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排序方式: 共有2100条查询结果,搜索用时 46 毫秒
21.
Blaylock GT Bolton T Brown JS Bunnell KO Burnett TH Cassell RE Coffman D Cook V Coward DH Dorfan DE Dubois GP Eigen G Eisenstein BI Freese T Gladding G Grab C Heusch CA Hitlin DG Izen JM Köpke L Li A Lockman WS Mallik U Matthews CG Mir R Mockett PM Mozley RF Nemati B Odian A Parker J Parrish L Partridge R Pitman D Sadrozinski HF Scarlatella M Schalk TL Schindler RH Seiden A Simopoulos C Stockdale IE Stockhausen W Thaler JJ Toki W Tripsas B Villa F Wasserbaech S Wattenberg A Weinstein AJ 《Physical review letters》1987,58(21):2171-2174
22.
The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution. 相似文献
23.
Paolo Calvini Andrea Gorassini Giorgio Luciano Enrico Franceschi 《Vibrational Spectroscopy》2006,40(2):177-183
Cellulose paper (Whatman no.1, chromatographic grade) was oxidised with 0.1 M sodium metaperiodate at different oxidation levels (0–11 days at room temperature), and analysed with FTIR before and after chemical treatments (reduction, further oxidation, alkaline hydrolysis). The deconvolution of infrared data allowed us to verify that periodate oxidises cellulose in isolated domains, leading to the decrease of crystallinity, in agreement with the results of wide angle X-ray scattering (WAXS). In particular, the alkaline hydrolysis (β-alkoxy fragmentation) followed by mild acid treatment removed the oxidised groups and recovered most of the crystallinity of cellulose, as determined by the FTIR crystallinity index. 相似文献
24.
Celebre G De Luca G Longeri M Pileio G Emsley JW 《The Journal of chemical physics》2004,120(15):7075-7084
The proton NMR spectra of two (13)C-labeled isotopomers of styrene dissolved in two liquid crystalline solvents have been obtained and analyzed to yield four sets each of 24 dipolar couplings. These couplings were then used to investigate the structure of the ring and the ene fragments of the molecule, and the position of the maximum, phi(0), in the ring-ene bond rotational probability distribution. To do this, the effect on the dipolar couplings of small-amplitude vibrational motion was taken into account using vibrational wave functions calculated by molecular orbital and density functional methods. It is concluded that the NMR data are consistent with the ring fragment, averaged over the ring-ene rotation, planar, while the ene fragment is not. The value of phi(0) is found to be 18.0 degrees +/-0.2 degrees for the two solutions, compared with a value of 27 degrees calculated by the molecular method MP2/6-31G(*). 相似文献
25.
Talhout R Villa A Mark AE Engberts JB 《Journal of the American Chemical Society》2003,125(35):10570-10579
The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance. 相似文献
26.
Bolm C Verrucci M Simic O Cozzi PG Raabe G Okamura H 《Chemical communications (Cambridge, England)》2003,(22):2826-2827
Quinoline-based C1-symmetric sulfoximines have been used as chiral ligands in copper-catalyzed asymmetric hetero Diels-Alder reactions leading to cycloadducts with up to 96% ee. 相似文献
27.
Volonterio A Bellosta S Bravin F Bellucci MC Bruché L Colombo G Malpezzi L Mazzini S Meille SV Meli M Ramírez De Arellano C Zanda M 《Chemistry (Weinheim an der Bergstrasse, Germany)》2003,9(18):4510-4522
Partially modified retro- (PMR) and retro-inverso (PMRI) psi[NHCH(CF(3))]Gly peptides, a conceptually new class of peptidomimetics, have been synthesized in wide structural diversity and variable length by aza-Michael reaction of enantiomerically pure alpha-amino esters and peptides with enantiomerically and geometrically pure N-4,4,4-trifluorocrotonoyl-oxazolidin-2-ones. The factors underlying the observed moderate to good diastereocontrol have been investigated. The conformations of model PMR-psi[NHCH(CF(3))]Gly tripeptides have been studied in solution by (1)H NMR spectroscopy supported by MD calculations, as well as in the solid-state by X-ray diffraction. Remarkable stability of turn-like conformations, comparable to that of parent malonyl-based retropeptides, was evidenced, as a likely consequence of two main factors: 1) severe torsional restrictions about sp(3) bonds in the [CO-CH(2)-CH(CF(3))-NH-CH(R)-CO] module, which is biased by the stereoelectronically demanding CF(3) group and the R side chain; 2) formation of nine-membered intramolecularly hydrogen-bonded rings, which have been clearly detected both in CHCl(3) solution and in some crystal structures. The former factor seems to be more important, as turn-like conformations were found in the solid-state even in the absence of intramolecular hydrogen bonding. The relative configuration of the -C*H(CF(3))NHC*H(R)- stereogenic centers has a major effect on the stability of the turn-like conformation, which seems to require a syn stereochemistry. X-ray diffraction and ab initio computational studies showed that the [-CH(CF(3))NH-] group can be seen as a sort of hybrid between a peptide bond mimic and a proteolytic transition state analogue, as it combines some of the properties of a peptidyl -CONH- group (low NH basicity, CH(CF(3))-NH-CH backbone angle close to 120 degrees, C-CF(3) bond substantially isopolar with the C=O) with some others of the tetrahedral intermediate [-C(OX)(O(-))NH-] involved in the protease-mediated hydrolysis reaction of a peptide bond (high electron density on the CF(3) group, tetrahedral backbone carbon). 相似文献
28.
Correa NM Zorzan DH D'Anteo L Lasta E Chiarini M Cerichelli G 《The Journal of organic chemistry》2004,69(24):8231-8238
Kinetics of the reduction of 3-chloroacetophenone (CAF) with sodium borohydride (NaBH(4)) were followed by UV-vis spectroscopy at 27.0 degrees C in different reverse micellar media, toluene/BHDC/water and toluene/AOT/water, and compared with results in an isooctane/AOT/water reverse micellar system. AOT is sodium 1,4-bis-2-ethylhexylsulfosuccinate, and BHDC is benzyl-n-hexadecyl dimethylammonium chloride. The kinetic profiles were investigated as a function of variables such as surfactant and NaBH(4) concentration and the amount of water dispersed in the reverse micelles, W(0) = [H(2)O]/[surfactant]. In all cases, the first-order rate constant, k(obs), increases with the concentration of surfactant as a consequence of incorporating the substrate into the interface of the reverse micelles where the reaction takes place. The reaction is faster at the cationic interface than at the anionic one probably because the negative ion BH(4)(-) is part of the cationic interface. The effect of the external solvent on the reaction shows that reduction is favored in the isooctane/AOT/water reverse micellar system than that with an aromatic solvent. This is probably due to BH(4)(-) being more in the water pool of the toluene/AOT/water reverse micellar system. The kinetic profile upon water addition depends largely on the type of interface. In the BHDC system, k(obs) increases with W(0) in the whole range studied while in AOT the kinetic profile has a maximum at W(0) approximately 5, probably reflecting the fact that BH(4)(-) is part of the cationic interface while, in the anionic one, there is a strong interaction between water and the polar headgroup of AOT below W(0) = 5 and, above that, BH(4)(-) is repelled from the interface once the water pool has formed. Application of a kinetic model based on the pseudophase formalism, which considers the distribution of the ketone between the continuous medium and the interface and assumes that reaction takes place only at the interface, has enabled us to estimate rate constants at the interface of the reverse micellar systems. At W(0) < 10, it was considered that NaBH(4) is wholly at the interface and, at W(0) >/= 10, where there are free water molecules, also the partitioning between the interface and the water pool was taken into account. The results were used to evaluate CAF and NaBH(4) distribution constants between the different pseudophases as well as the second-order reaction rate constant of the reduction reaction in the micellar interface. 相似文献
29.
Depecker G Patino N Di Giorgio C Terreux R Cabrol-Bass D Bailly C Aubertin AM Condom R 《Organic & biomolecular chemistry》2004,2(1):74-79
A cyclic molecule including a hexameric PNA sequence has been designed and synthesized in order to target the TAR RNA loop of HIV-1 through the formation of a "kissing complex". For comparison, its linear analogue has also been investigated. The synthesis of the cyclic and linear PNA has been accomplished following a liquid-phase strategy using mixed PNA and fully N-protected (aminoethylglycinamide) fragments. The interactions of this cyclic PNA and its linear analogue with TAR RNA have been studied and the results indicate clearly that no interaction occurs between the cyclic antisense PNA and TAR RNA, whereas a tenuous interaction has been detected with its linear PNA analogue. 相似文献
30.
In this paper we propose a method for carrying out variational transition state theory calculations without first obtaining
a converged minimum-energy path (MEP). We illustrate the method in two ways, first of all by employing an unconverged MEP
and secondly by using a dynamically optimized distinguished reaction path. Preliminary tests of the algorithm for the reactions
OH+H2→H2O+H and C2H5→C2H4+H are very encouraging.
Received: 22 January 1997 / Accepted: 11 March 1997 相似文献