Raccoon Bend field, Tex.


As an interesting footnote, Ceyer [291] has found that ethylene is hydrogenated by hydrogen absorbed in the bulk region just below a Ni(l 11) surface. In this case, the surface ethylenes are assumed to by lying flat, with the dissolved H atoms approaching the double bond from underneath.  [c.733]

The first term on the right of this equation is the average force from the adiabatic potential energy surfaces. The second term is a force due to the non-adiabatic coupling. This mean-field potential is inherent in the method. That it leads to practical problems can be seen by considering the case of a bound state coupled to a dissociative state. Non-adiabatic forces will cause the dissociative state to be populated. The mean-field force, however, gives a bound component to the experienced potential, which may prevent the trajectory from reaching the dissociative region. A discussion of this incorrect behavior is found in [199].  [c.292]

A useful device to prevent bumping of liquids during distillation consists of a glass tube, 2-3 mm. in diameter, bent in a U-form with one arm somewhat shorter than the other it should be long enough to extend from the bottom of the flask for a short distance into the neck in order that it should remain in an upright position (Fig. /, 3, 1, a). If for any reason a shorter U-tube is desired, a glass rod may be sealed on as in Fig. 1,3, 1, b. The short arm of the U-tube should be just above the level of the liquid in the flask, whilst the long arm should rest on the bottom of the flask just above the source of heat. With a large flask it is advantageous to employ two or three U-tubes, the short arm of one should be just above the fluid level at the start of the distillation the short arms of the other U-tubes should be of different lengths and below the initial level of the liquid.  [c.4]

The main reason for the deshielded nature of vinylic and aryl protons is related to the induced magnetic fields associated with tt electrons We saw earlier in Section 13 4 that the local field resulting from electrons in a C—H ct bond opposes the applied field and shields a molecule s protons The hydrogens of ethylene and benzene however he in a region of the molecule where the induced magnetic field of the tt electrons reinforces the applied field deshielding the protons (Figure 13 8) In the case of benzene this is described as a ring current effect that originates in the circulating tt electrons It has interesting consequences some of which are described in the boxed essay Ring Cur rents—Aromatic and Antiaromatic  [c.529]

In the plasma flame, much of the heating effect of the high-frequency electromagnetic field occurs in the outer skin of the flame, in common with all high-frequency electromagnetic heating. The hot electrons, ions, and neutrals mingle with cooler materials toward the center of the flame, and energy is transferred by conduction, convection, and radiation. The inner regions of the flame are somewhat cooler than the outer, but they are still very hot. At the center of the flame is a flow of cold argon gas carrying the sample, and it is the coolest region. At the outer periphery of the flame, coolant argon gas is used to prevent the very hot plasma from impinging on and melting the outer quartz tube. The rapidly flowing argon gas carries the really hot parts of the plasma beyond the ends of the concentric tubes so the latter do not become too hot. The three gas flows are shown on the diagram, together with an indication of the hotness of the flame in different regions. From hottest to coolest, the temperature ranges between 7000-8000 and 4000-5000 K, but these ranges depend a great deal on the actual conditions of argon gas flow and power input from the high-frequency field.  [c.90]

A typical interface is shown in Figure 14.2. The orifice in the sampler must be large enough to sample the center of the plasma flame while disturbing the plasma as little as possible. A diameter of about 1 mm is used normally, which is well in excess of the Debye length (A ) but not so large as to let too much plasma gas or even air into the interface region, as this would make it difficult to maintain a suitable vacuum behind the sampler. The Debye length is a measure of the width of the effective electric field of an ion and is given approximately by Equation 14.1, in which T is the electron temperature and is the number density of electrons (per milliliter).  [c.95]

In these equations, / q , Ffy C, andM represent the empirically adjusted constants associated with changes in bond lengths, angles, dihedrals, and nonbonded interactions. These terms plus 1. .. 3 nonbonded interactions, and cross-terms such as stretch—bend are considered in the most complex computational models as well as in the experimental force fields. Practically all of the early molecular mechanics force fields utilized force constants direcdy from vibrational spectroscopic studies (see background in Refs. 59 and 60). That is, for a particular interaction included in the force field, the force constant apphed to an interaction was one which had been experimentally determined. Although this method can be utilized, it is very difficult to develop a generalized force field for a broad spectmm of molecules, because not all experimental force fields are derived to the same level of accuracy, nor are they consistent, ie, having all force constants derived concurrently. For this reason AUinger (60) has suggested  [c.164]

The layers of the different polymers or resins may be combined in one of two ways. One is to use a combining block prior to the slot extmsion die. ParaUel openings within the block are fed from two or more extmders, one for each resin. The melts flow in laminar fashion through the die and onto the quench dmm. The film is processed conventionaUy or may then be oriented. Carefiil control of resin viscosity must be obtained to provide smooth flow, and the resins must be compatible in order to bond together properly. The second method uses a multimanifold die to bring the melt streams together within the die. This aUows use of resins with a wider difference in viscosity since fewer changes in flow patterns are necessary. Multimanifold dies may be flat or tubular. The most common types of coextmsion are AB, ABA, or ABC where A is one polymer system, B is another (of the same polymer type or different), and C is a third polymer type. Coextmsions of many, many layers lead to film products with a peadescent appearance. Where two polymers may not adhere sufficiendy, it is possible to extmde a tie or adhesive layer in the coextmsion. lonomer resins are often used as such tie layers.  [c.380]

I Junction Diode. Ap—n junction diode is formed when two adjacent areas of a single-crystal semiconductor are doped using opposite type impurities. At the junction interface, the carrier concentration gradient causes the majority carriers to diffuse across the junction where an equiUbrium is reached between the drift and diffusion of the carriers. This space charge region results in a built-in voltage typically on the order of the band gap energy of the semiconductor. This built-in field opposes the motion of the mobile majority carriers and bends the conduction and valence bands. An appHed forward bias, positive voltage on -type material, diminishes this barrier, allowing electrons to be injected from the / -region and holes from the -region. A forward bias nearly equivalent to the built-in potential is required to faciUtate appreciable injection, and consequently current flow through the diode (Eig. 2a).  [c.113]

Gravure inks, typically used for long press mns, are very fluid (low in viscosity) and dry by evaporation of solvent, leaving behind an ink film ca 10-p.m thick. Gravure inks are manufactured by milling dry pigment in the carrier system, consisting of volatile aromatic solvent, such as toluene, binders, and synthetic resins. Inks made by this procedure typically foUow the sequence of shot milling the concentrate at a high pigment level ranging from 25—35%, followed by thinning the concentrate with the addition of solvent, resin solution, and other additives. Gravure inks are also manufactured from dispersed pigment concentrates in the form of resin chips by dissolving them in the carrier solvent system. The bulk of gravure inks, however, are manufactured with dry pigment as a starting material (27,28).  [c.514]

Avalanche or tunnel breakdown occurs in the p—n junction for the large electric fields in the depletion region for sufftciendy large reverse bias. Increasing the doping on either side of the junction decreases the depletion width and lowers the avalanche breakdown voltage, although the actual breakdown field increases. As the electric field increases the slope of band energy with distance increases. When the distance between conduction and valence bands at constant band energy is <10 nm, electrons can tunnel from the valence to the conduction band. As shown in Figure 8, the energy barrier through which the electrons tunnel is essentially triangular, corresponding to Fowler-Nordheim tunneling. For doping levels >10 cm in siUcon the critical field for avalanche breakdown exceeds the threshold for tunneling and tunnel breakdown occurs. Junction avalanche breakdown can be useful because it can be nondestmctive. The junction breakdown voltage can be used as a reference voltage as in Zener diodes. Avalanche breakdown is also used for programming nonvolatile memories by hot-carrier injection. On the other hand, hot-carrier injection is a wear-out mechanism for MOSFETs.  [c.350]

A sequence of events taking place in the charge process has been described (16) demonstrating that during constant current charge, the surface double-layer region first produces a local interior space—charge field. As the semiconductor charge phase is extended into the interior, a distributed space—charge field is formed that is characterized by a combination of the semiconductor band stmcture and the mobiUty of dopant imperfections. When the state of charge increases, the magnitude of the space charge decreases. At the end of charge, there is only an ir (voltage) loss in the soHd, and the apphed field is mainly at the soHd electrolyte interface. If charging is continued until a steady-state oxygen evolution is attained, the distributed space charge disappears. The semiconductor is characterized by a flat band potential and, if the nickel electrode is left on open circuit, the space charge-field gradually decays through atom movements in the soHd phase, approximating a flat band potential condition.  [c.545]

The eadiest foamed graphite was made from exfoHated small crystals of graphite bound together and compacted to alow density (5—7). This type of foam is stmcturaHy weak and will not support loads of even a few newtons per square meter. More recently, carbon and graphite foams have been produced from resinous foams of phenoHc or urethane base by careful pyrolysis to preserve the foamed ceU stmcture in the carbonized state. These foams have good stmctural integrity, eg, a typical foam of 0.25 g/cm apparent density has a compressive strength of 9.3—15 MPa (1350—2180 psi) with thermal conductivity of 0.87 W/(m-K) at 1400°C. These properties make the foam attractive as a high temperature insulating packaging material in the aerospace field and as insulation for high temperature furnaces (see Insulation, thermal). Variations of the resinous-based foams include the syntactic foams where ceUular polymers or hoUow carbon spheres comprise the primary volume of the material bonded and carbonized in a resin matrix.  [c.527]

No less than 15 distinct chemical and physical mechanisms explain the various causes of color, ordered into five groups as in Table 3. In the first group, covered by quantum theory, there are incandescence, simple electronic excitations, and vibrational and rotational excitations. Most chemical compounds contain only paired electrons that requite very high energies to become unpaired and form excited energy levels this requites ultraviolet, hence there is no visible absorption and no color. Absorption color can, however, be derived from the easier excitation of unpaired electrons in transition-metal compounds and impurities, covered by ligand field theory in the second group. Absorptions from paired electrons can be shifted into the visible by increasing the size of the region over which the electrons are localized, as in organic compounds covered by molecular orbital theory in the third group this also explains various forms of charge transfer. In the fourth group there is color in metals and in semiconductors such as yellow cadmium sulfide, both pure and doped, covered by band theory this also covers color centers. In the final group there are four color-causing mechanisms explained by geometrical and physical optics.  [c.417]

In the region of laminar flow (Vr < 10), the same power is consumed by the impeller whether baffles are present or not, and they are seldom required The flow pattern may be affected by the baffles, but not always advantageously. When they are needed, the baffles are usually placed one or two widths radially off the tank wall, to allow fluid to circulate behind them and at the same time produce some axial deflection of flow.  [c.1628]

Inner shell. Just beneath the outer crust a brittle, black magnetite shell develops. The shell separates the region of high dissolved-oxygen concentration outside the tubercle from the very low dissolved-oxygen regions in the core and fluid-filled cavity below (Fig. 3.5). The shell is mostly magnetite and thus has high electrical conductivity. Electrons generated at the corroding floor are transferred to regions around the tubercle and to the shell, where cathodic reactions produce hydroxyl ion, locally increasing pH. Dissolved compounds with normal pH solubility, such as carbonate, deposit preferentially atop the shell where pH is elevated as in Reaction 3.2  [c.40]

With any iterative approach it is necessary to have convergence criteria in order to judge when to exit an iterative loop. In the case of the optimization of empirical force field parameters it is difficult to define rigorous criteria due to the often poorly defined and system-dependent nature of the target data however, guidelines for such criteria are appropriate. In the case of the geometries, it is expected that bond lengths, angles, and torsion angles of the fully optimized model compound should all be within 0.02 A, 1.0°, and 1.0° respectively, of the target data values. In cases where both condensed phase and gas-phase data are available, the condensed phase data should be weighted more than the gas-phase data, although in an ideal simation both should be accurately fit. It should be noted that, because of the harmonic nature of bonds and angles, values determined from energy minimization are generally equivalent to average values from MD simulations, simplifying the optimization procedure. This, however, is less true for torsional angles and for non-bond interactions, for which significant differences in minimized and dynamic average values can exist. With respect to vibrational data, generally a root-mean-square (RMS) difference of 10 cm or an average difference of 5% between the empirical and target data should be considered satisfactory. Determination of these values, however, is generally difficult, owing to problems associated with unambiguous assignment of the normal modes to the individual frequencies. Typically the low frequency modes (below 500 cm ) associated with torsional deformations and out-of-plane wags and the high frequency modes (above 1500 cm ) associated with bond stretching are easy to assign, but significant mixing of different angle bending and ring deformation modes makes assignments in the intermediate range difficult. What should be considered when optimizing force constants to reproduce vibrational spectra is which modes will have the greatest impact on the final application for which the parameters are being developed. If that final application involves MD simulations, then the low frequency modes, which involve the largest spatial displacements, are the most important. Accordingly, efforts should be made to properly predict both the frequencies and assignments of these modes. For the 500-1500 cm region, efforts should be made to ensure that frequencies dominated by specific normal modes are accurately predicted and that the general assignment patterns are similar between the empirical and target data. Finally, considering the simplicity of assigning stretching frequencies, the high frequency modes should be accurately assigned, although the common use of the SHAKE algorithm [95] to constrain covalent bonds during MD simulations, especially those involving hydrogens, leads to these modes often having no influence on the results of MD simulations.  [c.32]

The emergence of hybrid quantum mechanical-molecular mechanical (QM-MM) methods in recent years addresses this problem. Pioneering studies of this type were made by Warshel and Levitt [6]. The method entails the division of the system of interest into a small region that is treated quantum mechanically, with the remainder of the system treated with computationally less expensive classical methods. The quantum region includes all the atoms that are directly involved in the chemical reaction being studied, and the remainder of the system, which is believed to change little during the reaction, is treated with a molecular mechanics force field [7]. The atoms in each system influence the other system tlirough a coupled potential that involves electrostatic and van der Waals interactions [8-18]. Several molecular mechanics programs have been adapted to perform hybrid QM-MM simulations. In the majority of the implementations the quantum region has been treated either by empirical valence bond methods [19] or with a semiempirical method (usually AMI [20]). These implementations have been applied, for example, to study solvation [12,21], condensed phase spectroscopy [22], conformational flexibility [23], and chemical reactivity in solution [24,25], in enzymes [18,26-36], and in DNA [37].  [c.222]

In the RISM-SCF theory, the statistical solvent distribution around the solute is determined by the electronic structure of the solute, whereas the electronic strucmre of the solute is influenced by the surrounding solvent distribution. Therefore, the ab initio MO calculation and the RISM equation must be solved in a self-consistent manner. It is noted that SCF (self-consistent field) applies not only to the electronic structure calculation but to the whole system, e.g., a self-consistent treatment of electronic structure and solvent distribution. The MO part of the method can be readily extended to the more sophisticated levels beyond Hartree-Fock (HF), such as configuration interaction (Cl) and coupled cluster (CC).  [c.421]

An approach between a continuum model and an explicit solvation model is the Langevin dipole method, introduced by Warshel and Levitt [20, 21]. In the region beyond the solvent-accessible surface of the molecule, a grid of rotatable point dipoles is defined these represent the dipoles of the solvent molecules, which are not explidtly present. By using the Langevin equation (not shown), the size and direction of each dipole Pi can be determined, considering the fact that the electric field at each dipole has contributions from the solute and all other dipoles present in the system. The free energy of Langevin dipoles can be calculated according to Eq. (40)  [c.365]

Experimental data for mass transfer into gas streams agree approximately with Eq. (5-306) when the Schmidt number is close to unity and in smooth, straight tubes or along flat plates when the pressure drop is due entirely to sldn fric tion against the surface. It does not, however, agree for cases involving Torm drag as well as sldn friction. Also, it does not account for the mass-transfer resistance of the region of fluid near the liquid or solid boundaiy in which mass transfer occurs principally by molecular (as opposed to turbulent) motion.  [c.625]

An example of a PES apparatus is shown in Figure A3.5.3. A PES apparatus consists of (a) an ion source, (b) a fixed-frequency laser, (c) an interaction region, (d) an electron energy analyser and (e) an electron detector. Ion sources include gas discharge, sputtermg, electron-impact and flowing afterglow. The laser may be cw (tlie argon-ion laser operated at 488 mn is connnon) or pulsed (which allows frequency doubling etc.). Recent trends have been toward UV laser light because the negative ions of importance in practical chemistry (e.g., atmospheric chemistry and biochemistry) tend to be strongly bound and because the more energetic light allows one to access more electronic and vibrational states. The interaction region may include a magnetic field that routes detached electrons toward the energy analyser. The energy analyser is either a hemispherical electrostatic device or a time-of-flight energy analyser the latter is especially suited to a pulsed-laser system.  [c.802]

The total depth of focus is the sum of both. It mcreases with the wavelength of the light, depends on the numerical aperture and the magnification of the microscope. For X = 550 mn, a refractive index of 1 and a numerical aperture of 0.9, the depth of focus is in the region of 0.7 pm with a numerical aperture of 0.4 it increases to about 5 pm. Fligh-resolution objectives exclude the observation of details in the axial direction beyond their axial resolution. This is tnie for conventional microscopy, but not for scaiming confocal microscopy, since optical sectioning allows successive layers in the bulk to be studied. Similarly, the field of view decreases with increasing resolution of the objective in conventional microscopy, whereas it is independent of resolution in scaiming microscopy.  [c.1660]

In those instances in which the bond angle is very strongly deformed, the usual expansion of the potential energy function to a cubic or quartic equation can improve the fit to the actual bending energy, but, in MM3, it has been found expedient to define entirely new atom types with entirely new parameter sets. For example, the C—C—C angles in cyclopropane (60°) or cyclobutene (90°) are distorted beyond the limit of the quadratic expressions for bending of sp carbon atoms. Bending in cyclopropane is outside the range of even the cubic and quartic equations. Carbon atoms in cyclopropane and cyclobutene are given special atom type numbers (22 and 57, respectively, in the MM3 force field) and treated as though they have no relation to the sp carbon atom, which, energetically, they do not. For this reason, there are more than a dozen atom type numbers for the single element carbon in MM3. Carbon is unique in having so many atom type numbers because carbon is unique in the number of chemical combinations it enters into. In general, force fields are constmcted with an eye to achieving the greatest simplicity consistent with chemical reality and new atom types are admitted only grudgingly.  [c.117]

Another topic of heated debate comprised the extent of water penetration into the hydrocarbon interior Small-angle neutron scattering studies have resolved tliis matter by indicating tliat significant water penetration into the micellar core is unlikely " . However, at the interface, extensive contact between water and the hydrocarbon chain segments definitely occurs. The headgroups of the micelle are extensively hydrated. For ionic micelles, a large fraction of the counterions are located in the vicinity of the headgroups. These counterions normally retain their first hydration shell . The part of the surfactant that contains the hea(%roups and a variable fraction of the counterions is called the Stem region. This region comprises an appreciable electric field and a high concentration of ions (several molar) at the interface between the nonpolar interior and tire aqueous exterior of the micelle and can be expected to exhibit unique properties. For pyridinium iodides the polarity of this region has been probed with the aid of the interionic charge transfer band characteristic for these species. The results indicate a somewhat reduced polarity of tire Stem region compared to bulk water ". The important role of this region in solubilisation and micellar catalysis is reviewed in the next sections.  [c.127]

The primary photochemical act, subsequent to near-uv light (wavelengths <400 nm) absorption by Ti02 particles, is generation of electron—hole pairs where the separation (eq. 3) into conduction band electrons (e g ) and valence band holes (/lyB ) faciUtated by the electric field gradient in the space charge region. Chemically, the hole associated with valence band levels is constrained at  [c.403]

There are many materials, especially organic and metal-organic materials, which exhibit tme thermochromism, with a variety of sometimes debatable stmctural transition mechanisms it is difficult to summarize the whole with any continuity. For this reason, an effort is made to delineate the scope of the field by listing several thermochromic transitions (Table 1). Selected thermochromic material examples are accompanied in each instance by the corresponding transition stimulus for that case. Characteristically sharp transition temperatures, are indicated where appropriate. At the other extreme are examples of comparatively gradual transitions, associated for example with an equiUbrium or a changing bandwidth. The sharpness of the transition is one aspect by which the several mechanisms could be classified. On the other hand, it is useful also to group materials into metal-complex, inorganic, and organic classes. In this way, the variety of therm ochromic changes in each of the three material classes can easily be realized.  [c.170]

Resin Cements. Early resin cements formed by free radical polymerization, available since 1952, were based primarily on poly(methyl methacrylate) [9011-14-7] and its monomer (100). Relatively rapid setting times, high polymerization shrinkage, and difficulty of removing excess hardened cement from the interproximal spaces and from beneath free gingival margins are principal deficiencies of this type of resin cement (see Methacrylic polymers). More recent resin cements are based on high molecular weight, fluid, di- and multifunctional methacrylates, some containing relatively high loadings of fillers, such as fine glass powders.  [c.475]

The measurement of detergency can be approached from two different poiats of view. The theoretical approach is concerned with the relative quantity of soil bound to the substrate before and after washing. In this case, measurement is a necessary analytical procedure ia the study of the detergency mechanism. The second approach emphasizes the development of reproducible laboratory methods that predict the results of practical cleaning operations. In the development of new household-cleaning compositions, for example, the formulator must know whether his products outperform others under actual use conditions. ReaUsm, or accuracy as it is usually termed, is a prime requisite of any detergency test. It means good correlation between laboratory evaluation and the results of field testing. The practical field evaluation is usually made on the basis of specifications, sometimes implied rather than exphcitiy expressed, that determine whether or not the cleaning results were satisfactory. In removing spinning lubricants from wool yams, for example, the most satisfactory cleaning procedure is that which removes most soil from the substrate. In certain metal-cleaning operations, however, the satisfactory outcome is a piece of metal free of soHd soil but carrying an even and easily perceivable layer of mst-preventive oil. In judgiag the cleanness of white fabrics, more iaterest is usually shown ia fabric whiteness rather than ia its actual soil content. Thus, most detergency evaluations ia which white fabric is the substrate specify cleanness ia terms of fabric whiteness or reflectance.  [c.536]

See Figure 6.7(b). The tnaehine now operates in a constitnt h.p. region. The frequency is raised but the voltage is kept constant at its rated value (as it should not be raised beyond rated). I he flux will diminish while / and also /,r will remain almost the same. The torque therefore reduces so that the h.p. developed remains almost a constant (h.p. T.N). This is also known as the field-  [c.105]

Surface treatments such as earburising or nitriding give hard surface layers, which give good wear and fatigue resistance. In carburising, a steel component is heated into the austenite region. Carbon is then diffused into the surface until its concentration rises to 0.8% or more. Finally the component is quenched into oil, transforming the surface into hard martensite. Steels for nitriding contain aluminium when nitrogen is diffused into the surface it reacts to form aluminium nitride, which hardens the surface by precipitation hardening. More recently ion implantation has been used foreign ions are accelerated in a strong electric field and are implanted into the surface. Finally, laser heat treatment has been developed as a powerful method for producing hard surfaces. Here the surface of the steel is scanned with a laser beam. As the beam passes over a region of the surface it heats it into the austenite region. When the beam passes on, the surface it leaves behind is rapidly quenched by the cold metal beneath to produce martensite.  [c.155]

Figure 5 Continuum reaction field approaches for electrostatic free energies, (a) A two-step approach. The mutation introduces a positive charge near the center of a protein (shown in tube representation). The mutation in the fully solvated protein (left) is decomposed into two steps. Step I The mutation is performed with a finite cap of explicit water molecules (shown m stick representation) the system is otherwise suirounded by vacuum. Step II The two finite models (before and after mutation) are transferee into bulk solvent, treated as a dielectric continuum. The transfer free energy is obtained from continuum electrostatics. (From Ref. 25.) (b) Molecular dynamics with periodic boundary conditions on-the-fly reaction field calculation. One simulation cell is shown. For each charge q, interactions with groups within are calculated in microscopic detail everything beyond is viewed as a homogeneous dielectric medium, producing a reaction field on [55], The mutation is introduced using MD or MC simulations. As shown, for many of the charges the medium beyond r E is not truly homogeneous, being made up of both solvent and solute groups, (c) Spherical boundary conditions with continuum reaction field [56], The region within the sphere (large circle) is simulated with MD or MC and explicit solvent the region outside is treated as a dielectric continuum, which produces a reaction field on each charge within the sphere. If the sphere IS smaller than the protein (as here), the outer region is heterogeneous and the reaction field calculation IS rather difficult. Figure 5 Continuum reaction field approaches for electrostatic free energies, (a) A two-step approach. The mutation introduces a positive charge near the center of a protein (shown in tube representation). The mutation in the fully solvated protein (left) is decomposed into two steps. Step I The mutation is performed with a finite cap of explicit water molecules (shown m stick representation) the system is otherwise suirounded by vacuum. Step II The two finite models (before and after mutation) are transferee into bulk solvent, treated as a dielectric continuum. The transfer free energy is obtained from continuum electrostatics. (From Ref. 25.) (b) Molecular dynamics with periodic boundary conditions on-the-fly reaction field calculation. One simulation cell is shown. For each charge q, interactions with groups within are calculated in microscopic detail everything beyond is viewed as a homogeneous dielectric medium, producing a reaction field on [55], The mutation is introduced using MD or MC simulations. As shown, for many of the charges the medium beyond r E is not truly homogeneous, being made up of both solvent and solute groups, (c) Spherical boundary conditions with continuum reaction field [56], The region within the sphere (large circle) is simulated with MD or MC and explicit solvent the region outside is treated as a dielectric continuum, which produces a reaction field on each charge within the sphere. If the sphere IS smaller than the protein (as here), the outer region is heterogeneous and the reaction field calculation IS rather difficult.
An alternative approach to the link atom method is to use the frozen orbital approach developed by Rivail and coworkers [56] (the local self-consistent field, LSCF). The continuity of the electron density at the boundary region is maintained by a frozen orbital along the bond between the quantum and classical atoms. This frozen orbital is derived from calculaitons on model compounds, with the assumption that the orbitals from model compounds are transferable to the enzymatic system. A more generalized fonn of this implementation was presented by Gao et al. [57], in which a set of hybrid orbitals are used at the boundary region [this method is termed the generalized hybrid orbital (GHO) method by the authors]. The set is divided into auxiliary and active orbitals and acts as a basis set for the boundary atoms of the MM fragment. The active orbitals are optimized along with other orbitals on the QM atoms in the SCF cycle. In essence this method is an expansion of the approach of Rivail but has the advantage that the oribitals do not need to be parametrized for each specific problem.  [c.227]

The field of QM-MM simulations of chemical reactions has grown considerably from the initial proposals of Warshel and Levitt [6] in the 1970s to a technique that can now deliver quantitatively accurate reaction pathways for reactions in the active sites of enzymes. Currently, the computational chemist has several options for treatment of the quantum region. Which method is employed in any given simation is dependent on a number of factors. The computational expense of the density functional and ab initio methods dictate studies using these methods need to be carried out on parallel computers. Naturally, these methods are more accurate for studying the chemistry of the process under consideration, and in the case of metalloenzymes with transition metals it is almost essential to use density functional methods. Nonetheless, it is possible to get quantitative accuracy with semiempirical QM-MM studies, particularly when the quantum atoms and the van der Waals parameters are parametrized for the specific reaction at hand. Additionally, semiempirical QM-MM methods allow a dynamic study of the chemical reaction, which is currently beyond the higher level methods, even with parallel computers. The field continues to expand, and it is to be expected that advances in the speed of the quantum calculations, the accuracy of the treatment of the quantum/classical boundary region, and computational speed will come over the next decade and enable further insight to be gained into the mechanisms of biochemical processes.  [c.234]

Figure 10.14 Schematic diagrams of the DNA-binding zinc cluster region of the GAL4 subunit, (a) The zinc cluster contains two zinc atoms each bound to four cysteine residues, two of which bridge the zinc atoms. The diagram illustrates the number of amino acids in the loop regions between the cysteine ligands, (b) Richardson-type diagram of the DNA-binding region. The red region provides the sequence-specific DNA interactions. The zinc cluster stabilizes the structure to give the proper fold for DNA binding. Figure 10.14 Schematic diagrams of the DNA-binding zinc cluster region of the GAL4 subunit, (a) The zinc cluster contains two zinc atoms each bound to four cysteine residues, two of which bridge the zinc atoms. The diagram illustrates the number of amino acids in the loop regions between the cysteine ligands, (b) Richardson-type diagram of the DNA-binding region. The red region provides the sequence-specific DNA interactions. The zinc cluster stabilizes the structure to give the proper fold for DNA binding.

See pages that mention the term Raccoon Bend field, Tex. : [c.618]    [c.287]    [c.1572]    [c.2222]    [c.2368]    [c.444]    [c.521]    [c.631]    [c.109]    [c.35]    [c.145]    [c.349]    [c.360]    [c.261]    [c.108]    [c.169]   
Sourse beds of petroleum (1942) -- [ c.4 , c.399 ]