Intramolecular flexibility

Mahoney, M. W. Jorgensen, W. L., Quantum, intramolecular flexibility, and polarizability effects on the reproduction of the density anomaly of liquid water by simple potential functions, 7. Chem. Phys. 2001,115, 10758-10768... 

The intramolecular flexibilities of poly(1,4-phenylene oxide), polyi2,6-dimethyl-1,4-phenylene oxide), poly(2-methyl-6-phenyl-1,4-phenylene oxide), and poly 2,6-diphenyl-1,4-phenylene oxide) are evaluated through estimation of the resistance to rotation about the Cj 4—0 bonds in their backbones. A 6-12 potential is used to account for the van der Waals interactions between nonbonded atoms and groups encountered during the backbone rotations, while the twofold intrinsic potential to rotation about the C14—0 bonds resulting from the -electron delocalization is also included. 

O.V. Shishkin et al., Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs. J. Mol. Struct. 477, 15-21 (1999)... 

Application of Eq. 19 to the /7-HMX isotherm from simulations leads to the Us-Up curve shown in Fig. 11, where negative curvature in the simulation results is clearly evident (filled circles). While such behavior would be anomalous for metals, it is actually expected for pressures below about one GPa in the case of polyatomic molecular crystals, due to complicated molecular packings and intramolecular flexibility, and has in fact been reported for the high explosives pentaerythritol tetranitrate (PETN) where careful studies were performed for low levels of compression [77], By contrast, the experimental results for /3-HMX in the Us-Up plane do not exhibit significant curvature due to lack of data at pressures below about one Gpa [78], Thus, estimates of isothermal sound speeds, and hence isothermal bulk moduli, based on... 

Kleinpeter and Koch have recently introduced spatial magnetic properties as a measure of homoaromaticity. These are calculated as through-space NMR shieldings (TSNMRS) and visualized as iso-chemical shielding surfaces (ICSF). The structures, the intramolecular flexibility, and the and C NMR chemical shifts are calculated on the MP2/6-311 + G level of theory. TSNMRS of benzene and the cyclopropenylium cation as prototype aromatic molecules published earlier are used as references for homoaromaticity in a number of homoaromatic carbocations. The existence and the degree of homoaromaticity are deduced from the TSNMRSs by comparing the experimental and computed H and NMR NMR chemical shifts. 

While the crystals of these compounds necessarily have numerous intermolecular phenyl phenyl interactions, they do not in general demonstrate close sextuple embraces a porcupine embrace is aloof This is probably because the gold clusters are relatively globular, and not intramolecularly flexible. There are interesting supramolecular questions to be raised for these compounds. What is determining the molecular conformations It is evident that core compositions [X(AuP)J with n = 4, 5, and 6 are sterically feasible. However, rotation about X-Au-P bonds is related to the intramolecular phenyl-phenyl nonbonded interactions, and do these override any X-Au-P bonding influences And what is the relative influence of the intermolecular phenyl-phenyl interactions These questions are still unanswered. 

Similarly, the dynamic behavior of the complex [Ir3Rh(CO)6)/i2-GO)3(/t3-l,3,5-trithiane)] was studied by variable temperature H and NMR spectroscopy and also by 2-D exchange spectroscopy (EXSY) NMR spectroscopy <1994HCA1869>. However, only the apical and basal carbonyl groups are involved in the intramolecular flexibility of the system and not the 1,3,5-trithiane moiety. 

In terms of intramolecular flexibility, the poly(2,6-disub-stituted-1,4-phenylene oxides) are freely rotating chains [71] however, intermolecular steric effects may limit phe-nylene rotation in the solid state and periiaps account for the absence of detectable sub-Tg relaxational processes. For example, results of NMR measurements indicate that the phenylene rings of PPO can execute only small amplitude motions due to the relative stiffness and dense packing of the PPO chain and blockage from rings on adjacent chains. 

Eis, P.S., Lakowicz, J.R. Time-resolved energy transfer measurements of donor-acceptor distance distributions and intramolecular flexibility of a CCHH zinc finger peptide. Biochemistry 32, 7981-7993 (1995)... 

This raises the question of intramolecular flexibility which has not yet been adequately addressed. The potential energy surface involving intermolecular and intramolecular degrees of freedom is a formidable object and so far has been constructed for only a small number of small dimers. Methods for the inclusion of internal degrees of freedom have been suggested (Jankowski 2004, 2008 Jankowski and Ziolkowski 2006 Murdachaew et al. 2002), but so far have been applied to dimers of small systems only. This remains one of the outstanding problems with this approach. 

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