Molecular mechanics calculations, structural

J. H. Horner, P. J. Squatritto, N. McGuire, J. P. Riebenspies, and M. Newcomb, Organometallics, 10, 1741 (1991). Macrocycles Containing Tin. Crystal Structures and Molecular Mechanics Calculated Structures of Macrocyclic Lewis Acidic Hosts. 

Molecular mechanics calculations are deceptively simple to perform. Many software packages now make molecular mechanics as easy as specifying a molecular structure and saying go, at which point the calculation will run and very soon give a result. The dilhculty is in knowing which results to trust. 

Some properties, such as the molecular size, can be computed directly from the molecular geometry. This is particularly important, because these properties are accessible from molecular mechanics calculations. Many descriptors for quantitative structure activity or property relationship calculations can be computed from the geometry only. 

For crystalline polymers, the bulk modulus can be obtained from band-structure calculations. Molecular mechanics calculations can also be used, provided that the crystal structure was optimized with the same method. 

PW91 (Perdew, Wang 1991) a gradient corrected DFT method QCI (quadratic conhguration interaction) a correlated ah initio method QMC (quantum Monte Carlo) an explicitly correlated ah initio method QM/MM a technique in which orbital-based calculations and molecular mechanics calculations are combined into one calculation QSAR (quantitative structure-activity relationship) a technique for computing chemical properties, particularly as applied to biological activity QSPR (quantitative structure-property relationship) a technique for computing chemical properties... 

The distorted structure can be replaced by a more reasonable structure using an empir ical molecular mechanics calculation This calculation which is invoked m Spartan Build by clicking on Minimize, automatically finds the structure with the smallest strain energy (m this case a structure with realistic bond distances and a boat conformation for the SIX membered ring)... 

This text is similar to that of McCammon and Harvey (see below), but also provides a background for force field-based calculations and a more sophisticated discussion. Includes numerous examples of computing the structure, dynamics, and thermodynamics of proteins. The authors provide an interesting chapter on the complementary nature of molecular mechanics calculations and specific experimental techniques. 

This difference is shown in the next illustration which presents the qualitative form of a potential curve for a diatomic molecule for both a molecular mechanics method (like AMBER) or a semi-empirical method (like AMI). At large internuclear distances, the differences between the two methods are obvious. With AMI, the molecule properly dissociates into atoms, while the AMBERpoten-tial continues to rise. However, in explorations of the potential curve only around the minimum, results from the two methods might be rather similar. Indeed, it is quite possible that AMBER will give more accurate structural results than AMI. This is due to the closer link between experimental data and computed results of molecular mechanics calculations. 

The concept of a parameter set is an important (but often inconvenient) aspect of molecular mechanics calculations. Molecular mechanics tries to use experimental data to replace a priori computation, but in many situations the experimental data is not known and a parameter is missing. Collecting parameters, verification of their validity, and the relationship of these molecular mechanics parameters to chemical and structural moieties are all important and difficult topics. 

These results, which pertain to stable-ion conditions, provide strong evidence that foe most stable structure for foe norbomyl cation is foe symmetrically bridged nonclassical ion. How much stabilization does foe a bridging provide An estimate based on molecular mechanics calculations and a foermodynamic cycle suggests a stabilization of about 6 1 kcal/mol. An experimental value based on mass-spectrometric measurements is 11 kcal/mol. Gas-phase Itydride affinity and chloride affinity data also show foe norbomyl cation to be especially stable. ... 

Bicyclo[6.2.0]deca-2,4,6,8,10-pentaene has been synthesized, and a number of molecular orbital and molecular mechanics calculations have been performed to determine whether it is aromatic or antiaromatic. Consider the structure and discuss the following points. 

Two other steric parameters are independent of any kinetic data. Charton s v values are derived from van der Waals radii/ and Meyer s values from the volume of the portion of the substituent that is within 0.3 nm of the reaction center. The V values are obtained by molecular mechanics calculations based on the structure of the molecule. Table 9.7 gives v and value.s for some groups. As can be seen in the table, there is a fair, but not perfect, correlation among the Ei, v, and values. Other sets of steric values, (e.g., and have also been proposed. ... 

For calculations of electronic structures of azolides (CNDO, PCILO, EHMO, INDO and Molecular Mechanics Calculation) the interested reader should consult the relevant papers. 481... 

The final step in the molecular-mechanics calculation of molecular conformation involves the minimization of the energy Approximations are involved whose importance is not always clear. Usually, all first derivatives with respect to the various internal coordinates are set equal to zero - although these coordinates are often not independent (see Section 10.6). Furthermore, the final conformation obtained depends on the assumed initial structure. Therefore, (he method must be applied with care and a certain amount of chemical intuition. In spite of these uncertainties the molecular mechanics method has been employed with considerable success, particularly in the conformational analysis of branched alkanes. For molecules containing hetero-atoms, it can be applied, but with somewhat less confidence. 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

The synthesis, X-ray structure, NMR, and UV-visible spectroscopy, and electrochemistry of a macrocyclic platinum(II) complex containing the tetradentate 1,4,7,10-tetrathiacyclodecane ligand, [12]aneS4 (144) have been reported.350 Related complexes including [Pt([13]aneS4)]2+ and [Pt([16]aneS4)]2+ have also been prepared, and molecular mechanics calculations complemented... 

In their pursuit of determining solution structures of dinuclear copper complexes as carried out for complex (29) (Section 6.6.3.1.1). Comba reported complex (431) (r = 0.02 Cu-Cu 6.9 A, comparable with the values of 7.2 A predicted by molecular mechanics calculations and 6.7 A obtained from the simulated EPR spectrum).54 They reported369 complexes (432) (square planar) and (433) (Cu-Cu 3.35 A) as well. As part of studying magnetic properties of mono-, di-, and... 

The functionalization of zinc porphyrin complexes has been studied with respect to the variation in properties. The structure and photophysics of octafluorotetraphenylporphyrin zinc complexes were studied.762 Octabromoporphyrin zinc complexes have been synthesized and the effects on the 11 NMR and redox potential of 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetraarylporphyrin were observed.763 The chiral nonplanar porphyrin zinc 3,7,8,12,13,17,18-heptabromo-2-(2-methoxyphenyl)-5,10,15,20-tetraphenylporphyrin was synthesized and characterized.764 X-ray structures for cation radical zinc 5,10,15,20-tetra(2,6-dichlorophenyl)porphyrin and the iodinated product that results from reaction with iodine and silver(I) have been reported.765 Molecular mechanics calculations, X-ray structures, and resonance Raman spectroscopy compared the distortion due to zinc and other metal incorporation into meso dialkyl-substituted porphyrins. Zinc disfavors ruffling over doming with the total amount of nonplanar distortion reduced relative to smaller metals.766 Resonance Raman spectroscopy has also been used to study the lowest-energy triplet state of zinc tetraphenylporphyrin.767... 

Geometric Optimization. The structure of the molecule as built by CHEMLAB (or a input from other methods) can be optimized through either a full force field molecular mechanics calculation (MMII) or with the semi-empirical molecular orbital methods MINDO-3 and MNDO. 

Molecular mechanics calculations show the [3.3.3]propellanes to be thermodynamically favored over the other, intermediate, structures proposed above40, and presumably over the respective dispiran derivatives albeit we have not conducted the calculations for the abovementioned starting materials. 

A theoretical analysis is presented for the binding of the four dia-stereoisomers of benzo[a]pyrene diol epoxides (BPDEs) to N2(g), N6(a), 06(G) and NU(c). Molecular models for binding and stereoselectivity involving intercalation, intercalative covalently and externally bound forms are presented. Molecular mechanics calculations provide the energetics which suggest possible structures for the formation of each of the principal DNA-BPDE complexes. Stereographic projections are used to illustrate the molecular structures and steric fits. The results of previous calculations on intercalation and adduct formation of BPDE l(+) in kinked DNA (37) are summarized and extended to include the four diastereoisomers l( ) and II( ). The theoretical model is consistent with the observed experimental data. 

Estimates of the ultimate shear strength r0 can be obtained from molecular mechanics calculations that are applied to perfect polymer crystals, employing accurate force fields for the secondary bonds between the chains. When the crystal structure of the polymer is known, the increase in the energy can be calculated as a function of the shear displacement of a chain. The derivative of this function is the attracting force between the chains. Its maximum value represents the breaking force, and the corresponding displacement allows the calculation of the maximum allowable shear strain. In Sect. 4 we will present a model for the dependence of the strength on time and temperature. In this model a constant shear modulus g is used, thus r0=gyb. 

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