Nonlinear optical properties of dicyanomethylene‐derived heteroaromatic dyes: Semiempirical molecular orbital calculations and experimental investigations

The effect of conformation (E/Z isomerism), nature (donor/acceptor) of substituents, and endgroups (indandione, pyrazolone, pyrazoledione) on the molecular hyperpolarizability β_vec of dicyanomethylene (hetero)aromatic dyes is investigated by means of semiempirical (AM1, ZINDO) molecular orbital calculations. Unless Z isomers are stabilized by intramolecular hydrogen bonding, generally E conformers have larger β_vec's. Replacement of one nitrile group of the dicyanomethylene moiety by p‐aminoaryl rather than p‐R‐arylamino (R=NMe₂, MeO, H, NO₂) is found to be advantageous. Increasing the acceptor strength of 29 by successively replacing the carbonyl with dicyanovinyl groups leads to a maximum of β_vec for the derivative with one rather than two C(CN)₂ groups. With respect to endgroups, the indandione moiety generally is the least active group. Solvent effects are treated within the framework of the self‐consistent reaction field approximation. In most cases gas‐phase tendencies are either parallel or even reinforced if solvent effects are taken into account. The calculated results are compared with electric field induced second harmonic generation (EFISH) measurements. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 253–266, 2000     

Semiempirical calculations of binding enthalpy for protein–ligand complexes

A systematic semiempirical quantum mechanical study of the interactions between proteins and ligands has been performed to determine the ability of this approach for the accurate estimation of the enthalpic contribution to the binding free energy of the protein–ligand systems. This approach has been applied for eight test protein–ligand complexes with experimentally known binding enthalpies. The calculations were performed using the semiempirical PM3 approach incorporated in the MOPAC 97, ZAVA originally elaborated in Algodign, and MOPAC 2002 with MOZYME facility packages. Special attention was paid to take into account structural water molecules, which were located in the protein–ligand binding site. It was shown that the results of binding enthalpy calculations fit experimental data within ～2 kcal/mol in the presented approach. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Accurate parametrized variational calculations of the molecular electronic polarizability by NDDO‐based methods

The variational method for the calculation of the electronic polarizability of molecules within the NDDO‐based semiempirical MO methods MNDO, AM1, and PM3 was parametrized to improve its accuracy. A training set of 156 compounds was used to fit 34 parameters simultaneously for 12 elements using a simplex optimization. The resulting parameters were tested for a test set of 83 molecules and the calculated polarizabilities compared with the experimental data. For AM1, the RMS deviation between experimental and calculated polarizabilities was reduced from 2.99 (using the original variational treatment) to 0.70 ų for the test set and from 2.81 to 0.40 ų for the training set. MNDO and PM3 gave similar improvements. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 17–31, 1999     

Boronate affinity adsorption of cis‐diol‐containing biomolecules in nonaqueous solvent

Boronate affinity has attracted much attention in recent years. It has been broadly used for selective isolation and enrichment of cis‐diol‐containing molecules. Conventionally, the cis‐diols are adsorbed in mild alkaline aqueous solutions. In this work, for the first time, we found that boronate affinity adsorption could also be performed in nonaqueous solvent at nonbasic pH. Cis‐diol‐containing compounds present in herbal medicines were used for the adsorption test. The results indicated that all compounds obtained higher recoveries in the organic solvents (methanol, acetonitrile, ethyl acetate) compared with alkaline buffer. The adsorption of vicinal cis‐diol‐containing molecules in organic solvents could be accomplished rapidly, with high selectivity and high recoveries (>80%). These results shed light on the possibility of boronate affinity adsorption in nonaqueous solvents. The results are very important for the isolation and enrichment of cis‐diols, which have poor solubility in water, especially for those in herbal medicines. Copyright © 2015 John Wiley & Sons, Ltd.     

The synthesis of non‐symmetrical stilbene analogs of trans‐resveratrol using the same Pd catalyst in a sequential double‐Heck arylation of ethylene

We have developed a sequential and selective Pd‐catalyzed double‐Heck arylation of ethylene that results in non‐symmetrical nitro‐stilbene analogs of trans‐resveratrol at excellent yields. A catalytic system consisting of Pd(OAc)₂ and P(o‐tolyl)₃ permitted us to carry out the two consecutive Heck arylations without losing activity from the first to the second Heck reaction. After the first Heck arylation of ethylene, no isolation or additional catalyst loading is required for the second Heck arylation reaction. This protocol was applied to the synthesis of methylated trans‐resveratrol, which was obtained at a 65% overall yield. Copyright © 2011 John Wiley & Sons, Ltd.     

Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens

The new semiempirical methods, PDDG/PM3 and PDDG/MNDO, have been parameterized for halogens. For comparison, the original MNDO and PM3 were also reoptimized for the halogens using the same training set; these modified methods are referred to as MNDO' and PM3'. For 442 halogen-containing molecules, the smallest mean absolute error (MAE) in heats of formation is obtained with PDDG/PM3 (5.6 kcal/mol), followed by PM3' (6.1 kcal/mol), PDDG/MNDO (6.6 kcal/mol), PM3 (8.1 kcal/mol), MNDO' (8.5 kcal/mol), AM1 (11.1 kcal/mol), and MNDO (14.0 kcal/mol). For normal-valent halogen-containing molecules, the PDDG methods also provide improved heats of formation over MNDO/d. Hypervalent compounds were not included in the training set and improvements over the standard NDDO methods with sp basis sets were not obtained. For small haloalkanes, the PDDG methods yield more accurate heats of formation than are obtained from density functional theory (DFT) with the B3LYP and B3PW91 functionals using large basis sets. PDDG/PM3 and PM3' also give improved binding energies over the standard NDDO methods for complexes involving halide anions, and they are competitive with B3LYP/6-311++G(d,p) results including thermal corrections. Among the semiempirical methods studied, PDDG/PM3 also generates the best agreement with high-level ab initio G2 and CCSD(T) intrinsic activation energies for S(N)2 reactions involving methyl halides and halide anions. Finally, the MAEs in ionization potentials, dipole moments, and molecular geometries show that the parameter sets for the PDDG and reoptimized NDDO methods reduce the MAEs in heats of formation without compromising the other important QM observables.     

Quantum topology phase diagrams for the cis‐ and trans‐isomers of the cyclic contryphan‐Sm peptide

Within the quantum theory of atoms in molecules (QTAIM) framework we present a quantum topology phase diagram (QTPD) using the Poincaré–Hopf relation of a total of 17 all new QTAIM topologies of the cis‐ and trans‐isomers of the cyclic contryphan‐Sm peptide. The resultant QTPD consists of separate regions for the cis‐ and trans‐isomers that only overlap for topologies associated with the lowest energy minima of the cis‐ and trans‐isomers. We determine the QTAIM topologies of 29 “missing” isomers. A new, contracted formulation of the QTPD is presented, this contracted formulation includes the interamino acid bond critical points (BCPs) that link together the amino acid units, the disulphide bridge “pivot” BCP and side chain bonding interactions. The seven interamino acid BCPs linking the amino acid units coincide with the so‐called peptide backbone, the conventional qualitative approach to reduce the complexity of the peptide. We expand the interpretation of ellipticity to include the associated eigenvectors and find that higher values of the ellipticity ? are associated with a greater preference to conserve folding states. We quantify previous qualitative findings that suggested the disulfide bond is central to the folding behavior of the cyclic contryphan‐Sm peptide and why the cis‐isomer is the major form of the cyclic contryphan‐Sm peptide. © 2014 Wiley Periodicals, Inc.     

Study of phenothiazine and N‐methyl phenothiazine by infrared,raman, 1H‐, and 13C‐NMR spectroscopies

A complete vibrational analysis of the Fourier transform (FT) infrared (IR) and FT‐Raman spectra of both molecules was carried out using quantum chemical calculations. The structure of phenothiazine (PTZ) and N‐methylphenothiazine (N‐MePTZ) were studied by semiempirical, and ab initio methods. Different basis sets and two new procedures for scaling the frequencies of the ring modes were used. Vibrational data of the methyl group in N‐MePTZ were interpreted in terms of the different molecular conformations in the solid state. The ¹H‐ and ¹³C–nuclear magnetic resonance (NMR) data were interpreted in terms of the electron densities on the atoms and the stacking solute–solute association in dimethyl sulfoxide solution. Chemical shifts were related to the Merz‐Kollman atomic charges. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis‐ and trans‐2‐Butene

Noncovalent interactions of cis‐ and trans‐2‐butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2‐butene dimers, in butane dimers, and between 2‐butene and saturated butane. The results show the trend that interactions of 2‐butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2‐butene dimers are the weakest. The strongest calculated interaction energy is between trans‐2‐butene and butane, with a CCSD(T)/CBS energy of ?2.80 kcal mol^?1. Interactions in cis‐2‐butene dimers are stronger than interactions in trans‐2‐butene dimers. Interestingly, some of the interactions involving 2‐butene are as strong as interactions in a benzene dimer. These insights into interactions of cis‐ and trans‐2‐butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.     

Theoretical studies on the BN substituted fullerenes C70−2x(BN)x (x=1–3)—isoelectronic equivalents of C70

The equilibrium structures and relative stabilities of BN-doped fullerenes C_70−2x(BN)_x (x=1–3) have been studied at the AM1 and MNDO level. The most stable isomers of C_70−2x(BN)_x have been found out and their electronic properties have been predicted. The calculation results show that the BN substituted fullerenes C_70−2x(BN)_x have considerable stabilities, though they are less stable than their all carbon analog. For C₆₈BN, the isomers whose BN is located in the most chemically active bonds of C₇₀ (namely B and A) are among the most stable species, of which B is predicted to be the ground state. The stabilities of C₆₈BN decrease and the dipole moments increase with increasing the distance between the heteroatoms. For C₆₆(BN)₂, the lowest energy species is the isomer in which the B–N–B–N bond is formed; For C₆₄(BN)₃, the most stable species should have three BN units located in the same hexagon to form B–N–B–N–B–N ring. The ionization potentials and the affinity energies of the most stable species of BN-doped C₇₀ are almost the same as those of C₇₀ because of the isoelectronic relationship. The ionization potentials and affinity energies depend on the relative position of the heteroatoms in C₆₈BN, the chemical reactivities of the isomers whose heteroatoms are well separated should differ significantly from their all carbon analog.     

NANOPACK: Parallel codes for semiempirical quantum chemical calculations of large systems in the sp‐ and spd‐basis

A parallel implementation of the conventionally used NDDO (MNDO, AM1, PM3, CLUSTER‐Z1) and modified NDDO‐WF (CLUSTER‐Z2) techniques for semiempirical quantum chemical calculations of large molecular systems in the sp‐ and spd‐basis, respectively, is described. The atom‐pair distribution of data over processors forms the basis of the parallelization. The technological aspects of designing scalable parallel calculations on supercomputers (using ScaLAPACK and MPI libraries) are discussed. The scaling of individual algorithms and the entire package was carried out for model systems with 894, 1920, and 2014 atomic orbitals. The package speed‐up provided by different multiprocessor systems involving a cluster of Intel PIII processors, Alpha‐21264‐processor‐built machine MBC‐1000M, and Cray‐T3E is analyzed. The effect of computer characteristics on the package performance is discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Effect of trans‐ and cis‐isomeric defects on the localization of the charged excitations in π‐conjugated organic polymers

We use the long‐range‐corrected hybrid density functional theory models to study the effect of various conformational distortions of weak‐trans and strong‐cis nature on the spatial localization of charged states in poly(p‐phenylene vinylene) (PPV) and its derivative poly[2‐methoxy‐5‐(2′‐ethylhexyloxy)‐p‐phenylene vinylene] (MEH‐PPV). The extent of self‐trapping of positive (P⁺) and negative (P^?) polarons is observed to be highly sensitive to molecular conformation that, in turn, controls the distribution of atomic charges within the polymers. It is shown that, to reach good agreement with recent experimental data on lattice distortion for P⁺ and P^? excitations, the polarization of the medium plays a critical role. The introduction of weak‐trans defects along the MEH‐PPV chain breaks the observed symmetry for P⁺ and P^? excitations. The P^? states exhibit more spatial localization owing to lattice relaxation than their vacuum counterparts in contrast to P⁺. These observations suggest higher mobilities of holes than that of electrons in MEH‐PPV, in agreement with the experimental observations. The predicted binding, reorganization, and solvation energies for PPV and MEH‐PPV are analyzed for this difference in the response behavior of holes and electrons for trans and cis distortions. This study allows for a better understanding of charge‐transport and photophysical properties in π‐conjugated organic materials by analyzing their underlying structure–property correlations. © 2013 Wiley Periodicals, Inc. 1 1 This article is a U.S. Government work, and as such, is in the public domain in the United States of America.
J. Polym. Sci., Part B: Polym. Phys. 2013 , 51, 935–942     

Combined experimental and computational modeling studies on 3,5‐dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester

The title compound, 3,5‐Dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester, has been synthesized and structurally characterized by X‐ray single crystal diffraction, elemental analysis, IR spectra, and UV‐Vis spectrum. The crystal belongs to orthorhombic, space group P212121, with a = 5.3829(15), b = 11.193(3), c = 21.824(6) Å, V = 1315.0(6) ų, and Z = 4. The molecules are connected via intermolecular C–H···N hydrogen bonds into 1D infinite chains. The crystal structure is consolidated by the intramolecular C–H···S hydrogen bonds. Furthermore, Density functional theory (DFT) calculations of the structure, stabilities, orbital energies, composition characteristics of some frontier molecular orbitals and Mulliken charge distributions of the title compound were performed by means of Gaussian 03W package and taking B3LYP/6‐31G(d) basis set. The time‐dependent DFT (TD‐DFT) calculations have been employed to calculate the electronic spectrum of the title compound, and the UV‐Vis spectra has been discussed on this basis. The results show that DFT method at B3LYP/6‐31G(d) level can well reproduce the structure of the title compound. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Quantum chemical study of several monocyclic complex β‐lactam C‐3, C‐4, and N‐derivatives,and β‐ring model molecules

A quantum chemical study of several complex monocyclic 4‐benzoyl‐4‐phenyl‐β‐lactam derivatives was carried out using cyclobutane, azetidine, 2‐azetidinone, 1‐methyl‐2‐azetidinone, and 3‐methyl‐2‐azetidinone as model compounds. The optimum geometry was obtained for the different conformations. The planarity of the ring was discussed in terms of the influence of the substituents on the amide resonance. To better analyze the amide resonance and the activity of the β‐lactam ring, a vibrational study was also carried out. To examine the influence of solvent polarity on the carbonyl bands, the Fourier transform–infrared (FT‐IR) spectra of the β‐lactam monocyclic derivatives were recorded in CCl₄, C₆H₆, and CHCl₃ solutions. The normal vibrations of the β‐lactam ring in the model compounds were characterized and used in the analysis of the β‐ring of more complex derivatives. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Theoretical investigation on the reactivity of sulfur-centered heterocumulenes as dienophiles in Diels–Alder reactions and endo-lone-pair effect

AM1 and PM3 computations show that thiocarbonyl S-oxide and thiocarbonyl S,S-Dioxide undergo Diels–Alder cycloadditions with cyclopentadiene and anthracene to form thiabicyclic adducts through asynchronous transition structures (TSs) with C(DOUBLE BOND)S π* involving in the reaction at a very early stage. Calculated activation barriers indicate that the dienophilicity of these heterocumulenes decrease gradually with progressive addition of oxygen atom on thiocarbonyl sulfur, in reasonable agreement with experimental observations. Frontier Molecular Orbital (FMO) and deformation energy analyses reveal that the above trend is due to gradual destabilization of lowest unoccupied molecular orbital (LUMO) of the dienophile and increase of deformation energy of both diene and dienophile with increase of oxygen atoms around sulfur. Analysis of bond orders and TS geometries show that the TSs are neither “early” nor “late.” Chlorine substitution on these heterocumulenes does not seem to increase their reactivity contrary to expectations. The reactions of monosubstituted sulfines with cyclopentadiene pass through four very closely lying TSs and stereoselectively form four stereoisomeric products. For the above reason, the computed barriers show a mixed trend although the relative exothermicity of these reactions are in order. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 309–322, 1998     

细菌光合反应中心Q~A和Q~B间电子转移反应的量子化学研究

用量子化学半经验的AM1和密度泛函DFT(BELYP/6-31G(d))方法分别优化了质体醌MQ1(Q~A)、泛醌UQ1(Q~B)及其阳离子自由基的结构。用Nelsen方法计算了电子转移反应MQ1-UQ1→MQ1UQ^-~1的内重组能λi。用线性反应坐标方法构造了该电子转移反应的双势阱,两透热势能面在反应坐标R≈0.30处相交。对该电子转移体系进行闭壳层的单点计算,并用Koopmans定理计算了体系的分裂能△,得到△随线性反应坐标R的变化关系。结果表明,在R=0.342处△有一极小值,从而得到该电子转移反应的电子转移矩阵元Vrp,并由此确定了反应的过渡态。在此基础上,用两球模型计算了反应的溶剂重组能λ0。本文还计算了该电子转移反应的活化自由能△G。最后,根据Marcus电子转移理论计算了该反应的速率常数ket为5.93×10^4s^-^1,由此得到该反应的半衰期与文献报道的结果一致。     

Determination of Band Structure Parameters and the Quasi‐Particle Gap of CdSe Quantum Dots by Cyclic Voltammetry

Band structure parameters such as the conduction band edge, the valence band edge and the quasi‐particle gap of diffusing CdSe quantum dots (Q‐dots) of various sizes were determined using cyclic voltammetry. These parameters are strongly dependent on the size of the Q‐dots. The results obtained from voltammetric measurements are compared to spectroscopic and theoretical data. The fit obtained to the reported calculations based on the semi‐empirical pseudopotential method (SEPM)—especially in the strong size‐confinement region, is the best reported so far, according to our knowledge. For the smallest CdSe Q‐dots, the difference between the quasi‐particle gap and the optical band gap gives the electron–hole Coulombic interaction energy (J_e1,h1). Interband states seen in the photoluminescence spectra were verified with cyclic voltammetry measurements.