Examination of stabilty of molecular agglomerates in molecular crystals

We report an examination algorithm of stability of molecular aggregates based on the estimation of rigidity of intermolecular contacts in a crystal structure. The algorithm includes the intermolecular interaction energy calculation (in the atom-atom potential approximation) of a pair of molecules selected in the crystal structure. Further, the energy is minimized using a least-squares technique by varying the position and orientation of one of the molecules. The contact rigidity is quantitatively assessed by the minimized rms difference between the positions of the atoms in the original and optimized structures (Zorkii’s criterion). Every rigid contact revealed in the structure determines finite or infinite stable agglomerates. The paper presents the results of testing the computer program based on this algorithm with a number of real crystal structures previously determined by single crystal X-ray diffraction, and also the examples of the most common stable molecular agglomerates found with the aid of the program.     

Understanding molecular structure from molecular mechanics

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.     

Gaussian expansion method for molecular integrals of molecular properties

The finite Gaussian Expansion method for molecular integrals proposed by Taketa, O-ohata and Huzinaga has been extended to the integrals of molecular properties. The integral formulas of so-called moment, field and field gradient integrals have been derived. It has been numerically shown that in order to evaluate the field and the field gradient integrals based on Slater type orbitals, eight- or ten-term Gaussian expansions are sufficient but this method fails to attain sufficient effective numbers for the moment integrals.     

Polyvalent carbocyanine molecular beacons for molecular recognitions

Polyvalent carboxylate-terminating near-infrared (NIR) carbocyanine molecular beacons were prepared by homologation of reactive carboxyl groups of the beacon with imino diacetic acid. Their conjugation with unprotected d-(+)-glucosamine gave dendritic arrays of the carbohydrate on an inner NIR chromophore core. In vivo evaluation of the dendritic glucosamine constructs shows enhanced uptake in proliferating tumor cells relative to surrounding normal tissue. The structural framework of these polyvalent beacons permits the amplification by synergistic effects of a variety of bioactive motifs or chemical sensors in molecular recognition interactions without dramatic change of their desirable NIR spectral properties.     

Net signs of molecular graphs: Dependence of molecular structure

The concept of internal connectivity associates to each eigenvector of the molecular graph a graph with signed edges. We show that the respective edge signs can be deduced without knowing the graph eigenvectors. The dependence of the edge signs on molecular structure is elucidated. The sign of an edge whose end vertices are ν_r and ν_s is found to be the result of separate interactions through all paths connecting the vertices ν_r and ν_s. The analysis of the edge signs is particularly simple in the case of acyclic systems. © 1994 John Wiley & Sons, Inc.     

Two-dimensional molecular space with regular molecular structure

A novel two-dimensional molecular space (layered carboxylpropylamidephenylsilica, CPAPhS) with regular carboxyl groups was successfully synthesized through grafting carboxyl groups in the structure of layered (aminophenyl)silica using butanedioic anhydride. The carboxyl groups regularly arranged in the layered CPAPhS can react with various organic molecules with amino and hydroxyl groups through formation of reactive intermediate with catalyzers, such as SOCl2. In this research, an example was used to prove the reaction properties of regular carboxyl groups in layered CPAPhS. The layered CPAPhS was reacted with SOCl2 to form layered acyl chloridepropylamidephenylsilica (ACPAPhS) and then reacted with n-butylamine and n-butyl alcohol to form layered n-butylamidepropylamidephenylsilica (BAPAPhS) and n-butylesterpropylamidephenylsilica (BEPAPhS) with regular molecular structures. Layered CPAPhS showed the potential as a starting material for formation of a series of novel two-dimensional molecular space with various regular molecular structures, and as a solid acceptor for chemical reagent with amino and hydroxyl groups for chemical processes.     

Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics

The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction.     

The kinetic energy of molecular charge distributions and molecular stability

This paper examines the relationship between the topographical features of a molecular charge distribution and the kinetic energy of the system. Specifically, the spatial contributions to the kinetic energy are related to the Laplacian of the total charge density and to the gradients of the natural-orbital densities. It is concluded that a necessary requirement for molecular stability is the existence of a net negative curvature for the molecular charge distribution in the internuclear region. It is shown that the charge density accumulated in the internuclear region of a stable molecule is distributed in such a way as to keep the accompanying increase in the kinetic energy to a minimum. A comparison of the contributions to the kinetic energy from the atomic and molecular charge distributions indicates that in the formation of a stable molecule the contribution from the molecular charge density in the binding region is decreased relative to that of the atoms.     

Fine tuning of molecular rotor function in photochemical molecular switches

Molecular switches are used as scaffolds for the construction of controlled molecular rotors. The internal position of the switching entity in the molecule controls the dynamic behaviour of the rotor moiety in the molecule. Six new molecular motors with o-xylyl rotor moieties were prepared on the basis of an overcrowded alkene, and their dynamics were systematically studied by 2D EXSY NMR. Variation of the (hetero-)atoms in the upper and lower halves of the overcrowded alkene allows fine tuning of the rate of rotation of the o-xylyl rotor in the lower half of the molecule. For all rotors it was observed that the rotation barrier for the trans-isomer was higher than that of the corresponding cis-isomer. The results are analyzed and discussed in terms of differences in steric interactions in the presented system.     

Determination of molecular weight dependences and characterization of molecular weight distributions

Molecular weight dependences of the square of the radius of gyration as well as of the coefficients of diffusion and friction of monodisperse polystyrenes in toluene at 20°C are determined experimentally. For this purpose, the z-averages of these quantities and $\text{M}$_w as determined by light scattering were subjected to the polydispersity correction procedures as described previously. In addition, a method is suggested for the checking of known data with respect to molecular weight distribution, using measured values in conjunction with the polydispersity correction procedures.     

Prediction of molecular volume and surface of alkanes by molecular topology

Molecular volume and molecular surface are expressed as a function of topological degree in alkane graphs. This allows not only a straightforward approach to calculate such physicochemical magnitudes but also an interpretation of the role of the local vertex invariant (LOVI) or valence degree, delta, as well as the connectivity indices in the prediction of physicochemical properties. The interpretation is based on the concept of molecular accessibility (as introduced by Estrada, J. Phys. Chem. A 2002, 106, 9085) for which precise mathematical definitions are provided.     

Effects of molecular entanglements during electrospray of high molecular weight polymers

Concentration-dependent bimodal size distributions (comprised of single-molecule particles and multimolecule clusters) observed by microscopic examination of particles collected during electrospray (ES) of dilute solutions of high molecular weight polymers suggest that chain entanglement can interfere with the droplet subdivisions believed to be intrinsic to the electrospray process. The feasibility of such interference is discussed in the context of the spray model of Kebarle, along with its potential impact on the ES mass spectrometry of macromolecules.     

Non-empirical molecular orbital theory of the electronic structure of molecular crystals

A non-empirical molecular orbital treatment of molecular crystals, based on SCF perturbation theory and matrix partitioning methods is presented.     

Mechanism of molecular recognition on molecular imprinted monolith by capillary electrochromatography

The recognition mechanism of molecularly imprinted polymer (MIP) in capillary electrochromatography (CEC) is complicated since it possesses a hybrid process, which comprises the features of chromatographic retention, electrophoretic migration and molecular imprinting. For an understanding of the molecular recognition of MIP in CEC, a monolithic MIP in a capillary with 1,1'-binaphthyl-2,2'-diamine (BNA) imprinting was prepared by in situ copolymerization of imprinted molecule, methacrylic acid and ethylene glycol dimethacrylate in porogenic solvent, a mixture of toluene-isooctane. Strong recognition ability and high column performance (theory plates was 43,000 plates/m) of BNA were achieved on this monolithic MIP in CEC mode. In addition, BNA and its structural analogue, 1,1'-bi-2, 2'-naphthol, differing in functional groups, were used as model compounds to study imprinting effect on the resultant BNA-imprinted monolithic column, a reference column without imprinting of BNA and a open capillary. The effects of organic modifier concentration, pH value of buffer, salt concentration of buffer and column temperature on the retention and recognition of two compounds were investigated. The results showed that the molecular recognition on MIP monolith in CEC mode mainly derived from imprinting cavities on BNA-imprinted polymer other than chromatographic retention and electrophoretic migration.     

分子轨道法研究硅酸盐分子结构

Pauling提出的硅酸盐结构规则,原则上只适用于纯粹离子键化合物。硅酸盐中硅酸根与金属原子之间的化学键是离子键,但是硅氧键却没有证据说明它是离子键。 Stewart等从X射线衍射实验和轨道电负性理论论证,α-石英中Si—O键仅有25％的离子性。还有人认为Si—O键的离子性为31～37.5％。我们用CNDO/2法计算得