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101.
A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization. 相似文献
102.
Y. L. Tong 《Annals of the Institute of Statistical Mathematics》1987,39(1):289-297
Summary This paper concerns interval estimation of the critical value θ which satisfies
under the general linear model,Y
i
=μ(x
i
)+ε
i
(i=1,2,···), where
for
and the functional forms off
j
′
s are known. From an asymptotic expansion it is shown that, under reasonable conditions, the limiting distribution of
is normal. Thus in the large-sample case a confidence interval for θ can be obtained. Such a result is useful when one is
interested in carrying out a retrospective analysis rather than designing the experiment (as in the Kiefer-Wolfowitz procedure).
In Section 3 a sequential procedure is considered for confidence intervals with fixed width 2d. It is shown that, for a given stopping variableN,
is also asymptotically normal asd→0. Thus the coverage probability converges to 1−α (preassigned) asd→0. An example of application in estimating the phase parameter in circadian rhythms is given for the purpose of illustration.
Research partially supported by the NSF Grant DMS-8502346. 相似文献
103.
An end-channel amperometric detector with a guide tube for working electrode was designed and integrated on a home-made glass microchip. The guide tube was directly patterned and fabricated at the end of the detection reservoir, which made the fixation and alignment of working electrode relatively easy. The fabrication was carried out in a two-step etching process. A 30 μm carbon fiber microdisk electrode and Pt cathode were also integrated onto the amperometric detector. The baseline separation of dopamine (DA), catechol (CA) and epinephrine (EP) was achieved within 80 s. Relative standard deviations of not more than 5.2% were obtained for both peak currents and migration times of DA and CA (n=5). Using standard adding method, DA in tLrine and plasma samples was detected. The recoveries were in the range of 83%—103%. 相似文献
104.
Characterization of the non-stoichiometric and isomorphic hydration and solvation in FK041 clathrate
Hisashi Mimura Satoshi Kitamura Teruyuki Kitagawa Shigetaka Kohda 《Colloids and surfaces. B, Biointerfaces》2002,26(4):397-406
FK041 crystallizes as a non-stoichiometric hydrate or as solvated hydrates which were characterized as isomorphic clathrates by powder X-ray diffractometry. Moisture and organic solvent vapor sorption studies, differential scanning calorimetry and thermogravimetric analysis revealed that FK041 monohydrate forms a physically stable host crystal, which has lattice channels for guest water and/or organic solvent molecules. The hydration state varies non-stoichiometrically between dihydrate and tetrahydrate depending on the relative humidity and the mol content of the co-existing organic solvent, that is 2-propanol, ethanol, or acetone. These organic solvents are thought to replace a part of originally present water with a mol ratio of 1:3. 2-Propanol exhibited the most stable solvation, indicating that the size and shape of 2-propanol are the most preferable to the lattice channels. 相似文献
105.
The treatment of 3,4-dihydropyrimidin-2-ones with n-BuLi at −78 °C, followed by quenching with various electrophiles furnished N3-substituted derivatives, regioselectively. Further, N1,N3-diacyl derivatives were found to transfer N1-acyl groups to nucleophilic sites. 相似文献
106.
Min-Hsien Liu Cheng Chen Yaw-Shun Hong Chuan-Wen Liu 《Theoretical chemistry accounts》2005,113(1):35-41
Calculation methods, based on hybrid density-functional theory with the basis sets of B3LYP/ 6-311+G (2d, p)//B3LYP/6-31G(d, p)and B3LYP/6-31+G(d)//B3LYP/6-31G(d, p), were applied to determine the thermodynamic characteristics of various energetic nitro compounds. A parametric modification equation and the least-squares approach were used to identify 21 of the energetic research compounds. The atomization energies of these 21 compounds have an average relative error of 0.21–0.25% of the experimental values. The enthalpy (H f) and the Gibbs energy (G f) of formation have mean absolute errors of 10.8–11.4 kJ/ mol (2.6–2.7 kcal/mol) and 10.0–10.3 kJ/mol (2.4 kcal/ mol), respectively. The enthalpy and the Gibbs energy of formation obtained exceed those in the literature obtained by semiempirical calculations. The calibrated least-squares parameters and parametric equations were used to predict H f and G f for the five newly developed energetic nitro compounds for further applications.Acknowledgements. The authors would like to thank the National Science Council of the Republic of China for financial support of this work under grant no. NSC-91-2113-M-014-003. The National Center for High-Performance Computing providing the computation facility is also acknowledged. 相似文献
107.
Shyh‐Jong Chen Cheng Chen Yaw‐Shun Hong 《International journal of quantum chemistry》2005,103(2):198-214
This investigation conducted reaction channels of weakly bound complexes CO2…HF, CO2…HF…NH3, CO2…HF…NH2CH3, CO2…HF…NH(CH3)2, and CO2…HF…N(CH3)3 systems, using the Gaussian 98 package at the B3LYP/6‐311++G(3df,2pd) level. The syn‐fluoroformic acid or syn‐fluoroformic acid plus NH3 or amine conformers are more stable than the related anti‐fluoroformic acid or anti‐fluoroformic acid plus NH3 or amine conformers. However, the above‐mentioned weakly bound complexes are more stable than both the related syn‐ and anti‐type fluoroformic acid or acid plus NH3 or amine conformers and their related decomposed into CO2 + HF or CO2 + NHR3F (R?H, CH3) combined molecular systems. Five reaction channels of the weakly bound complexes exist. Each channel includes weakly bound complexes and their related above‐mentioned systems. Moreover, each reaction channel contains two transition states. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T13) is significantly higher than that of internal rotation (T23) between syn‐ and anti‐FCO2H (or FCO2H…NR3) structures. However, the above‐mentioned T13 can significantly decrease its energy by adding the third molecule NH3 or NR3 (R?H or CH3). The more CH3 that is substituted in NR3 of the reaction channel, the lower the activation energy of the transition state in the system is affected. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 相似文献
108.
Russell G. Ross 《Journal of inclusion phenomena and macrocyclic chemistry》1990,8(1-2):227-233
The thermal conductivity and the heat capacity per unit volumec
p
have been measured for the urea-hexadecane inclusion compound using the transient hot-wire method. Measurements were made under isobaric conditions at a pressure of 0.1 GPa and in the temperature range of 100–300 K. There was evidence for a phase transition at a temperature of about 160 K, in reasonable agreement with previous work. For the high-temperature phase was independent of temperature within ±1%. The low-temperature phase showed a weak temperature dependence, with (d In/d InT)
p
= –0.13. It was inferred that interaction between acoustic phonons and low-frequency vibrational excitations of the guest molecules made a major contribution to the thermal resistivity. For the quantityc
p
a weak maximum was observed in the region of the phase transition temperature.Dedicated to Dr D. W. Davidson in honor of his great contributions to the sciences of inclusion phenomena. 相似文献
109.
110.
病态分析体系有偏估计的研究 总被引:3,自引:0,他引:3
运用广义岭估计和Liukejian提出的有偏估计,对病态分析体系进行了数值模拟和实际光度测定,结果表明,广义岭估计显优于最小二乘估计,Liukejian法有功效,可和为解析病态分析体系的化学计量学方法。 相似文献