Molecular mechanics, physical

Physical studies of molecular mechanisms, physical and chemical phenomena and elucidation of changes in foam properties under the effect of external factors Studies on the chemical structure and morphology using methods of ectroscopy. X-ray analysis, microscopy, thermography, etc. 

The accuracy of a molecular mechanics or seim-eni pineal quantum mechanics method depends on the database used to parameterize the method. This is true for the type of molecules and the physical and chemical data in the database. Frequently, these methods give the best results for a limited class of molecules or phen omen a. A disad van tage of these methods is that you m u si have parameters available before running a calculation. Developing param eiers is time-consuming. 

Many molecular mechanics potentials were developed at a time when it was computationally impractical to add large numbers of discrete water m olecules to ih e calcu la Lion to sim ulate th e effect of ac ueous media. As such, tech n iq ties cam e into place that were intended to Lake into account the effect of solvent in some fashion. These tech niqiieswcre difficult to justify physically but they were used n cvcrth eless. 

W C, A Tempcz)rrk, R C Hawley and T Hendrickson 1990. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. Journal of the American Chemical Society 112 6127-6129. ensson M, S Humbel, R D J Froese, T Matsubara, S Sieber and K Morokuma 1996. ONIOM A Multilayered Integrated MO + MM Method for Geometry Optimisations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition. Journal of Physical Chemistry 100 19357-19363. 

The rotational isomeric state (RIS) model assumes that conformational angles can take only certain values. It can be used to generate trial conformations, for which energies can be computed using molecular mechanics. This assumption is physically reasonable while allowing statistical averages to be computed easily. This model is used to derive simple analytic equations that predict polymer properties based on a few values, such as the preferred angle... 

Molecular mechanical force fields use the equations of classical mechanics to describe the potential energy surfaces and physical properties of molecules. A molecule is described as a collection of atoms that interact with each other by simple analytical functions. This description is called a force field. One component of a force field is the energy arising from compression and stretching a bond. 

The absolute energy of a molecule in molecular mechanics has no intrinsic physical meaning values are useful only for com-... 

The HyperChem log file includes calculated dipole moments of molecules. To set the amount of information collected in the log file, change the value of the QuantumPrintLevel setting in the chem.ini file. Note that the sign convention used in the quantum mechanical calculation of dipoles is opposite to that used in molecular mechanics dipole calculations this reflects the differing sign conventions of physics and chemistry. 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Molecular mechanics methods are available in many computer programs, including MM3, HyperChem, Quanta, Sybyl, and Alchemy. There are many different molecular mechanics methods. Each one is characterized by its particular/orce eW. A force field has these components ... 

Ab initio methods, unlike either molecular mechanics or semi-empirical methods, use no experimental parameters in their computations. Instead, their computations are based solely on the laws of quantum mechanics—the first principles referred to in the name ah initio—and on the values of a small number of physical constants ... 

Molecular modeling itself can be simply described as the computer-assisted calculation, modulation, and visualization of realistic 3D-molecular structures and their physical-chemical properties using force fields/ molecular mechanics. 

Armrmanto, R., Schwenk, C.F. and Rode, B.M. (2003) Structure and Dynamics of Hydrated Ag (I) Ab Initio Quantum Mechanical-Molecular Mechanical Molecular Dynamics Simulation. The Journal of Physical Chemistry A, 107, 3132-3138. 

The three prototype mixed p agonist/S antagonists described in this chapter have excellent potential as analgesics with low propensity to produce tolerance and dependence. The pseudotetrapeptide DIPP-NH2[ ] has already been shown to produce a potent analgesic effect, less tolerance than morphine, and no physical dependence upon chronic administration. In preliminary experiments, the tetrapeptides DIPP-NH2 and DIPP-NH2[T] were shown to cross the BBB to some extent, but further structural modifications need to be performed in order to improve the BBB penetration of these compounds. The Tyr-Tic dipeptide derivatives can also be expected to penetrate into the central nervous system because they are relatively small, lipophilic molecules. In this context, it is of interest to point out that the structurally related dipeptide H-Dmt-D-Ala-NH-(CH2)3-Ph (SC-39566), a plain p-opioid agonist, produced antinociception in the rat by subcutaneous and oral administration [72], As indicated by the results of the NMR and molecular mechanics studies, the conformation of the cyclic p-casomorphin analogue H-Tyr-c[-D-Orn-2-Nal-D-Pro-Gly-] is stabilized by intramolecular hydrogen bonds. There-... 

An alternative approach is to replace an accurate but expensive first-principle-based technique by a reliable model potential. Such potentials, broadly referred to as molecular mechanics (MM), generally cannot account for bond-breaking, but can, in principle, account for the range of intermolecular interactions. However, using a fitted pair-wise potential may result in losing quantitative accuracy, predictability, and the underlying physics. 

Chemical kinetics deals with quantitative studies of the rates at which chemical processes occur, the factors on which these rates depend, and the molecular acts involved in reaction processes. A description of a reaction in terms of its constituent molecular acts is known as the mechanism of the reaction. Physical and organic chemists are primarily interested in chemical kinetics for the light that it sheds on molecular properties. From interpretations of macroscopic. kinetic data in terms of molecular mechanisms, they can gain insight into the nature of reacting systems, the processes by which chemical bonds are made and broken, and the structure of the resultant product. Although chemical engineers find the concept of a reaction mechanism useful in the correlation, interpolation, and extrapolation of rate data, they are more concerned with applications... 

---