characterised by their (1)H, (13)C and (77)Se NMR parameters. Coupling constants (1)J((77)Se,(13)C) were measured and calculated by DFT methods at the B3LYP/6-311+G(d,p) level of theory. The comparison of experimental and calculated coupling constants (1)J((77)Se,(13)C) included numerous selenium carbon compounds with largely different Se--C bonds, revealing a satisfactory agreement. Both the spin-dipole (SD) and the paramagnetic spin-orbital (PSO) terms contributed significantly to the spin-spin coupling interaction, in addition to the Fermi contact (FC) term.     

DFT Study for a Series of Less-Symmetrical Crown Ethers and Their Complexes with Alkali Metal Cations

A series of ring‐contracted (14‐crown‐5, 17‐crown‐6) and ring‐enlarged (16‐crown‐5, 17‐crown‐5, 19‐crown‐6, 20‐crown‐6) crown ethers and their complexes with alkali‐metal cations Na⁺ and K⁺ had been explored using density functional theory (DFT) at B3LYP/6‐31G* level in order to reveal the effects of the methylene‐chain length in a crown ether. The nucleophilicity of all crown ethers had been investigated by the Fukui functions. The quantum chemistry parameters, such as the energy gap (ΔE), the highest occupied molecular orbital energy (E_HOMO) and the lowest unoccupied molecular orbital energy (E_LUMO) for less‐symmetrical crown ethers and symmetrical frameworks (15‐crown‐5, 18‐crown‐6) had been calculated. In addition, the thermodynamic energies of complexation reactions had also been studied. The results of the DFT calculations show that the methylene‐chain length plays an important role in determining the structure characters of the crown ethers and also strongly influences the properties of the ethers. Some of the calculated results are in a good agreement with the experimental values.     

Singlet excitation energies of thiophene derivatives of fluorene: TD‐DFT study

Fluorene‐thiophene (FT)‐based oligomers and polymers and their derivatives are good candidates for organic blue light‐emitting diodes. In this work, the intrinsic properties of the ground and excited states of FT monomer and its derivatives are studied. The ground‐state optimized structures and energies are obtained using molecular orbital theory and density functional theory (DFT). The ground‐state potential energy curves or surfaces of FT and its derivatives are also obtained. All derivatives are nonplanar in their electronic ground states. The character and energy of the first 20 singlet–singlet electronic transitions are investigated by applying the time‐dependent density functional theory (TD‐DFT) approximations to the correspondingly optimized ground‐state geometries. The lowest singlet state is studied with the configuration interaction (singles) approach (CIS). Excitation energies are red shifted when the FT unit or its derivatives are extended longitudinally. CIS results suggest geometry relaxation in the first singlet excited state. When available, a comparison is made with experimental results. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations

The electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron-vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO-3G, 3-21G*, 6-31G*, CC-pVDZ, and 6-311G**), as well as the influence of applying the DFT TD-B3LYP and ab initio TD-HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD-HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD-B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries.     

DFT study of acceleration of electrocyclization in photochromes under radical cationic conditions: Comparison with recent experimental data

Radical cation formation is proposed for the rapid cyclization of 1, 2-bis[5-phenyl-2-methylthien-3-yl]cyclopentene and oligothiophene functionalized dimethyldihydropyrenes (DMDHP). Density functional theory calculations have been performed to rationalize the effect of a radical cation on the activation barrier of different classes of electrocyclic photochromes (DHP, dithienylethene, dihydroazulene and fulgide). For exact comparative analysis, the activation barrier of neutral (singlet) analogues at the same level of theory are also calculated. In addition, the concerted nature and aromaticity of transition states were investigated with the help of synchronicity (Sy.) and nuclear independent chemical shift values NICS(0) calculations, respectively, for both the radical cation and neutral systems. In case of the radical cation, thermal return of CPD to DHP, the activation barrier is very low (ΔH = 3.13 kcal mol^?1, ΔG = 4.01 kcal mol^?1) as compared to the neutral analogue (ΔH = 20.6 kcal mol^?1, ΔG = 20.98 kcal mol^?1), which is consistent with experimental observations. Similarly for dithenylethenes, radical cation formation has a large impact on the activation barrier (ΔH = 19.44 kcal mol^?1, ΔG = 22.29 kcal mol^?1). However, radical cation formation has almost negligible impact on the activation barrier of VHF-DHA and fulgide isomerization. The significant difference has been observed for synchronicity and NICS(0) values of all types of photochromes under radical cation conditions as compared to the neutral system.     

DFT study of the carbon‐ and nitrogen‐pivot lariat crown ethers and their complexes with alkali metal cations: Na+, K+

In this work, a quantum mechanical research of five lariat crown ethers(LCEs), 2‐methoxy‐15‐crown‐5( A ), N‐methoxy‐4‐aza‐15‐crown‐5( B ), N‐methoxy‐4‐aza‐18‐crown‐6( C ), N‐methoxyethyl‐4‐aza‐18‐crown‐6( D ), N,N′‐bis(2‐metho xyethyl)‐4,13‐diaza‐18‐crown‐6( E ), which are based on either 15‐crown‐5 or 18‐crown‐6 frameworks and contain various pendant arms extending from either carbon or nitrogen atoms on the crown frameworks, had been done using density functional theory with B3LYP/6‐31G* method to obtain the electronic and geometrical structures of the LCEs and their complexes with alkali metal ions: Na⁺ and K⁺. The nucleophilicity of LCEs had been investigated by the Fukui functions. For complexes, the match between the cation and cavity size, the status of interaction between alkali metal ions and donor atoms in the LCEs, and the sidearm effect of the LCEs had been analyzed through the other calculated parameters, such as, highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy, and energy gaps. In addition, the enthalpies of complexation reaction had been studied by the calculated thermodynamic data (298 K). The calculated results are all in a good agreement with the experimental data for the complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Magnetic exchange interactions in cyano‐bridged MoIII binuclear complexes: Broken‐symmetry and density functional theory calculations

Molecular magnetism in cyano‐bridged Mo^III binuclear complexes [Mo₂(CN)₁₁]^5? and [(Me₃tacn)₂Mo₂(CN)₅]⁺ (Me₃tacn?N, N′, N″‐trimethyl‐1,4,7‐triazacyclononane) has been calculated using Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Parr (B3LYP), a hybrid density functional theory (DFT), combined with a modified broken symmetry (BS) approach and the post–Hartree‐Fock (post‐HF) method difference‐dedicated configuration interaction (DDCI). We find B3LYP combined with broken‐symmetry approach (DFT‐BS) give the similar J values to those calculated by DDCI. So we use B3LYP combined with BS approach to investigate the magnetism above two molecules. Through calculations, we find that the absolute J values decrease with the increase of r (the Mo(2)‐C_brid and Mo(1)‐N_brid distances) and are linearly related to the differences of the squared spin populations [(ρ ? ρ)] on Mo^III atoms between the highest‐spin (HS) state and the broken symmetry (BS) state. Moreover, the absolute J values are linearly related to the sum of the square of the difference in energy of the unpaired electrons (ξ) with a limited variation of the r distance. We conclude that ξ can be used to scale the degree of the antiferromagnetic coupling interactions. At the end of the paper, the spin density distributions and the mechanisms of magnetic coupling interactions are analyzed by us. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of two‐dimensionally fused zinc porphyrins: DFT calculations

Electronic structures of D_4h square‐fused zinc porphyrin sheets of two types ( SA , SB ), where SA is a directly meso‐meso‐, β‐β‐, and β‐β‐linked array and SB is a directly β‐fused array, were compared using density functional theory (DFT). The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of oligomeric SA _n are characteristically delocalized at the cyclooctatetraene‐like sites composed of β‐pyrrolic carbons and their nearest‐neighbor nitrogens. Those of oligomeric SB _n remain solitary monomeric features, reflecting weakly interacting porphyrin units. These two‐dimensionally (2D) square‐fused sheets, especially for SA _n, show effective reduction of both the HOMO–LUMO energy gaps (E_g) and the lowest Q‐like excitation energies because of LUMO's greater stabilization with increasing number of porphyrins than the corresponding one‐dimensionally (1D) linear‐fused tapes. To estimate the minimum value of E_g, the electronic band structures of the infinite‐fused SA _∞ and SB _∞ were examined in detail using modern periodic DFT. Results indicate a full metal for SA _∞, with HOMO and LUMO bands crossing the Fermi level, and a semiconductor with E_g ≈ 0.5 eV for SB _∞. Furthermore, the phonon modes and the electron–phonon coupling (EPC) constant of SA _∞ were calculated throughout the Brillouin zone using density functional perturbation theory (DFPT), yielding a weak EPC constant, λ = 0.35. Within the standard phonon‐mediated BCS mechanism, the superconducting transition temperature, T_c is demonstrated using the McMillan formula, predicting ≈0.5 K. Results show that SA _∞ will become a rare synthetic metal/superconductor without a metal‐insulator transition coming from Peierls lattice instability because it has no serious imaginary phonon modes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Mechanism of action of aspartic proteinases: Application of transition-state analogue theory

Summary Applying the semiempirical MO methods AM1 and PM3 as well as the density functional theory to the model of the catalytic site composed of ca. 160–190 atoms, we have carried out studies aimed at the explanation of three aspects of the mechanism of action of aspartic proteinases: the site of dissociation within the catalytic diad COOH/COO^- (i) in the free enzyme and (ii) in the Michaelis complex, and (iii) the energy changes associated with the catalytic paths. We have found that the state of dissociation within the catalytic diad is ligand-sensitive. In the free enzyme and in the intermediate complexes, Asp³³ prefers to be dissociated with the outer oxygen of Asp²¹³ protonated, while in the Michaelis and product complexes the opposite holds true. This is in agreement with recent mechanistic hypotheses and with some experimental results by FTIR and NMR. The energy diagram for the catalysis indicates that electronic effects are responsible most of all for the relative reduction of energy of the intermediates and possibly transition states on the catalytic reaction path. The shape of the diagram qualitatively agrees with the transition-state analogue theory for the enzymatic reactions.     

IR spectrum and normal mode analysis of the antiAlzheimer''''s disease natural product Huperzine A: A quantum chemistry density-functional theory (DFT) investigation

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A study of DFT and surface enhanced Raman scattering in silver colloids for thymine

The vibrational spectrum of crystal thymine is calculated by density functional theory (DFT) at the B3LYP complex function. Considering the effect of intermolecular H-bonds, we add two water molecules that can form H-bonds with the CO and NH groups of thymine. The experimental spectra of normal Raman of thymine in solid state and surface enhanced Raman (SERS) of thymine adsorbed in silver colloids are presented in this study. The calculated Raman spectrum of thymine by DFT is in agreement with the experimental result of normal Raman spectrum. The appearance of new bands of thymine in SERS shows that molecules of thymine are adsorbed in the surface of silver nanoparticles with a perpendicular orientation through an oxygen atom (O7).     

Revealing the mechanism of Rh(I)‐catalyzed hydroformylation of 4‐pyridylethene derivatives: DFT study

A comprehensive theoretical investigation into the mechanism of 1‐phenyl‐1‐(4‐pyridyl)ethene hydroformylation, using a rhodium catalyst employing a nonlocal density functional method (B3LYP), was carried out. The calculated results show that it is strongly exothermic by >90 kJ/mol of the whole catalytic cycle, and the rate‐limited step is H₂ oxidative addition. The regioselectivity originates from olefin insertion into the Rh? H bond. The predominant product is the regiospecifically 3‐phenyl‐3‐(4‐pyridal)propanal determined both thermodynamically and kinetically. These are in agreement with practicality experimental studies. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Many‐body interactions of carbon monoxide cyclic oligomers: A computational study

Structural properties and energetics for the optimized carbon monoxide cyclic oligomers are analyzed at the correlated ab initio second‐order Møller–Plesset (MP2) and density functional methods (B3LYP and mPW1PW), using Dunning's cc‐pVXZ (X = D, T, Q) basis set, augmented with diffuse functions. Many‐body interactions of the stable carbon monoxide cyclic oligomers, (CO)₄ and (CO)₅ are computed at the MP2/aug‐cc‐pVTZ level. Contributions of two‐ to five‐body terms to each of these oligomers for their interaction energies, including corrections for basis set superposition error (BSSE) are investigated by using function counterpoise and its generalized version. It has been found that three‐body terms are attractive in nature and essential in order to describe the cooperative effects in the stable cyclic CO oligomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005