Big Chemical Encyclopedia

Chemical substances, components, reactions, process design ...

Articles Figures Tables About

Computational force field calculations

D information is available, e.g., in databases without experimental data, the different types of surfaces (sec below) can be calculated only after a 3D structure has been determined by a 3D structure generator, which might be followed by computational refinement, e.g., with a force-field calculation. [Pg.125]

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. [Pg.4]

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. [Pg.29]

The performance is (as expected) very good. MMX provides relative (and absolute) stabilities with a MAD of only 1.2 kcal/mol, which is better than the estimates from the combined theoretical methods in Table 11.31. Considering that force field calculations require a factor of 10 less computer time for these systems than the ab initio methods combined in Table 11.31, this clearly shows that knowledge of the strengths and weakness of different theoretical tools is important in selecting a proper model for answering a given question. [Pg.294]

Molecular mechanics (also known diS force-field calculations) is a method for the calculation of conformational geometries. It is used to calculate bond angles and distances, as well as total potential energies, for each conformation of a molecule. Steric enthalpy can be calculated as well. Molecular orbital calculations (p. 34) can also give such information, but molecular mechanics is generally easier, cheaper (requires less computer time), and/or more accurate. In MO calculations, positions of the nuclei of the atoms are assumed, and the wave equations take account only of... [Pg.178]

A Gst is the difference in free energy due to steric constants in reactant and transition state, k is the rate constant of the nonsterically constrained reaction. The contribution of the steric component to the transition-state energy cannot be deduced accurately from DFT calculations because van der Waals energies are poorly computed. Force field methods have to be used to properly account for such interactions. [Pg.16]

For a quantitative description of molecular geometries (i.e. the fixing of the relative positions of the atomic nuclei) one usually has the choice between two possibilities Cartesian or internal coordinates. Within a force field, the potential energy depends on the internal coordinates in a relatively simple manner, whereas the relationship with the Cartesian nuclear coordinates is more complicated. However, in the calculations described here, Cartesian coordinates are always used, since they offer a number of computational advantages which will be commented on later (Sections 2.3. and 3.). In the following we only wish to say a few words about torsion angles, since it is these parameters that are most important for conformational analysis, a topic often forming the core of force field calculations. [Pg.162]

A force field is considered transferable from an arbitrary molecule A to another molecule B if the agreement of properties calculated fori (geometrical, vibrational, thermochemical, and other properties) with the respective experimental values is as good as for A. In our calculations we are dealing with force fields which describe entire families of molecules. Within these families, properties of only a fraction of their members are known experimentally while it is our aim to predict the others computationally. It is therefore clear that the problem of transferability is of decisive importance for force field calculations of unknown systems or those with unknown properties or. Traditional vibrational spectroscopic force fields in most cases reproduce well the frequencies of a single molecule or a family of closely related molecules however, they are not transferable to molecules of different strain. Subsequently we comment on this point in somewhat more detail. [Pg.171]

The lion s share of the computer-time for the least-squares process has to be provided for forming the Z-matrix. The elements of this matrix are evaluated partly numerically and partly analytically in the calculations of Lifson and Warshel (17). In certain cases, strong parameter correlations may occur. Therefore caution is demanded when inverting the matrix C. Also from investigations other than consistent force-field calculations it is known that such correlations frequently occur among the parameters for the nonbonded interactions (34,35). Another example of force field parameter correlations was encountered by Ermer and Lifson (19) in the course of the calculation of olefin properties. When... [Pg.176]

Fig. 7. Computer-printout of a force-field calculation of ethylene ( initial and final refer to the results before and after the energy minimisation)... Fig. 7. Computer-printout of a force-field calculation of ethylene ( initial and final refer to the results before and after the energy minimisation)...
The computational verification and prediction of the conformations (tertiary structures) of polypeptides presents a considerable challenge for theoretical chemists. Attempts towards this goal have so far made use of force field calculations to a large extent. Levitt... [Pg.199]

In spite of its limitations, molecular mechanics (MM) is a technique that is widely used for the computation of molecular structures and relative stabilities. The advantage of MM over quantum mechanical methods is mainly based on the computational simplicity of empirical force field calculations, leading to a comparatively small computational effort for MM calculations. Therefore, even large... [Pg.130]

The term computational chemistry can refer in its broadest sense to a wide range of methods that have been developed to give insight into the fundamental behavior of chemical species. Such methods include, but are not necessarily limited to, those related to quantum mechanics (1), molecular mechanics (or force-field calculations) (2), perturbation theory (3), graph theory (4), or statistical thermodynamics (5). For the purposes of this chapter, comments will be restricted to force-field and quantum-based calculations, since these are the techniques that have been used in work on lignin. Furthermore, these methods have been reviewed in a very readable book by Clark (6). [Pg.268]

Note that in the leapfrog method, position depends on the velocities as computed one-half time step out of phase, thus, scaling of the velocities can be accomplished to control temperature. Note also that no force-field calculations actually take place for the fractional time steps. Forces (and thus accelerations) in Eq. (3.24) are computed at integral time steps, halftime-step-forward velocities are computed therefrom, and these are then used in Eq. (3.23) to update the particle positions. The drawbacks of the leapfrog algorithm include ignoring third-order terms in the Taylor expansions and the half-time-step displacements of the position and velocity vectors - both of these features can contribute to decreased stability in numerical integration of the trajectory. [Pg.72]

A valuable approach toward the determination of solution structures is to combine molecular mechanics calculations with solution experimental data that can be related to the output parameters of force field calculations 26. Examples of the combination of molecular mechanics calculations with spectroscopy will be discussed in Chapter 9. Here, we present two examples showing how experimentally determined isomer distributions may be used in combination with molecular mechanics calculations to determine structures of transition metal complexes in solution. The basis of this approach is that the quality of isomer ratios, computed as outlined above, is dependent on the force field and is thus linked to the quality of the computed structures. That is, it is assumed that both coordinates on a computed potential energy surface, the... [Pg.74]

The aim of the present contribution is to critically review computational work related to platinum antitumor drugs, published prior to 1998. After a section devoted to molecular-orbital calculations on platinum antitumor complexes and related compounds, we address force-field calculations on platinum adducts with DNA constituents that have been used (mainly in combination with NMR spectroscopy) to evaluate the structure of the adduct. A brief outlook concludes this chapter. [Pg.538]


See other pages where Computational force field calculations is mentioned: [Pg.4]    [Pg.27]    [Pg.223]    [Pg.184]    [Pg.177]    [Pg.184]    [Pg.191]    [Pg.200]    [Pg.39]    [Pg.132]    [Pg.45]    [Pg.66]    [Pg.81]    [Pg.483]    [Pg.759]    [Pg.149]    [Pg.60]    [Pg.62]    [Pg.142]    [Pg.319]    [Pg.404]    [Pg.56]    [Pg.57]    [Pg.132]    [Pg.15]    [Pg.37]    [Pg.69]    [Pg.92]    [Pg.142]    [Pg.304]    [Pg.139]    [Pg.75]    [Pg.207]   
See also in sourсe #XX -- [ Pg.229 ]




SEARCH



Field calculations

Force calculation

Force-field calculations

© 2024 chempedia.info