Tight‐binding molecular dynamics simulation of Si?H bond dissociation in silicon clusters

New model of Si? H bond dissociation is proposed and tested in the cluster Si₁₀H₁₆ by the simulation approach that combines classic molecular dynamics method and the self‐consistent tight‐binding electronic and total energy calculation one. It is shown that the monohydride Si? H bond is unstable with respect to silicon dangling bond and bend‐bridge Si? H? Si bond formation when this cluster traps the single positive charge and that hydrogen migrates through a path involving rather rotation around the Si? Si bond than the center of this bond (the bond‐centered position). These results can be useful for understanding hydrogen‐related phenomena at surfaces, interfaces, and internal voids of various hydrogenated silicon systems: electronic devices, silicon solar cells, and nanocrystalline and porous silicon. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 351–359, 2003     

希土离子(Ⅲ)与牛血清白蛋白的相互作用

在ｐＨ，６．３０，３７℃条件下，用离心超过滤法测定了１１种希土离子（Ⅲ）与牛血清白蛋白（ＢＳＡ）的专一性结合常数Ｋ３和非专一性结合常数Ｋｎｓ。并通过ＣＤ，ＵＶ，ＩＲ和荧光光谱研究了Ｔｂ（Ⅲ）和Ｅｕ（Ⅲ）与ＢＳＡ作用的机理。结果表明，Ｋ３和Ｋｎｓ分别与希土离子（Ⅲ）和二元，一元羧酸形成配合物的稳定常数随希土系列原子序数的变化规律相一致。结合部位分布在ＢＳＡ的亲水性表面，参与配位的基团只有谷氨酸，...     

Biocompatible polymers for antibody support on gold surfaces

The elimination or minimization of non-specific protein adsorption from serum is critical for the use of surface plasmon resonance (SPR) sensors for in vitro and in vivo analysis of complex biological solutions. The ultimate goals in this application are to minimize non-specific adsorption of protein and to maximize analyte signal. A reduction of the non-specific protein adsorption from serum of up to 73% compared to carboxymethylated-dextran 500 kDa (CM-dextran) was achieved following a survey of eight biocompatible polymers and 10 molecular weights of CM-dextran. These coatings minimize non-specific adsorption on the sensor while also serving as immobilization matrices for antibody fixation to the probes. Polymers including polysaccharides: CM-dextrans, CM-hyaluronic acid, hyaluronic acid, and alginic acid were investigated. Humic acid, polylactic acid, polyacrylic acid, orthopyridyldisuldfide–polyethyleneglycol–N-hydroxysuccinimide (OPSS–PEG–NHS), and a synthesized polymer; polymethacrylic-acid-co-vinyl-acetate (PMAVA) were also used. The non-specific protein adsorption reduction was measured over a 14 day period at 0 °C for each polymer. Calibration curves using some of these polymers were constructed to show the performance and low detection limit possibilities of these new antibody supports. For many of the polymers, this is the first demonstration of employment as an antibody support for an optical or surface active sensor. CM-dextran is the polymer offering the largest signal for the antigen detection. However, the biocompatible polymers demonstrate a greater stability to non-specific binding in serum. These biocompatible polymers offer different alternatives for CM-dextran.     

A theoretical study of the relative affinities of an aliphatic and an aromatic bisguanylhydrazone for the minor groove of double-stranded (dA-dT) n oligomers

The nonintercalative binding of an aliphatic and an aromatic bisguanylhydrazone (BGH) to the minor groove of double-stranded (dA-dT) _n oligomers is investigated by means of theoretical computations. The preferred binding arrangements of both BGHs are stabilized by a number of H-bonding interactions with sites O₂(T), N₃(A) and o₁ on the two strands, and require limited conformational rearrangements of the BGHs around their C-C single bonds. The intermolecular interaction energy is larger with the aliphatic BGH than with the aromatic one. The energy difference is, however, considerably reduced when the oligomer is lengthened: it passes from 16.1 kcal/mole at the heptamer level, to 7.9 kcal/mole at the undecamer level and to 4.6 kcal/mole when each strand of the undecamer is flanked with a complementary complete helical turn of phosphates, on both the 3 and 5 termini.The interaction energies of the BGHs with water molecules in the first hydration shell are, however, also larger with the aliphatic BGH, than with the aromatic BGH. This energy difference is further enhanced when one considers also the water molecules in the second shell. It becomes greater than the difference in the interaction energy of the two BGHs with (dA-dT) _n for large values of n. When the dehydration energy of BGHs is taken into account the overall energy balance is then more favorable for the interaction of the aromatic than of the aliphatic BGH with the polynucleotide. This last conclusion is in agreement with experimental results.     

Lipophilicity in PK design: methyl, ethyl, futile

Lipophilicity, often expressed as distribution coefficients (log D) in octanol/water, is an important physicochemical parameter influencing processes such as oral absorption, brain uptake and various pharmacokinetic (PK) properties. Increasing log D values increases oral absorption, plasma protein binding and volume of distribution. However, more lipophilic compounds also become more vulnerable to P450 metabolism, leading to higher clearance. Molecular size and hydrogen bonding capacity are two other properties often considered as important for membrane permeation and pharmacokinetics. Interrelationships among these physicochemical properties are discussed. Increasing size (molecular weight) often gives higher potency, but inevitably also leads to either higher lipophilicity, and hence poorer dissolution/solubility, or to more hydrogen bonding capacity, which limits oral absorption. Differences in optimal properties between gastrointestinal absorption and uptake into the brain are addressed. Special attention is given to the desired lipophilicity of CNS drugs. In examples using -blockers, Ca channel antagonists and peptidic renin inhibitors we will demonstrate how potency and pharmacokinetic properties need to be balanced.     

Novel Methods of Synthesis of Dibenzo[3n]crown-n and Their Cation Binding Studied by Fluorescence Spectroscopy. Part V

The dibenzo[3n]crown-n were synthesised starting from bis[2-(o-hydroxyphenoxy)ethyl]ether obtained from bis[2-(o-formylphenoxy)ethyl]ether via Baeyer-Villiger oxidation in H₂O₂/CH₃COOH in a good yield. The cyclic condensation ofbis[2-(o-hydroxyphenoxy)ethyl]etherwith tri- and tetraethylene glycol bisdichlorides andthe bisditosylate of pentaethylene glycol in DMF/Me₂CO₃ afforded the large cyclic ethers of dibenzo[21]crown-7, dibenzo[24]crown-8 and dibenzo[27]crown-9. The structures were analysed with IR, ¹H NMR, ¹³C NMR and low-resolution mass spectroscopy methods. The Na⁺, K⁺, Rb⁺ and Cs⁺ cations' recognition of the molecules were conducted withsteady-state fluorescence spectroscopy. The 1:1 association constants, K_a, in acetonitrile were estimated. Dibenzo[21]crown-7 was the best both for K⁺ and Rb⁺ binding but showed too small an effect on Cs⁺. Dibenzo[24]crown-8 exhibited the binding power in the order of Rb⁺ > K⁺ > Na⁺ > Cs⁺. However, dibenzo[27]crown-9 displayed marked binding with only K⁺ but not with Rb⁺ or with Cs⁺ cations probably due to the heavy atom effect of fluorescence quenching.     

Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors

An increasing number of docking/scoring programs are available that use different sampling and scoring algorithms. A reliable scoring function is the crucial element of such approaches. Comparative studies are needed to evaluate their current capabilities. DOCK4 with force field and PMF scoring as well as FlexX were used to evaluate the predictive power of these docking/scoring approaches to identify the correct binding mode of 61 MMP-3 inhibitors in a crystal structure of stromelysin and also to rank them according to their different binding affinities. It was found that DOCK4/PMF scoring performs significantly better than FlexX and DOCK4/FF in both ranking ligands and predicting their binding modes. Most notably, DOCK4/PMF was the only scoring/docking approach that found a significant correlation between binding affinity and predicted score of the docked inhibitors. However, comparing only those cases where the correct binding mode was identified (scoring highest among sampled poses), FlexX showed the best `fine tuning' (lowest rmsd) in predicted binding modes. The results suggest that not so much the sampling procedure but rather the scoring function is the crucial element of a docking program.     

Self-assembled metallocycles with two interactive binding domains

Five metallocycles 1 a-e have been self-assembled from S-shaped bispyridyl ligands 2 a-e and a palladium complex, [Pd(dppp)(OTf)(2)] (dppp=1,3-bis(diphenylphosphanyl)propane), and have been characterized by elemental analysis and various spectroscopic methods including (1)H NMR spectroscopy and electrospray ionization (ESI) mass spectrometry. These metallocycles all are monocyclic compounds, but can fold to generate two binding domains bearing hydrogen-bonding sites based on pyridine-2,6-dicarboxamide units. The binding properties of the metallocycles with N,N,N',N'-tetramethylterephthalamide (G) have been probed by means of ESI mass spectrometry and (1)H NMR spectroscopy. The results both in the gas phase and in solution are consistent with the fact that the metallocycles accommodate two molecules of the guest G. Thus, the ESI mass spectra clearly show fragments corresponding to the 1:2 complexes in all cases. (1)H NMR studies on 1 a and G support the formation of a 1:2 complex in solution; the titration curves are nicely fitted to a 1:2 binding isotherm, but not to a 1:1 binding isotherm. In addition, a Job plot also suggests a 1:2 binding mode between 1 a and G, showing maximum complexation at approximately 0.33 mol fraction of the metallocycle 1 a in CDCl(3). The binding constants K(1) and K(2) are calculated to be 1600 and 1400 M(-1) (+/-10 %), respectively, at 25 degrees C in CDCl(3), indicative of positively cooperative binding. This positive cooperativity was confirmed by the Hill equation, affording a Hill coefficient of n = 1.6. Owing to insufficient solubility in CDCl(3), for comparison purposes the binding properties of the metallocycles 1 b-e were investigated in a more polar medium, 3 % CD(3)CN/CDCl(3). (1)H NMR titrations revealed that the metallocycles all bind two molecules of the guest G with Hill coefficients ranging from 1.4 to 1.8. This positive cooperativity may be attributed to a structural reorganization of the second binding cavity when the first guest binds to either one of the subcavities present in the metallocycles.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.