Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Statistical-overlap theory for elliptical zones of high aspect ratio in comprehensive two-dimensional separations

The low prediction by statistical-overlap theory of the numbers of singlets and peaks in two-dimensional separations containing zones represented by either circles of small number or eccentric ellipses of any number is shown to result from use of probability expressions for unbound spaces of infinite extent. An exact theory is derived for the probability of singlet formation in a reduced two-dimensional space of unit length, width, and area. The probability is a weighted sum of the probabilities of singlet formation in the interior, edge, and corner regions of the space, which depend only on saturation. The weighting factors are the fractions of area associated with each region and depend on the number of zones, the aspect ratio, the saturation, and the ellipse's spatial orientation. The average numbers of doublets, triplets, and peaks in the space are approximated by combining these results with Roach's equations describing the clustering of circles in an unbound two-dimensional space. Simulations show that theory predicts the number of singlets, doublets, triplets, and peaks, when the number of zones is 25 or more, the aspect ratio is 100 or less, and the saturation is 2 or less. The relationship is derived between the aspect ratios of ellipses in the reduced space and actual separation space. Calculations are presented for comprehensive two-dimensional gas chromatography.     

Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals

Experimental and theoretical studies of electron densities and the corresponding derived entities such as electrostatic potentials have been the primary means of understanding the chemical nature and electronic properties of crystalline substances. Conventional crystal calculation methods such as the embedded cluster models are capable of performing calculations on small and medium-sized molecules, while periodic ab initio methods can treat crystals with up to 200 atoms per unit cell. A linear scaling method, viz. the molecular tailoring approach, has recently been developed for obtaining ab initio quality one-electron properties. In the present study, the molecular tailoring approach is employed to generate electron density, electrostatic potential and interaction density maps with the ibuprofen crystal as a test case. The interaction density and electrostatic potential maps produced in the present work succinctly bring out the actual crystalline environment around a given reference molecule by including the interactions with atoms in its neighborhood. The results obtained from the molecular tailoring approach may thus be expected to enhance our understanding of the environment in the crystalline material with reasonably small computational effort.Contribution to the Jacopo Tomasi Honorary Issue     

Growth of ramification-like ZnO rods in the presence of polyaniline

To obtain new materials with synergetic or complementary behaviors, polyaniline composite filled with ZnO rods in ramification-like structure was prepared by a hydrothermal approach. Comparative experiments of ZnO preparation in the presence of some metal ions were also carried out. The results indicated that the morphology of ZnO was strongly affected by the preparation condition. The method to grow ZnO rods in the presence of polyaniline offers a simple approach to obtain polyaniline composite filled with linear ZnO structure. The results of X-ray photoelectron spectroscopy show that the strong interaction between ZnO and polyaniline possibly exists to cause the charge transfer.     

Statistical treatment of proficiency testing data

 There are three stages to evaluating a laboratory's results in an interlaboratory proficiency test: establishing the correct result for the test item, determining an evaluation statistic for the particular result, and establishing an acceptable range. There are a wide variety of procedures for accomplishing these three stages and a correspondingly wide variety of statistical techniques in use. Currently in North America the largest number of laboratory proficiency test programs are in the clinical laboratory field, followed by programs for environmental laboratories that test drinking water and waste water. Proficiency testing in both of these fields is under the jurisdiction of the federal government and other regulatory and accreditation agencies. Many of the statistical procedures are specified in the regulations, to assure comparability of different programs and a fair evaluation of performance. In this article statistical procedures recommended in International Organization for Standardization Guide 43, Part 1, are discussed and compared with current practices in North America. Received: 22 April 1998 · Accepted: 12 May 1998     

Simple correction for perturbations of peak amplitudes in statistical models of overlap

Summary The application of statistical models of overlap (SMOs) to saturated separations is made possible by theory that addresses variable peak amplitudes. These amplitudes cause peak widths to vary, and this variation can be modeled by a random variable whose effect on the probability of overlap is expressed by a convolution integral. Modified probabilities of overlap are derived for both homogeneous and nonhomogeneous one-dimensional separations, and the new probabilities are compared to results determined from published computer simulations. The new theory can describe overlap at saturations that are 3 to 4 times larger than before. Previously reported experimental chromatograms are reinterpreted to show the capabilities of theory. The theoretical extension is an important step towards making SMOs into practical tools for screening analytical separations.     

To what extent can an uncertainty calculation be general?

 It is argued that results of uncertainty calculations in chemical analysis should be taken into consideration with some caution owing to their limited generality. The issue of the uncertainty in uncertainty estimation is discussed in two aspects. The first is due to the differences between procedure-oriented and result-oriented uncertainty assessments, and the second is due to the differences between the theoretical calculation of uncertainty and its quantication using the validation (experimental) data. It is shown that the uncertainty calculation for instrumental analytical methods using a regression calibration curve is result-oriented and meaningful only until the next calibration. A scheme for evaluation of the uncertainty in uncertainty calculation by statistical analysis of experimental data is given and illustrated with examples from the author's practice. Some recommendations for the design of corresponding experiments are formulated.     

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data

Single nucleotide polymorphism (SNP) arrays were used to detect chromosomal regions with DNA copy number alterations. Current statistical methods for microarray-based comparative genomic hybridization (array-CGH) analysis generally assume certain relationships among adjacent markers on the same chromosome, and these assumptions may be questionable. For an SNP-array-based CGH study, multiple normal reference SNP arrays were collected. In order to utilize these normal reference SNP arrays, we derived an empirical distribution of signal ratios for each SNP marker. With an assumed threshold value for the overall error rate control and the defined signal ratio ranges for chromosomal amplification and deletion, we proposed a procedure to identify chromosomal alteration regions based on several bootstrapped one-sample t-tests and the false discovery rate control. When we have multiple arrays for different individuals with the same disease, our method can also be used to detect SNP markers for chromosomal alteration regions that are common among these individuals. We applied our method to a published SNP array data set for breast carcinoma cell lines. For an individual with breast cancer, numerous chromosomal alteration regions were identified. Compared to results of previous studies, our method identified more chromosomal alteration regions, with some being implicated in the literature to harbor genes associated with breast cancer. For multiple cancer arrays, our results suggested the existence of common chromosomal alteration regions. However, a high proportion of false positives also indicated that genetic variations among different individuals with breast cancer can be present.     

Nonlinear Optical Properties of Tri—nuclear Transition Metal Clusters M—（μ—S）s—M′（M=Mo,W;M′=Cu,Ag,Au）

The static polarizabilities and the second-order hyperpolarizabilities of a series of tri-nuclear metal cluster models MS4(M′PPh3)2(M′PPh3)(M=Mo,W;M′=Cu,Ag,Au)have been calculated within the first-principle theoretical framework. The model clusters have two fragments of rhombic units and it is the charge ransfer from one of these moieties to the other that is responsible for nonlinear optical property. This kind of electronic delocaization, differentiated from that of planar π-system, is very interesting and is worthy for further investigation.     

Development of an Amperometric Sensor Highly Selective For Dopamine and Analogous Compounds Determination Using Bis(2,2′‐Bipyridil) Copper(II) Chloride Complex

The use of [Cu(bipy)₂]Cl₂?6H₂O as a biomimetic catalyst in the construction of an amperometric sensor for dopamine determination is reported. The sensor was prepared modifying a glassy carbon electrode with a Nafion membrane doped with [Cu(bipy)₂]Cl₂?6H₂O complex. The sensor presented a higher response in 0.25 mol L^?1 phosphate buffer solution (pH 7.0), with an applied potential of ?50 mV (vs. SCE). In the optimized operational conditions, a linear response range between 35 and 240 μmol L^?1, with a sensitivity of 2.02±0.07 nA l μmoL^?1 cm^?2 and detection limit of 8.0 μmol L^?1 were typically observed for the sensor. The response time presented for this sensor was 0.5 s, presenting the same response for at least 40 successive measurements, with good repeatability (3.0%) expressed as relative standard deviation for n=6. The difference of the response between four sensor preparations was 4%. A detailed investigation about the sensor response for other sixteen phenolic compounds and interfering species were carried out. The sensor was applied in the determination of dopamine in pharmaceutical preparation with success.