And force-field calculations

The molecular mechanics technique has been called by many different names, including Westheimer method, strain-energy method, conformational energy calculations, empirical potential energy calculations, atom-atom pair potential method, and force field calculations. Empirical force field is widely used, but somewhat long, and many authors omit empirical, leading to confusion with spectroscopic force field calculations. Molecular mechanics (11) now appears to be favored (10a) and is used (abbreviated as MM) throu out this chapter. 

The structures and conformations of 1,3,5,7-tetroxocanes and its derivatives have been extensively studied by X-ray diffraction, dynamic NMR, IR and Raman spectroscopy, dipole moment measurements and force-field calculations. 1,3,5,7-Tetroxocane gives monoclinic crystals with four molecules in the unit cell. The conformation is a crown (Figure 2) with approximate C v and exact C2 symmetry (74BCJ583). 

With (Z)-alkenes, the most crowded inside position should preferentially be occupied by the medium group (OR ) and the small group (H), respectively, the large group (R) being placed anti (Scheme 6.48). In the case of (Fl-alkenes, the results were rationalized in terms of the inside-alkoxy model. Ab initio and force field calculations provide further support for this proposal (265). The transition... 

Medium-ring saturated monocyclic diamines (12) have pKa values > 12 in aqueous solution (88CC1528), (12, n = m = 4) has the highest pK[ resulting from internal hydrogen bonding as suggested by NMR measurements and force-field calculations. 

Insight II is a 49-module molecular modeling package that examines ligand docking and force field calculations. 

In general, the stereoelectronic influence of substituents in [2 + 2]-photocycload-dition reactions is minor, and the preferred ground-state conformation often accounts for the formation of the major diastereoisomer. Inspection of molecular models and force field calculations provide a good picture of possible transition states leading via 1,4-biradicals to cyclobutane products. The total synthesis of (+)-guanacastepene represents another recent example for the use of stereoselective intramolecular cyclopentenone-olefin photocycloadditions in natural products synthesis [32]. 

Molecular-orbital calculations performed on platinum antitumor complexes and related species, and force-field calculations carried out on their adducts with nucleic acids are reviewed. The aim of the author is to point out the methodological difficulties encountered in these calculations, and to comment on the (sometimes problematic) results which they have yielded. 

Problem of Multiple Minima. Combined Use ofNMR Spectroscopy and Force-Field Calculations. Chemical Shifts as Structural Indicators... 

Zemer and coworkers suggested the fifth isomer, the vinylcyclopropenyl cation 219, to be the most stable of the isomeric (CH)5+ cations (MP2/6-31G //6-31G level), but subsequent high-level ab initio calculations (G2 level of theoryfound almost identical energies for 218 and 219. In agreement with the latter conclusion, recent ab initio [MP2(full)/6-31G ] and force field calculations have shown ° that 218 is 1.2 kcal moT lower in energy than... 

Thiophene has 2 symmetry and the 21 fundamental vibrations are distributed between four symmetry species as follows iA + iA2+lB + 3B2. All vibrations are active in the Raman spectrum, but those of A2 symmetry are inactive in the infrared spectrum. The INS spectrum of thiophene has been modelled by ab initio and force field calculations [141]. The calculated spectrum and the experimental spectra of pure solid thiophene and thiophene adsorbed by a M0/AI2O3 catalyst are shown in Fig. 7.35. The vibrational modes involving significant hydrogen atom displacements are shovm in Fig.7.36. 

F. Fillaux, J.P. Fontaine, M.H. Baron, G.J. Kearley J. Tomkinson (1993). Chem. Phys., 176, 249-278. Inelastic neutron scattering study of the proton dynamics in N-methylacetamide and force-field calculation at 20 K. 

Catalysis and Sorption software provided in several modules capable of all molecular modelling tasks Molecular graphics and force-field calculations. 

Molecular graphics studies and force field calculations were carried out with the program Discover [5] to determine the minimum energy pathway for the diffusion of o-, p-... 

In the present study, we report our molecular graphics investigations and force field calculations for the diffusion of isomers of IBEB in mordenite, mazzite and faujasite. The dimensions of the pores in these zeolites as well as the molecules are listed in Table 1. Using... 

Both AMI and force-field calculations of 4-methyl-4/f-pyran and 4-methylcoumarin anion were employed as approximate models for a transition-state study of the alkaloid-induced enantioselective electroreduction of 4-methylcoumarin (93LA609). 

The emphasis in this review is on ab initio methodologies, although semiempirical and force-field calculations will be mentioned occasionally. We will concentrate on recent studies which generally use elaborate ab initio methods. Such methods are better suited to tackle, with a reasonable level of confidence, problems where experimental data are scarce and cannot be used to guide and to calibrate the calculations. 

Quantum calculations and force-field calculations [ 126] on oin exocyclic tetraenes 11,16, 17, and (2.2.2]hericene (18) and their Diels-Alder adducts (or model compounds of them) suggested that the s-czs-butadiene moieties in these systems are aU planar and that the 1,4-distance between the extremities of the dienes does not vary between a tetraene and its monoadducts. Ra-diocrystaUography of crystalline derivative [ 150,151 ], as well as variable temperature circular dichroism (CD) data for enantiomerically pure (+)-(7R)-7-deutero-2,3,5,6-tetramethylidenebicyclo[2.2.2]octane and (+)-(7S)-7-methyl-2,3,5,6-tetramethylidenebicyclo[2.2.2]octane confirmed these predictions. 

Stmetnre obtained from rotational constants and force field calculations. ... 

The conformation of uncomplexed [18]crown-6 found in the crystalline state has been shown by IR spectroscopy to be predominant also in solution and force-field calculations have essentially confirmed the same structure 241.2 9) interestingly, it was found that the ordered Dsa [18]crown-6 conformation observed in the potassium complex would be lower in energy by 7 kJ mor were it not for the aforementioned unfavorable electrostatic interactions The tendency to remove the latter by complexation of a cation and thus enable the ligand to adopt a low-energy conformation might contribute considerably to the high affinity of [18]crown-6 to potassium ions. 

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