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Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations 总被引:1,自引:0,他引:1
Raymond J. Abraham Guy H. Grant Ian S. Haworth Paul E. Smith 《Journal of computer-aided molecular design》1991,5(1):21-39
Summary The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples.In substituted methanes (CH3X, CF3X, CCl3X) the effects of varying the electronegativity of the substituents and the - and -substituent contributions are clearly illustrated for a variety of substituent groups X.The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges ( and contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed.The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N-methyl-amides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods.The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.For previous parts in this series, see Refs. 1-7. 相似文献
45.
Chen D Wang R Arachchige I Mao G Brock SL 《Journal of the American Chemical Society》2004,126(50):16290-16291
This communication describes a spin-coating method to nucleate organic molecular rods of uniform size from an inorganic nanoparticle at a solid surface. The particle-rod hybrid structure spontaneously forms when a film is spin coated from a mixed 2-propanol solution of arachidic acid (AA) and nanoparticles of cadmium selenide capped by mercaptoundecanoic acid (MUA-CdSe) on graphite. AFM images show that MUA-CdSe nanoparticles nucleate single crystalline rods of AA with a cross section of a single unit cell of the C-form. The solution-based process potentially allows the precise tuning of the wetting profile of the solution on the surface-attached nanoparticle, which provides the reservoir for the growth of the single crystalline rods. The results suggest that nanoparticles can be regarded as nanoseeds for the nucleation of guest crystals. It should be possible to further functionalize the AA rods by electrostatic complexation with metal or organic ions. 相似文献
46.
Julio C. Facelli David M. Grant Josef Michl 《International journal of quantum chemistry》1987,31(1):45-55
A new method is presented to analyze the IGLO (individual gauge for localized orbitals) bond contributions in 13C chemical shielding. The IGLO bond contributions calculated in the molecular frame are rotated to a local bond frame, in which one component is selected along the bond. This procedure removes the explicit angular dependence of the IGLO bond contributions and allows a comparison of the bond contributions in different molecules. The results provide a new method to study the electronic basis of shielding interactions. The problems associated with the multiple gauge origins used in the IGLO method are discussed in their relationship to the bond contribution analysis. 相似文献
47.
Seasonal fluctuation of DNA photodamage in marine plankton assemblages at Palmer Station, Antarctica
Meador J Jeffrey WH Kase JP Pakulski JD Chiarello S Mitchell DL 《Photochemistry and photobiology》2002,75(3):266-271
Ultraviolet radiation-induced DNA damage frequencies were measured in DNA dosimeters and natural plankton communities during the austral spring at Palmer Station, Antarctica, during the 1999-2000 field season. We found that the fluence of solar ultraviolet-B radiation (UV-B) at the earth's surface correlated with stratospheric ozone concentrations, with significant ozone depletion observed because of "ozone hole" conditions. To verify the interdependence of ozone depletion and DNA damage in natural microbial communities, seawater was collected daily or weekly from Arthur Harbor at Palmer Station, Antarctica, throughout "ozone season," exposed to ambient sunlight between 0600 and 1800 h and fractionated using membrane filtration to separate phytoplankton and bacterioplankton populations. DNA from these fractions was isolated and DNA damage measured using radioimmunoassay. Under low-ozone conditions cyclobutane dimer concentrations in bacterioplankton and phytoplankton communities were maximal. DNA damage measured in dosimeters correlated closely with ozone concentrations and UV-B fluence. Our studies offer further support to the theory that stratospheric deozonation is detrimental to marine planktonic organisms in the Southern Ocean. 相似文献
48.
Polymers such as poly(ethylene glycol) (PEG) have proven use in a variety of applications including organic synthesis. We now disclose our investigations into the recently disputed report that PEG tartrate esters can reverse the enantioselectivity of the Sharpless asymmetric epoxidation reaction. The results presented herein have clarified that the enantioselectivity of this reaction can be reproducibly reversed solely as a function of the molecular weight of the appended PEG. By preparing a range of tartrate ligands with varying PEG chains lengths, the reversal was found to occur within a molecular weight change of only 800. As the PEG chain did not affect the inherent chirality of the ligand, the enantioreversal was proposed to occur as a result of two Ti-ligand complexes which differ in their molecularity of ligand, one monomeric in ligand and the other dimeric. Support for this hypothesis was given through equilibrium measurements which revealed that the predominant species in Ti/PEG tartrate ester mixtures is a distinct 2:1 Ti-ligand complex, as opposed to the 2:2 Ti-ligand complex of traditional Sharpless asymmetric epoxidations. In total, these data represent an unrecognized property of PEG-supported catalysts that could open up new venues in the control of asymmetric reactions by means of achiral appended polymers. 相似文献
49.
Solid-state synthesis of a conducting polythiophene via an unprecedented heterocyclic coupling reaction 总被引:2,自引:0,他引:2
Meng H Perepichka DF Bendikov M Wudl F Pan GZ Yu W Dong W Brown S 《Journal of the American Chemical Society》2003,125(49):15151-15162
Prolonged storage ( approximately 2 years) or gentle heating (50-80 degrees C) of crystalline 2,5-dibromo-3,4-ethylenedioxythiophene (DBEDOT) affords a highly conducting, bromine-doped poly(3,4-ethylenedioxythiophene) (PEDOT), as confirmed by solid-state NMR, FTIR, CV, and vis-NIR spectroscopies. The novel solid-state polymerization (SSP) does not occur for 2,5-dichloro-3,4-ethylenedioxythiophene (DCEDOT), and requires a much higher temperature (>130 degrees C) for 2,5-diiodo-3,4-ethylenedioxythiophene (DIEDOT). X-ray structural analysis of the above dihalothiophenes reveals short Hal.Hal distances between adjacent molecules in DBEDOT and DIEDOT, but not in DCEDOT. The polymerization may also occur in the melt but is significantly slower and leads to poorly conductive material. Detailed studies of the reaction were performed using ESR, DSC, microscopy, and gravimetric analyses. SSP starts on crystal defect sites; it is exothermic by 14 kcal/mol and requires activation energy of approximately 26 kcal/mol (for DBEDOT). The temperature dependence of the conductivity of SSP-PEDOT (sigma(rt) = 20-80 S/cm) reveals a slight thermal activation. It can be further increased by a factor of 2 by doping with iodine. Using this approach, thin films of PEDOT with conductivity as high as 20 S/cm were fabricated on insulating flexible plastic surfaces. 相似文献
50.
The electronic absorption spectra of a series of alkoxy-styryl substituted terthiophenes, their corresponding sexithiophenes, and the oxidation products of both have been measured. The terthiophenes studied sigma-dimerize to sexithiophenes during the oxidation process and there is clear evidence of sexithiophene radical cations, dications, and pi-dimers in the electronic absorption spectra. The oxidation of concentrated solutions produces predominantly pi-dimer bands, as expected. The absorption spectrum of the styryl-functionalized sexithiophene dication without alkoxy substitution closely resembles that of unsubstituted sexithiophene, while alkoxy substitution induces changes in the wavelength of the dication band maximum and the overall band shape. Time-dependent density functional theory (TDDFT) calculations have shown that styryl-based molecular orbitals are important in the transitions of the neutral molecules as well as the charged species, the dication in particular. Kinetics analyses confirm the stabilization effect induced by the alkoxy substituents. The presence of a reversible pi-dimer equilibrium was verified by cyclic voltammetry. It is clear from the experimental observations and the theoretical calculations that both the styryl and alkoxy groups are influencing the electronic properties of this class of molecules. 相似文献