Bonding constraints

The second application of the CFTI approach described here involves calculations of the free energy differences between conformers of the linear form of the opioid pentapeptide DPDPE in aqueous solution [9, 10]. DPDPE (Tyr-D-Pen-Gly-Phe-D-Pen, where D-Pen is the D isomer of /3,/3-dimethylcysteine) and other opioids are an interesting class of biologically active peptides which exhibit a strong correlation between conformation and affinity and selectivity for different receptors. The cyclic form of DPDPE contains a disulfide bond constraint, and is a highly specific S opioid [llj. Our simulations provide information on the cost of pre-organizing the linear peptide from its stable solution structure to a cyclic-like precursor for disulfide bond formation. Such... 

The SHAKE method for bond constraints reduces the number of degrees of freedom during the initial stages of simulations it is good for minimizing solvent bath overhead. 

Pogozheva ID, Lomize AL, Mosberg HI. Opioid receptor three-dimensional structures from distance geometry calculations with hydrogen bonding constraints. Biophys J 1998 75 612-634. 

Hopefully, we make our point. The confidence curve is NOT fashioned out of granite - it has to be applied with understanding and circumspection. It will always have the same basic shape but we have to be prepared to take a view on how wide it should be in every individual situation Matters become a great deal more complex when we come up against structures that are sterically crowded (i.e., structures where bond constraints force various moieties into close proximity with one another). 

For freely jointed chains, if all intramolecular interactions other than bonding constraints are neglected, such an ideal system is still tractable. In this case,... 

This programme turns DQF-COSY and HMBC spectra into bond constraints. Then it turns C DEPT spectra and the molecular formula into building blocks such as -CH3 and -CH2-. These are then assembled into as many complete structures as are compatible with the bond constraints. CISOC-SES is designed to be as compatible with real-world spectra with their attendant ambiguities as possible. CISOC-SES is a result of collaborative work with Bodenhausen et al. who had previously tackled the problem indepen-dently. CISOC-SES has since been commercialized as NMR-SAMS by Spectrum Research, EEC. 

Both the LINK and the BOND constraints are ideal for specifying or excluding the chemistry at a particular bond. For example, one could easily exclude the formation of peptide bonds between specific components to generate peptidomimetics. However, the most prevalent use is to eliminate bonded heteroatoms or other unstable chemical species. 

PHARM constraint I I ft CMPNTS constraint ATYPE constraint BOND constraint... 

Rp2 =0.188, Rai=0.195, and Ra2=0.171. These results suggest that pj can be eliminated but do not allow for selection between the other three. However examination of the intermolecular contacts shows only model a2 is fully acceptable, whereas serious short contacts occur for the other three. Non-bonded. constraints were incorporated in the refinements but these were not successful in removing the bad contacts nor was the situation improved by refinement using the full data including 41 unobserved reflections (at w = 1/2). ... 

The refined structure had residuals R=0.244, R"=0.274. The amide groups are approximately perpendicular to the chain axis and form hydrogen bonds N-H...0=C, as indicated by the polarized infrared spectrum. The 06-H group is close to the gt conformation but is not hydrogen bonded and has a short 06 05 contact. Elimination of the short contact with a non-bonded constraint increases the residuals to R=0.250, R"=0.288, an insignificant change. However the 06-H groups remain unbonded, contrary to infrared indications. 

The major source of the disorder energy is the bond strain within the random network. Phillips (1979) proposed a model to explain the relation between network coordination and disorder. A four-fold continuous random network is overcoordinated, in the sense that there are too many bonding constraints compared to the number of degrees of freedom. The constraints are attributed to the bond stretching and bending forces, so that for a network of coordination Z , their number, NciZJ is. 

It may seem surprising to apply thermal equilibrium concepts to amorphous silicon, because the amorphous phase of a solid is not the equilibrium phase. However, a subset of bonding states may be in equilibrium even if the structure as a whole is not in its lowest energy state. The attainment of equilibrium is prevented by bonding constraints on the atomic structure. The collective motion of many atoms is required to achieve long range crystalline order and the topological constraints are formidable. On the other hand the transformation of point defects requires the cooperation of only a few atoms. Therefore any partial thermal equilibrium may be expected at point defects or impurities. 

In standard MD, the highest frequency motions dictate the timestep in the system. Bond vibrations are typically frozen out by using bond constraints, such as SHAKE [46] in order to increase the timestep used from Ifs to 2 fs. 

A typical excluded volume effect is the occurence of nontrivial power laws. As a first (jx miple lei us consider the average size of an isolated polymer coil consisting of n segments. We assume e rch segment to consist of several monomtirs, so that any bond constraints among the directions of sub-... 

---