For macromolecules

Most LB-forming amphiphiles have hydrophobic tails, leaving a very hydrophobic surface. In order to introduce polarity to the final surface, one needs to incorporate bipolar components that would not normally form LB films on their own. Berg and co-workers have partly surmounted this problem with two- and three-component mixtures of fatty acids, amines, and bipolar alcohols [175, 176]. Interestingly, the type of deposition depends on the contact angle of the substrate, and, thus, when relatively polar monolayers are formed, they are deposited as Z-type multilayers. Phase-separated LB films of hydrocarbon-fluorocarbon mixtures provide selective adsorption sites for macromolecules, due to the formation of a step site at the domain boundary [177]. 

Kremer K and Binder K 1988 Monte Carlo simulations of lattice models for macromolecules Comp. Phys. Rep. 7 259... 

D. E. Humphreys, R. A. Friesner, and B. J. Berne. A multiple-time-step molecular dynamics algorithm for macromolecules. J. Phys. Cfiem., 98(27) 6885-6892,... 

Wisdom, J. The Origin of the Kirkwood Gaps A Mapping for Asteroidal Motion Near the 3/1 Commensurability. Astron. J. 87 (1982) 577-593 Tuckerman, M., Martyna, G. J., Berne, J. Reversible Multiple Time Scale Molecular Dynamics. J. Chem. Phys. 97 (1992) 1990-2001 Tuckerman, M., Berne, J. Vibrational Relaxation in Simple Fluids Comparison of Theory and Simulation. J. Chem. Phys. 98 (1993) 7301-7318 Humphreys, D. D., Friesner, R. A., Berne, B. J. A Multiple-Time Step Molecular Dynamics Algorithm for Macromolecules. J. Chem. Phys. 98 (1994) 6885-6892... 

Humphreys D D, R A Friesner and B J Berne 1994. A Multiple Time-step Molecular Dynami Algorithm for Macromolecules. Journal of Physical Chemistry 98 6885-6892. 

AMBER was first developed as a united atom force field [S. J. Weiner et al., J. Am. Chem. Soc., 106, 765 (1984)] and later extended to include an all atom version [S. J. Weiner et al., J. Comp. Chem., 7, 230 (1986)]. HyperChem allows the user to switch back and forth between the united atom and all atom force fields as well as to mix the two force fields within the same molecule. Since the force field was developed for macromolecules, there are few atom types and parameters for small organic systems or inorganic systems, and most calculations on such systems with the AMBER force field will fail from lack of parameters. 

Unconstrained optimization methods [W. H. Press, et. al.. Numerical Recipes The Art of Scientific Computing, Cambridge University Press, 1986, Chapter 10] can use values of only the objective function, or of first derivatives of the objective function, second derivatives of the objective function, etc. HyperChem uses first derivative information and, in the Block Diagonal Newton-Raphson case, second derivatives for one atom at a time. HyperChem does not use optimizers that compute the full set of second derivatives (the Hessian) because it is impractical to store the Hessian for macromolecules with thousands of atoms. A future release may make explicit-Hessian methods available for smaller molecules but at this release only methods that store the first derivative information, or the second derivatives of a single atom, are used. 

Laue Method for Macromolecule X-Ray Diffraction. As indicated above it is possible to determine the stmctures of macromolecules from x-ray diffraction however, it normally takes a relatively long period of data collection time (even at synchrotrons) to collect all of the data. A new technique, the Laue method, can be used to collect all of the data in a fraction of a second. Instead of using monochromated x-rays, a wide spectmm of incident x-rays is used. In this case, all of the reflections that ate diffracted on to an area detector are recorded at just one setting of the detector and the crystal. By collecting many complete data sets over a short period of time, the Laue method can be used to foUow the reaction of an enzyme with its substrate. This technique caimot be used with conventional x-ray sources. 

Several devices are available commercially to measure mobihty. One of these (Zeta-Meter Inc., New York) allows direct microscopic measurement of individual particles. Another allows measurement in more concentrated suspensions (Numinco Instrument Corp., Monroeville, Pa.). The state of the charge can also be measured by a streaming-current detecdor (Waters Associates, Inc., Framingham, Mass.). For macromolecules, more elaborate devices such as the Tisehus moving-boundaiy apparatus are used. 

A very simple version of this approach was used in early applications. An alchemical charging calculation was done using a distance-based cutoff for electrostatic interactions, either with a finite or a periodic model. Then a cut-off correction equal to the Born free energy, Eq. (38), was added, with the spherical radius taken to be = R. This is a convenient but ill-defined approximation, because the system with a cutoff is not equivalent to a spherical charge of radius R. A more rigorous cutoff correction was derived recently that is applicable to sufficiently homogeneous systems [54] but appears to be impractical for macromolecules in solution. 

K. Kremer, K. Binder. Monte Carlo simulation of lattice models for macromolecules. Comp Phys Rep 7 259-310, 1988. 

Unfortunately, even for low molecular weight material it is difficult to obtain clear experimental evidence for a roughening transition [71]. This is mainly due to the fact that during growth the interface generally assumes a metastable shape and relaxation times are long and increase with crystal size. Therefore we certainly cannot expect a definitive answer for macromolecules. We shall therefore just make several comments which hopefully will be of use when reading the literature. 

The term polysaccharide has also been widely used for macromolecules containing glycose or alditol residues in which both glycosidic and phosphate diester linkages are present. 

Langer, R., Brem, H., and Tapper, D., BiocompatibiUty of polymeric delivery systems for macromolecules, J. Biomed. 

Jones TA. A graphics model building and refinement system for macromolecules. JAppl Cryst 1918 11 268. 

A related experiment TOCSY (Total Correlation Spectroscopy) gives similar information and is relatively more sensitive than the REIAY. On the other hand, intensity of cross peak in a NOESY spectrum with a short mixing time is a measure of internuclear distance (less than 4A). It depends on the correlation time and varies as . It is positive for small molecules with short correlation time (o r <<1) and is negative for macromolecules with long correlation time (wr >>l) and goes through zero for molecules with 1 Relaxation effects should be taken into consideration for quantitative interpretation of NOE intensities, however. 

The positive nOe observed in small molecules in nonviscous solution is mainly due to double-quantum relaxation, whereas the negative nOe observed for macromolecules in viscous solution is due to the predominance of the zero-quantum 1% cross-relaxation pathway. 

Matrix Assembler (ADMA) method, introduced for the generation of ab initio quality approximate density matrices for macromolecules [142-146], and for the computation of approximate macromolecular forces [146], among other molecular properties. 

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