The structural theory and physical organic chemistry

Woolley's revolutionary proposal that quantum mechanics does not sanction the concept of “molecular structure”—which is but only a “metaphor”—has fundamental implications for physical organic chemistry. On the one hand, the Uncertainty Principle limits the precision with which transition state structures may be defined; on the other, extension of the structure concept to the transition state may be unviable. Attempts to define transition states have indeed caused controversy. Consequences for molecular recognition, and a mechanistic classification, are also discussed.     

A critical review of spectral and related physical properties of the hollow cathode discharge

Investigations made over the last fifty years, of the electrical properties which differentiate a hollow cathode d.c. discharge from one before a plane cathode, have been summarized. The wide range of dimensions and pressure conditions used by different workers have been considered, and related where possible to results, to give a more unified picture. Data are collected on energies and densities of electrons, and of positive ions, in hollow cathode cavities, with a view to establishing the principles governing spectral line emission. Results of measurements on spectral line intensities, of carrier gases and of atoms sputtered from the cathode, are discussed in relation to the activity, already considered, of electrons and positive ions. The gaps and contradictions in present knowledge of conditions for useful light emission are indicated.     

The adsorptivity of organic substances with various physico-chemical properties

The adsorption isotherms of benzene,n-hexane, cyclohexane, and 1,2-dibromo-1,1,2,2-tetrafluoroethane on a nonporous carbon adsorbent, carbon black, were calculated from the results of a gas-chromatographic experiment at 373 K. A general equation of adsorption isotherm for vapors of organic substances on nonporous sorbents that was proposed earlier is shown to be valid in the range of relative pressures,p/p _s, of 10^–7–1 and temperatures of 293–373 K.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1381–1383, August, 1993.     

Preparation of pure dinitromethane and its physical properties

Summary Treatment of the potassium salt of dinitromethane with hydrogen fluoride in ether gave a fairly stable dinitromethane that could be distilled; its physical properties were determined.Translated from Izvestiya Akademii Nauk SSSR, Khimicheskaya, No. 12, pp. 2220–2221, December, 1965     

论物质的分子结构与临界温度

分析了Thodos等的理论方法及公式的不足后,利用分子物理学和光谱学的理论与实验研究成果,根据及Dieterici方程,解出T_c∝1/f(K);根据Kirchhoff定律d(△H)/dT=△C_p,导出.经用120种不同结构类型的无机化合物验算,平均误差0.68％;当以405种有机化合物验证时,平均误差0.450％,优于文献中各式.     

Facile macrocyclizations to beta-turn mimics with diverse structural, physical, and conformational properties

On-resin S(N)Ar reactions were performed to prepare the macrocyclic beta-turn mimics 1a-n (Scheme 1 and Table 1). These reactions occurred more efficiently than completely analogous macrocyclization reactions that do not involve an iodinated aromatic electrophile. The synthesis was also modified to allow introduction of an alkyne via a solid-phase Sonogashira reaction (giving compound 2, Scheme 2) and an aryne via a solid-phase Suzuki reaction (giving compound 3, Scheme 2). Conformational analyses of three illustrative compounds, i.e., 1i, 2, and 3, were performed using a combination of NMR, circular dichroism, and computer-aided molecular simulation methods. Overall, the preferred conformations of all three molecules tended to be type-I-like beta-turns, but for compound 3 interaction of the electron cloud of the aryl substituent with the oxygen lone pairs seems to cause differences in the preferred orientation of the turn frameworks. This study illustrates how iodinated electrophiles can be used in solid-phase S(N)Ar reactions to increase the molecular and conformational diversity in a library.     

High-performance organic field-effect transistors: molecular design, device fabrication, and physical properties

In the past decade, tremendous progress has been made in organic field-effect transistors (OFETs). Their real applications require further development of device performance. OFETs consist of organic semiconductors, dielectric layers, and electrodes. Organic semiconductors play a key role in determining the device characteristics. The properties of the organic semiconductors, such as molecular structure and packing, as well as molecular energy levels, can be properly controlled by molecular design. Therefore, we designed and synthesized a series of organic molecules. The synthesized organic semiconductors exhibit excellent field-effect properties due to strong intermolecular interactions and proper molecular energy levels. Meanwhile, the influence of the device fabrication process, organic semiconductor/dielectric layer interface, and organic layer/electrode contact on the device performance was investigated. A deep understanding of these factors is helpful to improve field-effect properties. Furthermore, single-crystal field-effect transistors are highlighted because the single-crystal-based FETs can provide an accurate conducting mechanism of organic semiconductors and higher device performance as compared with thin film FETs.     

The effect of physical organic properties on hydrophobic fields

Summary Physical organic structural properties of small molecules and macromolecules such as bond count, branching and proximity between multiple polar fragments contribute significantly to measured hydrophobicity (log P). These structural properties are encoded in the Rekker and Leo methods of calculating log P as structural-dependent factors. Regardless of the size of the atom primitive set, methods predicting log P with only atom primitives can miss subtle structural detail within series of related compounds. The HINT (Hydropathic INTeractions) model for inter- and intramolecular noncovalent interactions calculates atom-based hydrophobic constants, but uses all Leo-type factors in the calculation rather than a large set of atom primitives. Two types of applications of HINT are discussed: evaluation of the binding of an inhibitor (A74704) to HIV-1 protease, where it is shown that modeling of the protonation state (i.e., Asp²⁵, Asp¹²⁵) in the protein can strongly influence perceived substrate binding; and the use of HINT to calculate a third (hydropathic) field for CoMFA can yield a statistically enhanced and predictive model for molecular design.     

A molecular-dynamics study of structural and physical properties of nitromethane nanoparticles

The structural and physical properties of nanoparticles of nitromethane are studied by using molecular dynamics methods with a previously developed force field. [Agrawal et al., J. Chem. Phys. 119, 9617 (2003).] This force field accurately predicts solid- and liquid-state properties as well as melting of bulk nitromethane. Molecular dynamics simulations of nanoparticles with 480, 240, 144, 96, 48, and 32 nitromethane molecules have been carried out at various temperatures. The carbon-carbon radial distribution function, dipole-dipole correlation function, core density, internal enthalpy, and atomic diffusion coefficients of the nanoparticles were calculated at each temperature. These properties were used to characterize the physical phases and thus determine the melting transitions of the nanoparticles. The melting temperatures predicted by the various properties are consistent with one another and show that the melting temperature increases with particle size, approaching the bulk limit for the largest particle. A size dependence of melting points has been observed in experimental and theoretical studies of atomic nanoparticles, and this is a further demonstration of the effect for large nanoparticles of complex molecular materials.     

Diamondoids approach to electronic,structural, and vibrational properties of GeSi superlattice nanocrystals: a first-principles study

Germanium silicide diamondoids are used to determine electronic, structural, and vibrational properties of GeSi superlattice nanocrystals and bulk as their building block limit. Density functional theory at the generalized gradient approximation level of Perdew, Burke, and Ernzerhof (PBE) with 6-31G(d) basis including polarization functions is used to investigate the electronic structure of these diamondoids. The investigated molecules and diamondoids range from GeSiH₆ to Ge₆₃Si₆₃H₉₂. The variation of the energy gap is shown from nearly 7 eV toward bulk value which is slightly higher than the average of Si and Ge energy gaps. Variations of bond lengths, tetrahedral, and dihedral angles as the number of atoms increases are shown taking into account the effect of shape fluctuations. Localized and delocalized electronic charge distribution and bonds for these molecules are discussed. Vibrational radial breathing mode (RBM) converges from its initial molecular value at 332 cm^?1 to its bulk limit at 0 cm^?1 (blue shift). Longitudinal optical-highest reduced mass mode (HRMM) converges from its initial molecular value 332 cm^?1 to experimental bulk limit at 420.7 cm^?1 (red shift). Hydrogen vibrational modes are nearly constant in their frequencies as the size of diamondoids increases in contrast with lower frequency Ge–Si vibrational modes. GeSi diamondoids can be identified from surface hydrogen vibrational modes fingerprint, while the size of these diamondoids can be identified from Ge–Si vibrational modes.     

Low temperature physical properties of the organic conductor, (Dimet)2i3 after thermal treatment

The effect of thermal treatment on the electrical conductivity was studied for a quasi-one-dimensional organic conductor, (DIMET)₂I₃ (DIMET=dimethyl(ethylenedithio)tetrathiafulvalene). After heating the samples up to a temperature between 340 and 370 K, the electric resistivity was measured at low temperature down to 2 K and under pressure up to 1.6 Gpa. (DIMET)₂I₃ shows irreversible decrease in the electric resistivity between 350 and 356 K on heating. It was found that the heating above 350 K suppresses the spin-density-wave transition at 40 K and another metal-insulator transition appears at 18 K. This revised version was published online in August 2006 with corrections to the Cover Date.     

Perylene-3,4,9,10-tetracarboxylic acid diimides: synthesis, physical properties, and use in organic electronics

Perylene-3,4,9,10-tetracarboxylic acid diimides (perylene diimides, PDIs) have been used as industrial pigments for many years. More recently, new applications for PDI derivatives have emerged in areas including organic photovoltaic devices and field-effect transistors. This Perspective discusses the synthesis and physical properties of PDI derivatives and their applications in organic electronics.     

Relationship between the molar volume and enthalpy of formation, polarizability, and ionization potential of CHNO-containing organic substances

A new approach to revealing a relationship between various physicochemical properties of organic compounds is suggested. The basic principle of this approach consists in that deviations of experimental values of various molecular parameters from linear dependences for the constituent elements are due to intramolecular forces of the same nature.