Theory on the molecular characteristic contour (II)——Molecular intrinsic characteristic contours of several typical organic molecules

Shape and size of a molecule are the most fun-damental concepts in modern chemistry, and its appli-cations, especially about molecular surface area and molecular volume, are numerous in many fields[1—10]. Most properties of a molecule, including the proc…     

Protonation effects on electron transport through diblock molecular junctions:A theoretical study

Diblock oligomers are widely used in molecular electronics. Based on fully self-consistent nonequilib-rium Green's function method and density functional theory, we study the electron transport properties of the molecular junction with a dipyrimidinyl-diphenyl (PMPH) diblock molecule sandwiched between two gold electrodes. Effects of different kinds of molecule-electrode anchoring geometry and protona-tion of the PMPH molecule are studied. Protonation leads to both conductance and rectification en-hancements. However, the experimentally observed rectifying direction inversion is not found in our calculation. The preferential current direction is always from the pyrimidinyl to the phenyl side. Our calculations indicate that the protonation of the molecular wire is not the only reason of the rectification inversion.     

State-crossing from a Locally Excited to an Electron Transfer State(SLEET) Model Rationalizing the Aggregation-induced Emission Mechanism of (Bi)piperidylanthracenes

Luminogens with aggregation-induced emission(AIE)characteristics(or AIEgens)have been widely used in various applications due to their excellent luminescent properties in molecular aggregates and the solid state.A deep understanding of the AIE mechanism is critical for the rational development of AIEgens.In this work,the“state-crossing from a locally excited to an electron transfer state”(SLEET)model is employed to rationalize the AIE phenomenon of two(bi)piperidylanthracenes.According to the SLEET model,an electron transfer(ET)state is formed along with the rotation of the piperidyl group in the excited state of(bi)piperidylan-thracene monomers,leading to fluorescence quenching.In contrast,a bright state exists in the crystal and molecular aggregates of these compounds,as the intermolecular interactions restrict the formation of the dark ET state.This mechanistic understanding could inspire the deployment of the SLEET model in the rational designs of various functional AIEgens.     

Theoretical study of low-lying excited states of molecular aggregates. I. Development of linear-scaling TD-DFT

The project aims to develop an integrated linear-scaling time-dependent density functional theory (TD-DFT) for studying low-lying excited states of luminescent molecular materials, especially those fluorescence and phosphorescence co-emitting systems. The central idea will be "from fragments to molecule" (FF2M). That is, the fragmental information will be employed to synthesize the molecular wave function, such that the locality (transferability) of the fragments (functional groups) is directly built into the algorithms. Both relativistic and spin-adapted open-shell TD-DFT will be considered. Use of the renormalized exciton method will also be made to further enhance the efficiency and accuracy of TD-DFT. Solvent effects are to be targeted with the fragment-based solvent model. It is expected that the integrated TD-DFT and program will be of great value in rational design of luminescent molecular materials.     

MISCIBILITY IN COPOLYMER/HOMOPOLYMER BLENDS

In order to study the miscibility of a copolymer with its corresponding homopolymers, varieties of multicomponent polymers including simple graft, muhibranch, diblock, triblock and four-arm block copolymers and so-called ABCPs were synthesized and characterized. The morphologies of the blends comprising the copolymers and the corresponding homopolymers were examined by electron microscopy. It is concluded that besides molecular weight, architecture of a copolypaers has apparent effect on the miscibility, i.e. the more complex is molecular architecture, the greater is conformation restriction in microdomain formation and the less is solubility of homopolymer in corresponding domains. In addition, a density gradient model is suggested for describing the segment distribution of the bound and free chains in block-homopolymer systems. Using this model, Helfand's theory is extended to the blends of copolymer and homopolymer predicting the miscibility which is in good agreement with the experimental results.     

CRYSTAL STRUCTURE DETERMINATION OF MUNG BEAN TRYPSIN INHIBITOR Lys FRAGMENT-BOVINE TRYPSIN COMPLEX——MOLECULAR REPLACEMENT,ELECTRON DENSITY MAP AT 3.0 ■ RESOLUTION

The orientation and position of the trypsin molecule in the complex crystal cell mung bean trypsin inhibitor Lys fragment (MBILF)-bovine trypsin (BTRY) have been successfully determined by molecular replacement method with the model of the refined bovine trypsin molecule.Starting from the BTRY coordinates which were oriented and located in the correct azimuth and position in the complex cell according to the result from rotation function and translation function, sim-weighted Fourier map with coefficients 2|F_o|-|F_c| at 3.0 resolution was calculated.Besides the electron density which is obviously attributed to itself, in the vicinity of the active site of BTRY the dense contour levels corresponding to the MBILF and its boundary could be clearly seen in this map. The size of MBILF was approximately estimated at 15×15×25.     

Theoretical Study on Reactivity of Electron Transfer in Model—System of Oxidation of α—Amino Carbon—centered Radical by O2

Electron transfer reaction between a simplified model model molecule of α－amino carbon-centered radical and O2 has studied with ab initio calculations at the MP2/6-31 G^**//UHF/6-31 G^** level,The reactant complex and the ion pair complex have been optimized and employed to perform calculation of the reaction heat and the reorganization energy,Solvent effects have been considered by applyning the conductor-like screening model,Theoretical results show that the highly endothermic charge separation process ,in which one electron transfers from the α－amino carbon-centered radical to O2,so as to form an ion pair complex,is difficult to occur in gas-phase,By apply-ing an external electronic field to prepare the charge-locallized molecular orbitals,the charge-separated state has been obtained using the initial-guess-induced self-consistent field technique,The theoretical investigations indicate that the solvent effect in the process of the oxidation of α-animo carbon-centered radical by O2 is remarkable.From the rate constant estima-tion ,it can be predicted that the oxidation of the model donor molecule by O2 can proceed,but not very fast.A peroxyl radi-cal compound has been found to be a competitive intermediate in the oxidation process.     

Preparation and Intramolecular Electron Transfer of A Covalently Linked Zinc Porphyrin-Methyl Viologen (MV2+) Complex

Porphyrins and methyl viologen(MV~(2+)) are widely used as a photosensitizer and an electron acceptor respectively in photoinduced electron transfer systems. Literatures covered numerous examples of photochemical studies of porphyrins covalently linked to various electron acceptor units, such as viologen, which functioned as both a photosensitizer and an electron acceptor in the same molecule. However, the length of the linked chain between porphyrin and viologen is very important. To improve the rate of photoin-     

A theoretical study on nitration mechanism of benzene and solvent effects

Aromatic nitration is an important and canonical example of electrophilic substitution in organic chemistry. The research on nitration mechanism is also very important for synthesis of explosives since benzene molecule is a basic unit to build up into the energetic material. Besides the electrophilic substitution mechanism, there is an electron transfer mechanism[1,2]. The nitronium ion (NO+ 2), however, is a generally accepted active nitrating agent in the aromatic nitration. Therefore, the …     

A generalized mathematical model for non-catalytic gas-solid reactions

Based on a general classification and characteristic comparison of the existing models, a new model for non-catalytic gas-solid reactions is proposed and a general formulation for the model in terms of the solid conversion, X, is presented in this paper. The model, referred to the generalized model, is demonstrated to be applicable to any solid reactant of general structure ranging from highly porous to nonporous materials. It is shown that the generalized model incorporates the grain and pore structure for a solid pellet and can be reduced to the grain and random pore models as extreme cases.     

A NEURAL NETWORK STUDY ON GLASS TRANSITION TEMPERATURE OF POLYMERS

In this paper, an atificial neural network model is adopted to study the glass transition temperature of polymers. Inour artificial neural networks, the input nodes are the characteristic ratio C_∞, the average molecular weigh M_e betweenentanglement points and the molecular weigh M_(mon) of repeating unit. The output node is the glass transition temperature T_g,and the number of the hidden layer is 6. We found that the artificial neural network simulations are accurate in predicting theoutcome for polymers for which it is not trained. The maximum relative error for predicting of the glass transitiontemperature is 3.47%, and the overall average error is only 2.27%. Artificial neural networks may provide some new ideas toinvestigate other properties of the polymers.     

Study on Pair Correlation Energies of Isoelectronic Systems F^－, HF and H2F^＋

The intrapair and interpair correlation energies of F-, HF and H2F^ systems are calculated and analyzed using MP2-OPT2 method of MELD program with cc-PVSZ^* basis set. From the analysis of pair correlation energies of these isoelectronlc sysoterns, it is found that the 1sF^2 pair correlation energy is trans-ferable in these three isociectronic systems. According to the definition of pair correlation contribution of one electron pair to a system, the pair correlation contribution values of these three systems are calculated. The correlation contribution values of inner electron pairs and H—F bonding electron pair in HF molecule with those in H2F^ system are compared. The results indicate that the bonding effect of a molecule is one of the im-portant factors to influence electron correlation energy of the system. The comparison of correlation energy contributions in-cluding triple and quadruple excitations with those only includ-ing singles and doubles calculated with 6-311 G(d) basis set shows that the higher.excitation correlation energy contribution gives more than 2 % of the total correlation energy for these sys-tems.     

Molecular Frame Photoemission： Probe of the Photoionization Dynamics for Molecules in the Gas Phase

Molecular frame photoemission is a very sensitive probe of the photoionization （PI） dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions （MFPADs）. We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the Ⅰ（χ, θe, Фe） MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and （θe, Фe） the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization （DPI） of D2 at two photon excitation energies, hv=19 eV, where direct PI is the only channel opened, and hv=32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.     

A DFT Study of Thiophene Adsorption on the Rh（111） Surfaces

Thiophene adsorption on the Rh(111) surfaces has been investigated by density functional theory.The results show that the adsorption at the hollow and bridge sites is the most stable.The molecular plane of the thiophene ring is distorted,the C=C bond is stretched to 1.448  and the C-C bond is shortened to 1.390.The C-H bonds tilt 22～42oaway from the surface.The calculated adsorption geometries are in reasonable agreement with population analysis and density of states.The thiophene molecule obtains 0.74 electrons,reflecting the interaction between the lone pair of sulfur and the d-orbitals of metal.The reaction paths and transition states for desulfurization of the molecule have been investigated.The bridge adsorption structure of thiophene leads to a thiol via an activated reaction with an energetic barrier of 0.30 eV.This second step is slightly difficult,and dissociation into a C4H4 fragment and a sulfur atom is possible,with an energetic barrier of 0.40 eV.     

2D-QSAR Studies on the Norcantharidin Analogues as Protein Phosphatase 1 and 2A Inhibitors

The Two-dimensional Quantitative Structure-activity Relationship(2D-QSAR) of a series of novel norcantharidin analogues,which exhibit inhibitory activities of protein phosphatase 1 and 2A(PP1 and PP2A),has been studied with a combined method of ab initio(HF),molecular mechanics(MM+) and statistics.The established 2D-QSAR model(Eq.1) for PP1 shows a reasonable regressive performance(R2 = 0.749),and the hydrophobic property of this molecule plays a decisive role in determining the inhibitory activity of PP1.In addition,the established 2D-QSAR model(Eq.2) for PP2A also shows an acceptable regressive performance(R2 = 0.701),and the dipole moment of the molecule determines the inhibitory activity of PP2A.     

COMPUTER SIMULATIONS ON UNPERTURBED CONFIGURATIONAL DIMENSIONS OF POLY (METHYL ACRYLATE)

A full-relaxation optimization of molecule and the popular MM2 force field are em-ployed to obtain the geometry parameters and the conformational energy surface of a mesoor a racemic dyad of poly(methyl acrylate) (PMA) with a specified carbonyl-bond orien-tation in side-groups. It is found that the conformational energy maps calculated hereconsiderably differ from those calculated with the rigid molecular model as reported in theearlier studies. The g~- state cannot be omitted in the obtained contour maps. Two impor-tant conformers tg~- and g~(-t) with energy minima were newly detected for a racemic dyad.The analysis on the conformations with energy minima confirmed that the ester groupsare not always perpendicular to the plane defined by the two adjacent skeletal bonds andmay change their relative orientations to meet the requirement of lower energies duringthe conformational state transition. Instead of the early way of adjusting the interactionenergy parameters to fit the experimental data, we attempt to predict unperturbed chaindimensions via the reliable force field and the configurational statistical mechanics. Theproposed scheme with three rotational states identified from the contour maps allowed usto satisfactorily reproduce the experimental dimensions of random PMA chains.     

CoMFA 3D-QSAR Analysis of Epothilones Based on Docking Conformation and Alignment

Epothilones belong to a class of novel microtubule stabilizing and anti-mitotic agents, which have a paclitaxel-like mechanism of action. A three-dimensional quantitative structure-activity relationship （3D-QSAR） model was built for epothilones by the method of comparative molecular field analysis （CoMFA） combined with the flexible docking technology. The docking CoMFA model gave a good cross-validated value of q2=0.784 with an optimized component of 6 and the conventional correlation coefficient of r^2=0.985. The statistical results show that the model has good ability to predict the activity of the studied compounds. At last, the docking CoMFA model was analyzed through contour maps complemented with MOLCAD-generated active site potential surface in the α,β-tubulin receptor, which can provide important information for the structure-based drug design.     

QSAR Study and VolSurf Characterization of Human Intestinal Absorption of Druge

The prediction of human intestinal absorption is a major goal in the design,optimization,and selection of candidates for the develoment of oral drugs.In this study,a computerized method(VolSurf with GRID) was used as a novel tool for predicting human intestinal absorption of test compound,and for determining the critical molecular properties needed for human intestinal absorption.The tested molecules consisted of 20 diverse drug-like compounds.Partial least squares(PLS) discriminant analysis was used to correlate the experimental data with the theoretical molecular properties of human intestinal absorption.A good correlation(r^2=0.95,q^2=0.86) between the molecular modeling results and the experimental data demonstrated that human intestinal absorption could be predicted from the three-dimensional(3D) molecular structure of a compound .Favorable structureal properties identified for the potent intestinal absorption of drugs included strong imbalance between the center of mass of a molecule and the barycentre of its hydrophilic and hydrophobic regions and a definitive hydrophobic region as well as less hydrogen bonding donors and acceptors in the molecule.     

Behavior of macromolecules in adsorbed layers

A model for describing the behavior ot macromoiecuies in aosoroea layers is developed by introducing a concept of distribution density of layer thickness U based on stochastic process and probabilistic statistics. The molecular behavior of layers adsorbed on clay particle surfaces is discussed; the random distribution and its statistics of the layer thickness are given by incorporating experimental results with an ionic polyelectrolyte with the molecular weight of 1.08×106and chain charged density of 0.254.     

2D-QSAR Studies on the Norcantharidin Analogues as Protein Phosphatase I and 2A Inhibitors

The Two-dimensional Quantitative Structure-activity Relationship （2D-QSAR） of a series of novel norcantharidin analogues, which exhibit hnhibitory activities of protein phosphatase 1 and 2A （PP1 and PP2A）, has been studied with a combined method of ab initio （I/F）, molecular mechanics （MM＋） and statistics. The established 2D-QSAR model （Eq. 1） for PP1 shows a reasonable regressive performance （R2= 0.749）, and the hydrophobic property of this molecule plays a decisive role in determining the inhibitory activity of PP1. In addition, the established 2D-QSAR model （Eq. 2） for PP2A also shows an acceptable regressive performance （R2= 0.701）, and the dipole moment of the molecule determines the inhibitory activity of PP2A.