Molecular information

Since the early 20th century, chemists have represented molecular information by molecular models. The human brain comprehends these representations of graphical models with 3D relationships more effectively than numerical data of distances and angles in tabular form. Thus, visualization makes complex information accessible to human understanding easily and directly through the use of images. 

The investigation of molecular structures and of their properties is one of the most fascinating topics in chemistry. Chemistry has a language of its own for molecular structures which has been developed from the first alchemy experiments to modem times. With the improvement of computational methods for chemical information processing, several descriptors for the handling of molecular information have been developed and used in a wide range of applications. 

The most common application of dynamic SIMS is depth profiling elemental dopants and contaminants in materials at trace levels in areas as small as 10 pm in diameter. SIMS provides little or no chemical or molecular information because of the violent sputtering process. SIMS provides a measurement of the elemental impurity as a function of depth with detection limits in the ppm—ppt range. Quantification requires the use of standards and is complicated by changes in the chemistry of the sample in surface and interface regions (matrix efiects). Therefore, SIMS is almost never used to quantitadvely analyze materials for which standards have not been carefiilly prepared. The depth resoludon of SIMS is typically between 20 A and 300 A, and depends upon the analytical conditions and the sample type. SIMS is also used to measure bulk impurities (no depth resoludon) in a variety of materials with detection limits in the ppb-ppt range. 

Dynamic SIMS is used to measure elemental impurities in a wide variety of materials, but is almost new used to provide chemical bonding and molecular information because of the destructive nature of the technique. Molecular identihcation or measurement of the chemical bonds present in the sample is better performed using analytical techniques, such as X-Ray Photoelectron Spectrometry (XPS), Infrared (IR) Spectroscopy, or Static SIMS. 

SALI compares fiivorably with other major surface analytical techniques in terms of sensitivity and spatial resolution. Its major advantj e is the combination of analytical versatility, ease of quantification, and sensitivity. Table 1 compares the analytical characteristics of SALI to four major surfiice spectroscopic techniques.These techniques can also be categorized by the chemical information they provide. Both SALI and SIMS (static mode only) can provide molecular fingerprint information via mass spectra that give mass peaks corresponding to structural units of the molecule, while XPS provides only short-range chemical information. XPS and static SIMS are often used to complement each other since XPS chemical speciation information is semiquantitative however, SALI molecular information can potentially be quantified direedy without correlation with another surface spectroscopic technique. AES and Rutherford Backscattering (RBS) provide primarily elemental information, and therefore yield litde structural informadon. The common detection limit refers to the sensitivity for nearly all elements that these techniques enjoy. 

LIMS is primarily used in failure microanalysis applications, which make use of its survey capability, and its high sensitivity toward essentially all elements in the periodic table. The ability to provide organic molecular information on a microanalyt-ical scale is another distinctive feature of LIMS, one that is likely to become more important in the future, with improved knowledge of laser desorption and ionization mechanisms. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

One example of such constructive cross talk can be found in the growing literature on quantitative structure-pharmacokinetic relationships (QSPKR). Reports on how to predict pharmacokinetics from molecular information, or how to link pharmacokinetic parameters with molecular features, have appeared in both the pharmacokinetic [61] and the toxicological [62] literature. Others are extending this to pharmacodynamics as well [63], and the approaches look promising. 

The Volta potential is defined as the difference between the electrostatic outer potentials of two condensed phases in equilibrium. The measurement of this and related quantities is performed using a system of voltaic cells. This technique, which in some applications is called the surface potential method, is one of the oldest but still frequently used experimental methods for studying phenomena at electrified solid and hquid surfaces and interfaces. The difficulty with the method, which in fact is common to most electrochemical methods, is lack of molecular specificity. However, combined with modem surface-sensitive methods such as spectroscopy, it can provide important physicochemical information. Even without such complementary molecular information, the voltaic cell method is still the source of much basic electrochemical data. 

Lehn, J. M. (1990) Perspective in supramolecular chemistry - from molecular recognition towards molecular information-processing and selforganization. Angew. Chem. Int. Ed., 29, 1304-1319. 

It has been proposed that local anesthetics pass nerve membrane by neutral species despite the clinical adminsitration of the cationic form. Experimental molecular information is required for a better understanding of the mechanism. Thus the NMR information can be useful to the anesthetic discharging in membranes. 

The development of experimental methods over the last 50 years has been at the forefront of new strategies that emerged, driven by the need to obtain molecular information relevant to the structure of catalyst surfaces and the dynamics of surface reactions. The ultimate aim was in sight with the atomic resolution that became available from STM, particularly when this was coupled with chemical information from surface-sensitive spectroscopies. 

To a computer scientist, VS is nothing but another text mining, only the bits and bytes stored that contain molecular information adopt a format quite different from natural language and without adequate warning cannot be quickly interpreted. It is not that modem day text does not contain text that is not natural language, but that they are adequately flagged and do not stop the NLP software. For example,... 

Mass spectrometry can be specific in certain cases, and would even allow on-line QA in the isotope dilution mode. MS of molecular ions is seldom used in speciation analysis. API-MS allows compound-specific information to be obtained. APCI-MS offers the unique possibility of having an element- and compound-specific detector. A drawback is the limited sensitivity of APCI-MS in the element-specific detection mode. This can be overcome by use of on-line sample enrichment, e.g. SPE-HPLC-MS. The capabilities of ESI-MS for metal speciation have been critically assessed [546], Use of ESI-MS in metal speciation is growing. Houk [547] has emphasised that neither ICP-MS (elemental information) nor ESI-MS (molecular information) alone are adequate for identification of unknown elemental species at trace levels in complex mixtures. Consequently, a plea was made for simultaneous use of these two types of ion source on the same liquid chromatographic effluent. 

Raman microscopy has the ability to investigate regions down to 1 pm, and, by the aid of fibre optics, remote sampling is possible. The molecular information... 

An interesting feature of polarized IR spectroscopy is that rapid measurements can be performed while preserving molecular information (in contrast with birefringence) and without the need for a synchrotron source (X-ray diffraction). Time-resolved IRLD studies are almost exclusively realized in transmission because of its compatibility with various types of tensile testing devices. In the simplest implementation, p- and s-polarized spectra are sequentially acquired while the sample is deformed and/or relaxing. The time resolution is generally limited to several seconds per spectrum by the acquisition time of two spectra and by the speed at which the polarizer can be rotated. Siesler et al. have used such a rheo-optical technique to study the dynamics of multiple polymers and copolymers [40]. 

Although many questions are still open, peptide nucleic acids are easier to synthesize via simple reaction routes than is natural RNA. The PNAs have another important advantage they are achiral and uncharged, i.e., they contain no chiral centres in the polymeric backbone (see Sect. 9.4). Unfortunately, however, they do not fulfil all the necessary conditions for molecular information storage and transfer. Thus, the search for other possible candidates for a pre-RNA world continues. 

It has long been realised that infrared (IR) spectroscopy would be an ideal tool if applied in situ since it can provide information on molecular composition and symmetry, bond lengths and force constants. In addition, it can be used to determine the orientation of adsorbed species by means of the surface selection rule described below. However, IR spectroscopy does not possess the spatial resolution of STM or STS, though it does supply the simplest means of obtaining the spatially averaged molecular information. 

DI-MS using El was applied to the characterisation of natural substances in ancient adhesives to obtain molecular information on these substances in order to identify them [19]. DI-MS has considerable potential for extending the knowledge of the various natural resources used by prehistoric people for making adhesives. 

Computer simulations of confined polymers have been popular for several reasons. For one, they provide exact results for the given model. In addition, computer simulations provide molecular information that is not available from either theory or experiment. Finally, advances in computers and simulation algorithms have made reasonably large-scale simulations of polymers possible in the last decade. In this section I describe computer simulations of polymers at surfaces with an emphasis on the density profiles and conformational properties of polymers at single flat surfaces. 

In the first part of this paper several novel approaches to the alignment problem of second-order nonlinearity will be presented. The molecular information which guided and motivated these efforts, and others described in this symposium, derives from third-order nonlinear optical experimentation (EFISH and others). In the second... 

AG(E)2468>. The application of distinct self-assembly processes to form grid-type and double-helical structures has potential in understanding and controlling molecular information an interesting discussion has been presented <00CEJ2103>. 

Protein molecular organization on solid matrices has intensively been explored in various manners. Although most of these researchers have not paid attention on retainment of protein functions, this chapter focuses on artificially designed protein organizates which are capable of molecular recognition and molecular information transduction. 

Molecular communication is the characteristic information system in the bioinformation networks. The endocrine system, which is one of intermolecular information networks, may represent the feature of molecular communication. The gland is a collection of specialized cells that synthesize, store, and release hormones. A hormone, molecular information, is released into the extracellular fluid and transported via the blood to two types of cells target cells where the hormone acts, and other cells that degrade the hormone as schematically presented in Fig.l. In some systems the target cell and the degradation site are in the same organ or even the same cell. Both activities may even be located on the same plasma membrane. The receptor for the hormone is located on the surface of the plasma membrane. 

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