Portion-wise addition

In a small dry flask, fitted with a short reflux condenser and a calcium chloride or cotton wool guard tube, place 0 4 g. of dry magnesium turnings, a minute crystal of iodine and a solution of 1 ml. (or 0 01 mol) of the alkyl halide in 10-15 ml. of anhydrous ether. If the reaction does not start immediately (as indicated by the disappearance of the iodine colour), warm for a short period in a beaker of warm water allow the reaction to proceed spontaneously, moderating it if necessary by immersing the flask in cold water. When the reaction has ceased, decant the nearly clear liquid from any solid material into another flask, and fit the reflux condenser into it. Add, portion-wise, through the condenser a solution of 0 - 5 ml. of phenyl- or a-naphthyl-isocyanate in 15 ml. of anhydrous ether, shaking the flask after each addition. AUow the mixture to stand for 10 minutes and then add 30 ml. of hydrochloric acid drop wise and with vigorous shaking and cooling in ice. (Alternatively, pour the reaction mixture cautiously into 20 ml. of ice water containing 1 ml. of concentrated hydrochloric acid, and shake the mixture well.) Transfer to a separatory funnel, shake well, then discard the lower aqueous layer. Dry the ethereal solution with a little anhydrous magnesium sulphate and distil oflF the ether. Recrystallise the residue methyl alcohol, ethyl alcohol, petroleum ether, ether or hot water are suitable recrystallisation solvents.  [c.291]

Waving lotions frequently are formulated with a number of additives with the intention of enhancing the efficacy and the aesthetics of the process. Thus surfactants of the nonionic type are used to improve the wetting of hair and penetration, a hydrogen bond breaking agent such as urea [57-13-6] is added to intensify the swelling of hair, ammonium sulfate [7783-20-2] is used to decrease sweUing, and latex emulsions and polyacrylates are employed as opacifiers. Conditioning materials used include mineral oil [8012-95-1J, lanolin [8020-84-6] and hydrolyzed protein the addition of cationic polymers has been patented (56,57). Perfuming of the thioglycolate lotions, although essential and desirable, is very difficult as the odor of the mercaptan is augmented by the unpleasant smell of the reduced hair. The latter is particularly evident in the case of sulfite lotions which are usually odorless.  [c.459]

The economic disposal of oilseed meal presents a problem for almost every new oilseed. The large-volume oilseeds such as soy and peanut are particularly valuable because their oilseed meals contain large amounts of protein, which can be used almost direcdy for animal or even human food (see Feeds AND feed additives). Many oilseeds contain toxic or other undesirable materials complicating use. For example, the crambe seed contains toxic and allergenic substances that must be removed before being fed to monogastric animals. A large part of the research on crops and oilseeds is devoted to upgrading the seed meal once the oil has been obtained by conventional pressing and solvent extraction methods. The seeds may be cooked first to release the oil. Cooking is often by direct contact with steam.  [c.449]

A molecular dynamics simulation consists of numerically solving the equations of motion of a set of particles (atoms), given the forces on the particles. Classical MD simulations that solve Newton s equations of motion generate trajectories belonging to the microcanonical [constant number of particles, volume, and energy (NVE)] statistical mechanical ensemble. It is generally desirable to perfonn simulations in other ensembles such as the isobaric-isothermal ensemble (constant NPT). In addition to being the natural choice for correspondence with typical experimental conditions, the NPT ensemble is useful for validating force fields by checking their ability to reproduce important structural parameters known from experimental measurements, such as the surface area per lipid, the interlamellar spacing, and the membrane thickness, and for predicting these quantities when they are not known (e.g., in membrane-protein systems). Constant pressure and temperature are enforced in simulations by controlling the fluctuations of the particle kinetic energy and system volume, respectively, and there are various ways to do this. The best algorithms, in terms of their ability to rigorously generate the NPT ensemble, are based on the extended system approach [46], in which additional dynamic variables are introduced, for example a time-dependent friction coefficient ( thermostat ) to control the temperature and a piston to control the pressure. The equations of motion and a conserved energy are consistently formulated so that the microcanonical distribution function for the extended phase space gives the isobaric-isothermal distribution function for the particles after integration over the additional dynamic variables [47].  [c.470]

Hydrogen as it occurs in nature is predominantly composed of atoms in which the nucleus is a single proton. In addition, terrestrial hydrogen contains about 0.0156% of deuterium atoms in which the nucleus also contains a neutron, and this is the reason for its variable atomic weight (p. 17). Addition of a second neutron induces instability and tritium is radioactive, emitting low-energy particles with a half-life of 12.33 y. Some characteristic properties of these 3 atoms are given in Table 3.1, and their implications for stable isotope studies, radioactive tracer studies, and nmr spectroscopy are obvious.  [c.34]

Consequently, a series of virtual sources is generated. These sources are distributed along the reflecting surface of the flaw, locating the surface to within the resolution of one Fresnel zone. In addition, the actual distribution of the sources along the reflecting surface indicate whether the reflector is spherical and smooth, or flat and sharp-edged. As shown in Figure 3 a rounded reflector generates a center-weighted virtual source distribution. This is essentially a specular reflection that is stronger at the center of the flaw. In contrast pointed edges, as are found in cracks, reflect strongly by diffraction, and the virtual source distribution for such defects is edge-weighted (Figure 4). Note that in both cases the method can only measure the portion of the flaw surface that reflects into the receiving transducer - this is particularly significant for a rounded flaw, for which only a small portion of the flaw surface reflects into the transducer (Figure 3).  [c.165]

Proteins are clearly not homopolymers because many energy scales are required to characterize tire polypeptide chain. Besides tire excluded volume interactions and hydrogen bonds tire potential between tire side chain depends on tire nature of tire residues [1]. Therefore, as a caricature of proteins tire heteropolymer model is a better approximation. A convenient limit is tire random heteropolymer for which approximate analytic treatments are possible [11]. In a random heteropolymer tire interactions between tire beads are assumed to be randomly distributed. Some of tire interactions are attractive (which are responsible for conferring globularity to the chain) while otliers are repulsive and tliese residues are better accommodated in an extended confonnation. In proteins water is a good solvent for polar residues while it is a poor solvent for hydrophobic residues. (In a good solvent contacts between tire monomer and solvent are favoured whereas in a poor solvent tire monomers are attracted to each otlier.) Because only 55% of tire residues in proteins are hydrophobic it is clear tliat in a typical protein energetic fmstration plays a role. In addition because of chain connectivity tliere is also topological fmstration. This arises because residues tliat are proximal tend to fonn stmctures on short-lengtli scales. The assembly of such short-lengtli scale stmctures would typically be incompatible witli tire global fold giving rise to topological fmstration. Even if energetic fmstrations are eliminated a polypeptide chain (in fact any biomolecule) is topologically fmstrated [7].  [c.2644]

If proteins are so full of internal near-constraints , we may take the analysis even a step further and investigate whether the protein is built from building blocks that can be approximated as rigid bodies. If there are n rigid building blocks, there are at most 6(n— 1) internal degrees of freedom, most of which are likely to be additionally constrained. Recently Hayward [142, 143] has devised an automatic procedure that detects rigid bodies and characterizes the mutual motion of each pair, given at least two different conformations of the protein. These conformations can either be obtained from X-ray data, or from an essential dynamics analysis of a MD simulation.  [c.24]

The remarkable achievement of this work is that such a simple additivity scheme can reproduce a quantitative value for such a complicated process as the binding of a ligand to its protein receptor, which involves a series of events such as desolvation of the ligand and of the protein from water molecules, conformational changes in the ligand and the protein, and alignment of functional groups in the ligand with binding sites in the protein.  [c.327]

For biomolecular systems, the protein under consideration is placed in the center of a box of explicitly defined water molecules. This box is normally regular (all angles are equal to 90", but other geometries, e.g., a truncated octahedron, can be used also) and surrounded by its periodic images. Therefore, the box of real water molecules no longer has a border with the vacuum, which reduces related artifacts and additionally improves the bulk properties of the simulated solvent. To conserve the number of atoms (i.e., the total mass) in the system, a water molecule leaving the real box must be added again. One very important condition for periodic boundary calculation is that an atom of the real molecule must not interact with another real atom and its image at the same time (minimum image convention). For that reason, spherical cutoffs for the non-bonding interactions shotild be defined which have to be smaller than half the smallest box dimension.  [c.366]

The impetus for this secorrd edition is a desire to include some of the new techniques that have emerged in recent years and also extend the scope of the book to cover certain areas that were under-represented (even neglected) in the first edition. In this second volume there are three topics that fall into the first category (density functional theory, bioinformatics/protein structure analysis and chemoinformatics) and one main area in the second category (modelling of the solid state). In addition, of course, a new edition provides an opportunity to lake a critical view of the text and to re-organise and update the material. Thus whilst much remains from the first edition, and this second book follows much the same path through the subject, readers familiar with the first edition will find some changes which I hope they will agree are for the better.  [c.11]

The probable mechanism of this change is first proton addition to one oxygen atom of the pinacol to give (I), which loses water to give the carbonium ion (II). I he group R then migrates to give the isomeric ion (III), which loses a proton, giving the pinacolone (IV ).  [c.152]

For purification, transfer the acid to a 150 ml. flask containing 60 ml. of water, boil the mixture under reflux, and then add acetic acid in 5 ml. portions down the condenser until almost all the solid has dissolved avoid an excess of acetic acid by ensuring that the solvent action of each addition is complete before the next portion is added. A small suspension of insoluble impurity may remain. Add 2 g. of animal charcoal, boil the solution again for 10-15 minutes, and then filter it through a preheated Buchner funnel. Cool and stir the filtrate, which will deposit pale cream-coloured crystals of the acid. Collect as before and if necessary repeat the recrystallisation. Yield of pure acid, 9 g. m.p. 227-229°.  [c.201]

Aminoazobenzene is a very weak base, and consequently it will not form salts with weak organic acids, such as acetic acid, although it will do so with the strong mineral acids, such as hydrochloric acid. Aminoazobenzene is a yellowish-brown compound, whilst the hydrochloride is steel blue. The colour of the latter is presumably due to the addition of the proton to the phenyl-N-atom, the cation thus having benzenoid and quinonoid forms  [c.208]

In a 2 litre bolt-head flask, equipped with an efficient mechanical stirrer, place 60-5 g. (50 ml.) of pure nitrobenzene and a solution of 30 g. of ammonium chloride in 1 litre of water. Stir vigorously and add 75 g. of a good quality zinc powder (about 90 per cent, purity) in small portions over a period of 5 minutes. The main reaction occurs about 5 minutes after the addition and the temperature rises. When the temperature reaches about 65°, add enough ice to the weU-stirred mixture to reduce the temperature to 50-55°. Filter the solution through a Buchner funnel twenty minutes after the first portion of zinc powder was introduced wash the zinc oxide residues with 600-700 ml. of boiling water.  [c.630]

Hydrogenation of styrene oxide over palladium in methanol 66 gives exclusively 2-phenylethanol, but in buffered alkaline methanol the product is l-phenylelhanol. If alcoholysis of the epoxide by the product is troublesome, the problem can be eliminated by portion-wise addition of the epoxide to the reaction, so as always to maintain a high catalyst-to-substrate ratio. The technique is general for reactions in which the product can attack the starting material in competition with the hydrogenation.  [c.139]

Conjugate acid (Section 1 13) The species formed from a Brpnsted base after it has accepted a proton Conjugate addition (Sections 1010 and 1812) Addition reaction in which the reagent adds to the termini of the con jugated system with migration of the double bond synony mous with 1 4 addition The most common examples include conjugate addition to 1 3 dienes and to a 3 unsaturated car bonyl compounds  [c.1279]

Dispersing agents such as sodium salts of polymerized alkylarenesulfonates [9084-06-4] or [8061-51-6] are surface-active agents which only weakly reduce the surface tension. Wetting agents such as sodium lauryl sulfate [151 -21 -3] more strongly reduce surface tension. Dispersing agents are used when a large quantity of surface area must be treated with surfactant without the mixture entrapping bubbles wetting agents are used to adjust the amount of fabric penetration or the flow of the latex mixture. Thickeners are used to prevent the settling of additives and can be organic polyelectrolytes or inorganic smectites [12199-37-0]. CoUoidal stabilizers such as casein are also used but are falling into disfavor because of the desire to avoid protein which can cause anaphylactic shock in sensitive individuals. Various antifoams prevent air entrapment and preservatives help avoid growth of microbes that could create slime or odors (see Industrial antimicrobialagents). Once formulated with additives, the mbber article is formed by adding acid-generating geUants to natural mbber or calcium nitrate [10124-37-5] to polychloroprene.  [c.228]

Although the role of vitamin K in blood clotting has cleady been demonstrated and involves carboxylation of multiple proteins in addition to prothrombin and includes factor VII, factor IX, and factor X, proteins containing Gla residues have been found in other tissues. For example, in 1975, Hauschka isolated an EDTA-soluble protein fraction of chick bones and identified the presence of Gla (84). Additional work sequenced the protein, which was called bone Gla protein or osteocalcin (85). The properties of the protein and its function in bone mineralisation have been extensively studied (86,87). However, its specific function is not completely understood. In addition, vitamin K-dependent carboxylase activity has been observed in cell cultures. For example, a vitamin K-dependent protein has been identified in a screen for growth arrest specific gene products. This protein, Gas6, has been identified as  [c.156]

Figure 2.20. NMR spectra of trans-and c/s-4-fert-butylcyclohexanol (23a and 23b) [(CD3)2CO, 25 °C, 400 MHz for H, 100 MHz for C]. (a) H decoupled NMR spectrum (NOE suppressed, comparable signal intensities) (b) H NMR spectrum (c) section of (b) (Sh = 3-4) with integrals (d) partial spectrum (c) following D2O exchange. The integrals (c) and the signal intensities (a) give the trans cis isomer ratio 71 29. Proton 1-H (Sh = 3.40) in the trans isomer 23a forms a triplet (10.8 Hz, two anti protons in 2,2 -positions) of quartets (4.3 Hz, two syn protons in 2,2 -positions and the OH proton as additional coupling partner) following D2O exchange a triplet (10.8 Hz) of triplets (4.3 Hz) appears, because the coupling to OH is missing. In the cis isomer 23b proton 1-H forms a sextet (3.0 Hz, four synclinal protons in 2,2 -positions and OH) which appears as a quintet following D2O exchange because the coupling to OH is then lost Figure 2.20. NMR spectra of trans-and c/s-4-fert-butylcyclohexanol (23a and 23b) [(CD3)2CO, 25 °C, 400 MHz for H, 100 MHz for C]. (a) H decoupled NMR spectrum (NOE suppressed, comparable signal intensities) (b) H NMR spectrum (c) section of (b) (Sh = 3-4) with integrals (d) partial spectrum (c) following D2O exchange. The integrals (c) and the signal intensities (a) give the trans cis isomer ratio 71 29. Proton 1-H (Sh = 3.40) in the trans isomer 23a forms a triplet (10.8 Hz, two anti protons in 2,2 -positions) of quartets (4.3 Hz, two syn protons in 2,2 -positions and the OH proton as additional coupling partner) following D2O exchange a triplet (10.8 Hz) of triplets (4.3 Hz) appears, because the coupling to OH is missing. In the cis isomer 23b proton 1-H forms a sextet (3.0 Hz, four synclinal protons in 2,2 -positions and OH) which appears as a quintet following D2O exchange because the coupling to OH is then lost
The attachment of the cyclopentapeptide lactone rings to the carboxy functions at C-1 and C-9 of the actinocin heterocycle B can be deduced from the HMBC plot d Protons 1-H (S = 7.35) and 8-// ([c.247]

Typical medical adhesives are highly compliant in order to minimize the risk for mechanical skin irritation and to maximize wet-out. At the same time, the materials are chosen to be cleanly removable from the skin surface even after extended wear. Traditional medical tapes used cloth backings with natural rubber-based adhesives. Due to limited breathability, and especially the irritation of certain skin types, these rubber-based adhesives have been increasingly replaced with synthetic adhesives. Since natural rubber is not tacky by itself, adhesives have to be compounded with anti-oxidants and tackifiers. Natural rubber also contains a protein, which can trigger severe allergenic response in certain people. The presence of small molecules like stabilizers, curatives, plasticizers and tackifiers has been of significant concern in the formulation of a PSA for skin contact. For this reason, inherently tacky polymers like silicones, polyisobutylenes, polyvinylethers and especially acrylics have become the standard PSAs used against skin. Acrylic PSAs have the additional benefit that they can be formulated to obtain a wide range of properties without compromising their excellent skin adhesion. For example, by choosing more hydrophilic formulations, the moisture vapor transmission rate of  [c.526]

The zinc. salts of these acids are extensively used as additives to lubricating oils to improve their extreme-pressure properties. The compounds also act as antioxidants, corrosion inhibitors and detergents. Short-chain dialkyl dithiophosphates and their sodium and ammonium salts are used as flotation agents for zinc and lead sulfide ores. The methyl and ethyl derivatives (RO)2P(S)SH and (RO)2P(S)CI are of particular interest in the large-scale manufacture of pesticides such as parathion, malathion, dimethylparathion, etc. For example parathion. which first went into production as an insecticide in Germany in 1947. is made by the following reaction sequence  [c.509]

Toluene is mixed with a haloid combination of butane and boiled with addition of chloride or bromide of aluminium. Water is added to the product and it is then distilled with steam, and that portion which distils over at a temperature between 170° and 200° C. is taken and treated with fuming nitric acid and fuming sulphuric acid. The resulting product is washed with water and crystallised from alcohol.  [c.288]

Toluene is mixed with a haloid combination of butane and boiled with addition of chloride or bromide of aluminium. Water is added to the product and it is then distilled with steam, and that portion which distils over at a temperature between 170° and 200° C. is taken and treated with fuming nitric acid and fuming sulphuric acid. The resulting product is washed with water and crystallised from alcohol.  [c.288]

Most samples require some initial ex situ preparation before insertion into a vacuum chamber [45]. A bulk single crystal must first be oriented [48], which is usually done with back-reflection Laue x-ray diffraction, and then cut to expose the desired crystal plane. Samples are routmely prepared to be within +1° of the desired orientation, but an accuracy of+1/4° or better can be routinely obtained. Cutting is often done using an electric discharge machine (spark cutter) for metals or a diamond saw or slurry drill for semiconductors. The surface must then be polished. Most polishing is done mechanically, with alumina or diamond paste, by polishing with finer and finer grits until the finest available grit is employed, which is usually of the order of 0.5 pm. Often, as a final step, tlie surface is electrochemically or chemi-mechanically polished. In addition, some samples are chemically reacted in solution in order to remove a large portion of the oxide layer that is present due to reaction with the atmosphere. Note that tliis layer is referred to as the native oxide.  [c.302]

The methods have in turn launched the new fields of nanoscience and nanoteclmology, in which the manipulation and characterization of nanometre-scale structures play a crucial role. STM and related methods have also been applied with considerable success in established areas, such as tribology [2], catalysis [3], cell biology [4] and protein chemistry [4], extending our knowledge of these fields into the nanometre world they have, in addition, become a mainstay of surface analytical laboratories, in the worlds of both academia and industry.  [c.1676]

The temi ellipsometry was first coined by Rothen in 1945 [25] to refer to the measurement of thm films of materials by monitoring the light reflected from them at some incident angle 0. The method is illustrated in figure Bl.26.9. The teclmique was used extensively before this [26], In the simplest case, the film is transparent with refractive index n, such that light can be reflected or transmitted at the first interface. The transmitted beam propagates tlirough the material and is reflected from the substrate. The reflected portion of the beam can either subsequently reflect from the fihn/air interface or reflect once again into the film and undergo fiirtlier reflections. The multiple beams are eventually emitted together so that, in general they are attenuated and one of the parameters that can most simply be measured is the reflectivity of the fihn. In addition, because of the phase shifts that occur because of path length differences as the beam passes tlirough the film, there is also a change of the phase of this beam which depends on the film thickness d and the wavelengdi of the light, X. The way in which this phase change can be measured will be described below. Each of these values, that is, the reflectivity and the phase shift, depend on the polarization of tire radiation (see below). Wlien the light is polarized parallel to the surface it is said to be s polarized and when it is  [c.1878]

Natural proteins are made up of twenty amino acid residues. An important question, from the perspective of protein design, is how many distinct types of residues are required for protein-like behaviour Such a selection cannot be made arbitrarily because in natural proteins one should have polar, hydrophobic, and charged residues. In addition, for optimal packing of the core, hydrophobic residues with different van der Waals radii may be required. To explore the potential simplification of the number of residues Wang and Wang [27] have carried out a highly significant study using lattice models and standard statistical potentials for the contact interaction elements B-j (C2.5.1). They discovered that a grouping of amino acid residues into five categories mimics the folding behaviour found using the standard twenty residues. To demonstrate this they used a cubic lattice with A = 27 and mostly focused on the maximally compact stmctures as ground states. Thus, stmctures such as ones given in figure C2.5.6 are not explicitly considered. Nevertheless, the demonstration that a suitable set of five amino acid residue types is sufficient is an important result which should have implications for the protein design problem—the generation of primary sequences that can fold to a chosen target folded stmcture.  [c.2658]

To prove this, we eonsider the following three regions (see Fig. 3) In the first region, designated ai2, is located the main portion of the interaction, t]2, between states 1 and 2 with the point of the conical intersection at Ci2. In the second region, designated as a23, is located the main portion of the interaction, t23, between states 2 and 3 with the point of the conical intersection at C23. In addition, we assume a thud region, ctq, which is located in-between the two and is used as a buffer zone. Next, it is assumed that the intensity of the interactions due to the components of t23 in On and due to ti2 in a23 is 0. This situation can always be achieved by shrinking ai2(cT23) toward its corresponding center Ci2(C23). In cto, the components of both ti2 and I23 may be of arbitrary magnitude but no conical intersection of any pair of states is allowed to be there.  [c.669]

The second discussion point is how the actual quantum system is to be described should one follow the time evolution of the time-dependent Schrodinger equation (TDSE) that allows mixed states to evolve, or should one insist on selecting a pure state, taking care of (sudden) transitions between states by some additional action in order to satisfy the time evolution of probabilities of states as dictated by the TDSE The former approach was followed, among others, by Bala et al. in wave packet dynamics applied to proton transfer in phospholipase A2 [109,110] and by us in the Density Matrix Evolution (DME) method which describes the mixed time-dependent wave function on asimple, appropriately chosen, basis set. [105, 111, 112, 113,114, 106, 115]. DME is obviously not capable of giving a correct response of the classical environment to quantum transitions, but is perfectly able to describe initial late processes or quantum systems that only weakly influence their environment. In fact, DME is the common method used in the evolution of nuclear spin magnetization [116]. The latter approach has led to the surface hopping method pioneered by Pechukas [117], with a modern formulation by Tully [118]. The basic idea is that the dynamics of a pure quantum state is followed, simultaneous with the classical dynamics of the environment. At every step the probability of a transition to another quantum state is calculated and such transitions are realized on a stochastic basis. When a transition is made, velocities are scaled to conserve total energy. The method has been  [c.17]

This section summarizes the results of a study of internal hydration of protein molecules, based on a very simple approach, in which only the intermolecular energy of protein and ligand was considered, and also describes the Dowser tool that was developed as a result of that study [37]. Water molecules inside cavities in proteins constitute integral parts of the structure. In most of the filled cavities, the internal water molecules are held with two or more hydrogen bonds, while cavities without hydrogen bonding groups on the surface are empty. Due to experimental error and interpretative uncertainty of electron density maps, internal water positions cannot always be unequivocally assigned the problem is worse for structures determined at lower resolution. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating the energy of introducing a water molecule into a cavity, using the known structure of the protein and standard molecular mechanics energies. In a survey of a number of proteins, it was found that a threshold value of the water-protein interaction energy at -12 kcal/mol distinguished hydrated from empty cavities. In one instance of two independent crystallographic determinations of the same structure [2, 24], we were able to conclude on the basis of these energies and additional crystallographic information (occupancy and B-factor) that in one structure many more buried water sites had been assigned than were, in fact, physically present.  [c.136]

TINKER is a modular molecular modeling package designed for molecular mechanics, dynamics, and several other energy-based structural manipulation calculations. The software in its actual version is distributed with several parameter sets AMBER94/96, CHARMM27, MM2 1991), MM3(2000), OPLS-AA, and OPLS-UA), which makes it an ideal tool for their comparison on the investigation system. In addition, the authors are actively developing their own protein force field (also called TINKER) which is based on polarizable atomic multipole electrostatics [20]. In the actual release, only the TINKER parameters for the polarizable water model are included. According to the authors, this model is "equal or better to the best available water models for many bulk and cluster properties [21]. Worth mentioning is the large number of modules provided for tasks like potential surface scanning, global optimization, solvent treatment, normal mode analysis, and many  [c.350]

The Ewald method has been widely used to study highly polar or charged systems. Its use is considered routine for many types of solid-state materials. It is increasingly used foi calculations on much larger molecular systems, such as proteins and DNA, due both tc the increases in computer performance and to the new methodological advances we have just discussed [Darden et al. 1999]. For example, an early application of the peirticle-mesl Ewald method was the molecular dynamics simulation of a crystal of tlie protein bovine pancreatic trypsin inhibitor [York et al. 1994]. The full crystal environment was reproduced with four protein molecules in the unit cell, together with associated water molecules anc chloride counterions. Over the course of the 1 ns simulation the deviation of the simulated structures from the initial crystallographic structure was monitored. Once equilibrium was achieved this deviation (measured as the root-mean-square positional deviation) settled down to a value of 0.63 A for all non-hydrogen atoms and 0.52 A for the backbone atoms alone. By contrast, an equivalent simulation run with a 9 A residue-based cutoff showed e deviation of more than 1.8 A. In addition, the atomic fluctuations calculated from the Ewald simulation were in close agreement with those derived from the crystallographic temperature factors, unlike the non-Ewald simulation, which was significantly overestimated due to the use of the electrostatic cutoff. The highly cheirged nature of DNA makes it particularly important to deal properly with the electrostatic interactions and simulations using the particle-mesh Ewald approach are often much more stable, with the trajectories remaining much closer to the experimental structures [Cheatham et al. 1995].  [c.353]

A wide variety of problems have been studied using the finite difference Poisson-Boltzmann (FDPB) method. In addition to the numerical values that the method can provide, significant insights can often be gleaned by graphical examination of the electrostatic potential around the molecule [Honig and Nicholls 1995]. It is often found that the electrostatic potential around a protein calculated using the FDPB method differs significantly from that obtained with a uniform dielectric model. The location of the charged and polar groups in the protein and the shape of the molecule (which determines the shape of the boundary between the regions of high and low dielectric) significantly influence the shape of the potential. Tliis  [c.622]

Add 2 g. of anthracene and 1 g. maleic anhydride to 25 ml. of dry xylene, and boil the mixture under reflux during the early stages of the heating, keep the mixture gently shaken until a clear solution is obtained, otherwise a portion of the reagents may adhere to the base of the flask and darken because of local overheating. After boiling for 20 minutes, cool the solution, when the addition product will rapidly crystallise. Filter at the pump, and drain well. (Yield of crude material, which is almost pure, ca, 2-7 g.) Recrystallise from about 50 ml. of xylene with the addition if necessary of a small quantity of animal charcoal filter the solution through a small preheated funnel, as the solute rapidly crystallises as the solution begins to cool. Place the recrys-  [c.292]

Method A (Friedel and Crafts reaction). Assemble an apparatus (1) consisting of a 500 ml. round-bottomed flask, a two-way addition tube (Fig. II, 1, 8, c) and a reflux condenser (see Fig. II, 13, 9 but with the separatory funnel replaced by a well-fitting cork) attach a water trap to the top of the condenser to absorb the hydrogen chloride produced in the reaction (compare Figs. Ill, 28, 1 and II, 8, 1). Place 38 -5 g. (35 ml.) of redistilled benzyl chloride and 150 ml. of dry benzene (see Section IV,2, Note 1) in the flask. Weigh out 12 g. of anhydrous aluminium chloride (Section IV,2, Note 2) into a dry-stoppered test-tube with the minimum exposure to the atmosphere. Cool the flask in a bath of crushed ice and add about one-fifth of the aluminium chloride. Shake the mixture a vigorous reaction will set in within a few minutes and hydrogen chloride will be evolved. When the reaction has subsided, add a further portion of the aluminium chloride and repeat the process until all has been introduced. The mixture should be kept well shaken and immersed in a freezing mixture during the addition. Finally reflux the mixture on a water bath for 30 minutes. Allow to cool. Cautiously add 100 g, of crushed ice, followed by 100 ml. of water in order to decompose the aliuninium complex. Shake the mixture well, transfer to a separatory funnel, and nm oflF the lower aqueous layer. Wash the upper layer  [c.513]

An alternative method of preparation consists in dissolving the aniline in 4 times its weight of glacial acetic acid in a beaker, and running in slowly from a tap funnel, while the solution is well stirred with a mechanical stiiTer, the theoretical amount of bromine dissolved in twice its volume of glacial acetic acid. The beaker should be cooled in ice during the addition as the reaction is exothermic. The final product (a pasty mass) should be coloured yellow by the addition of a little more bromine if necessary. Pour into excess of water, filter at the pump, wash well with water, press thoroughly, and dry. The yield of tribromoaniline, m.p. 119-120°, is quantitative. Recrystalli a small portion from methylated (or rectified) spirit m.p. 120°.  [c.579]

Place 20 -4 g. (20 ml.) of aniline in a 250 ml. conical or round-bottomed flask and cautiously add 74 g. (40 ml.) of concentrated sulphuric acid in small portions swirl the mixture gently during the addition and keep it cool by occasionally immersing the flask in cold water. Support the flask in an oil bath, and heat the mixture at 180-190° (fume cupboard) for about 5 hours (1). The sulphonation is complete when a test portion (2 drops) is completely dissolved by 3-4 ml. of ca. 2N sodium hydroxide solution without leaving the solution cloudy. Allow the product to cool to about 50° and pour it carefully with stirring into 400 g. of cold water or of crushed ice. Allow to stand for 10 minutes, and collect the precipitated sulphanilic acid on a Buchner funnel, wash it well with water, and drain. Dissolve the crude sulphanilic acid in the minimum volume of boiling water (450-500 ml.) if the resulting solution is coloured, add about 4 g. of decolourising carbon and boil for 10-15 minutes. Filter through a hot water funnel (Fig. 77, 7, 6) or through a Buchner funnel and flask which have been preheated by the filtration of boiling distilled water. Upon cooling, the sulphanilic acid dihydrate separates in colourless crystals. When the filtrate is quite cold, filter the crystals with suction, wash with about 10 ml. of cold water, and press thoroughly with a wide glass stopper. Dry between sheets of special absorbent paper or in a desiccator containing anhydrous calcium chloride in the latter case, the water of crystallisation (and hence the crystalline form) is lost. The yield of sulphanilic acid is 20-22 g. The substance does not melt sharply and no attempt should be made to determine the melting point the crystals are efflorescent.  [c.586]

See pages that mention the term Portion-wise addition : [c.205]    [c.359]    [c.371]    [c.562]    [c.568]    [c.211]    [c.257]    [c.379]    [c.603]    [c.616]   
Hydrogenation methods (1985) -- [ c.139 ]