Dipeptide molecules

The condensation reaction between two amino acid molecules, usually in the form of active esters, produces a dipeptide molecule (equation 16). The resulting amide bond (—CONH—) is often referred to as a peptide bond. This condensation reaction can be repeated to give a polypeptide chain (18). In naming the sequence of amino acid residues in the chain the customary habit of starting from the N-terminal (free amino) end will be adopted. Synthetic polypeptides made from a single amino acid type, i.e. R1 = R2 = R3 = = R" in (18), are known as homopolypeptides. Cyclic peptide molecules are also known and can occur naturally. 

Prior to our current investigations, we studied the structure of the dipeptide molecules that make up proteins. Based on the data supplied by the Cambridge database, the dipeptides were shown to adopt many types of arrangement mode in their crystalline state [9], Furthermore, it was shown that water, methanol,... 

By crystallization of a mixture of the dipeptide (2) and racemic methyl lactate from methanol, asymmetric recognition occurred to give an inclusion compound that contains the (S)-form of methyl lactate in 89 % ee [20], X-ray crystallographic study of the inclusion compound was able to elucidate that the dipeptide molecules... 

When allylic alcohols were used as a guest molecule instead of the ethers (THF and diethyl ether), the arrangement of the dipeptide molecules was changed to an antiparallel / -sheet-like structure. By crystallization from methanol-methallyl alcohol, we obtained the single crystal of an inclusion compound, which consisted of 2, methanol, and methallyl alcohol. The X-ray structure shows an antiparallel mode... 

Figure 7. Formation of the sheet structure in inclusion crystals with a Lewis base guest or a Lewis acid guest, (a) Formation of one-dimensional ribbon by head-to-tail arrangement (salt formation) of the dipeptide molecules, (b) Two-dimensional arrangement of the ribbons under the influence of the guest.

As shown in Figure 4 of section 2, the dipeptide molecules are arranged in a parallel / -sheet-like structure which is constructed by ionic pairing of carboxyl and amino groups via a hydrogen bonding network one terminal COO bridged two +NH3... 

The type of bond holding the amino acid units together in a dipeptide molecule is called ... 

Two amino acid molecules combine to form a dipeptide molecule. The reaction that occurs is ... 

Fig. 1.7 Illustration of the alanine dipeptide molecule. The central dihedral angles P and 4> are shown which are relevant to describing the conformational states...

We implement each of the methods in the NAMD-lite package [170, 302], and observe the effect of discretization error (if any) on computed averages. We initially consider the alanine dipeptide molecule in a vacuum, without boundary conditions, at T = 300 K for a fixed time interval of 2.5 ns. The CHARMM22 forcefield [246] (giving parameters for the governing potential energy functions) is used to compute force interactions. 

In order to provide a more realistic comparison to practical molecular dynamics simulation, we immerse the alanine dipeptide molecule in a sphere of flexible TIP3P water (10 A radius, total system contains 424 atoms, see Fig. 7.8) and equilibrate for 1 ns at 300K to generate an initial configuration. Simulations were completed with each scheme considered in the unsolvated case, using a lOA cutoff for the electrostatic and van der Waals potentials. 

Preparation of cryogels [297] based on the self-assembled dipeptide molecules, study of rheological properties and macroporous morphology of resulting cryogels... 

Figure 19 Spiral assembly of AV (a) and VA (b) dipeptide molecules that form a channel and illnstration of pore space in the materials. (Reproduced from Ref. 102. Wiley-VCH, 2004 and Ref. 103. American Chemical Society, 2006.)...

The crystal structure for AI contains somewhat disordered co-crystallized water molecules in a 1 1 ratio with dipeptide molecules (7 ). This corresponds to a maximum 8% water content within the crystal pores, although it may be noted that solvent content can vary depending upon recrystallization conditions. An AI sample was found to lose 2% of its weight after 5 days of exposure to 1.33 X 10 Pa (10" Torr), corresponding to 25% or more of the water residing within the pores, depending on the initial occupancy. Solvents within the dipeptide nanotubes can be removed (75,79), necessarily changing the hydrophobic interactions between solvent and peptide molecules. Crystal... 

In summary, AI is known to retain water in its pores which interacts hydrophobically with the dipeptide molecules, while it is known that lA loses intra-crystalline water in air in a matter of minutes. Line shifts of 1 cm accompany crystal dehydration in the AI spectrum compared to little noticeable shift in the lA spectrum on vacuum exposure. Therefore, the shifts in the AI spectrum are taken to indicate that water has been removed under vacuum from the AI structure whereas little if any water was present to remove from the lA structure. These results indicate that the low frequency THz modes are sensitive to changes in the weak hydrophobic interactions of water in these structures. 

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