Alanine Dipeptide Results

The vacuum potential results, corresponding to the limit of zero viscosity, are shown in Fig. 41a. At zero viscosity, the dihedral angle 41 oscillates with a period of approximately 0.63 ps. When the conditions are changed to represent water at 300 K (i.e., the solvent-modified potential-of-mean-force surface is used and r) = 1.0 cP), the dominant effect is that the dihedral motion has a periodicity of about 3.7 ps (see Fig. 41b). The solvent influence observed in these simulations is consistent with an earlier molecular dynamics study of 

The influence of solvent viscosity on the dynamics of small biopolymers, like the alanine dipeptide, is clearly illustrated by the results given here. However, it is necessary to determine whether for larger biopolymers like globular proteins, the solvent influence on the dynamics can also be related to the viscosity alone. Below we provide evidence to the contrary. It is found that the solvent does not affect all atoms and all of their dynamical properties in the same way. Thus, a description based on only the solvent viscosity is not adequate, even disregarding possible alterations in the potential of mean force. 

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OS 24] [R 5] [P 16/Dmab-y0-alanineand Emoc-yS-alanine were reacted to give a dipeptide [5], After cleavage of the Emoc function, Emoc-yS-alanine was added to such a dipeptide resulting in tripeptide formation with 30% yield [5]. 

Fig. 4.5. Free energy profile of alanine dipeptide as a function of

As an example, this approach was applied to the calculation of the PMF for alanine dipeptide as a function of the two torsion angles

resulting free energy surface is shown in Fig. 4.5. Bilinear Qi elements were used to approximate the free energy. Control points were chosen such that there are four of them around each data point. This was done in order to increase the smoothness and quality of the reconstructed free energy. The position of the Q i nodes and control points is shown in Fig. 4.6. 

Figure 10.8 Structure of a dipeptide. The peptide bond joins glutamic acid and alanine by condensation of the a-carboxyl group of glutamic acid and the a-amino group of alanine. The resulting dipeptide is called glutamylalanine, which can be abbreviated to NH2-Glu-Ala-COOH or Glu-Ala.

We compute free energy surfaces in the (f,f ) space, 3/(Hc,HN) dipolar couplings and radial distribution functions (RDF) which show that (1) PM3 is incapable of reproducing the conformational distribution of alanine dipeptide (2) the peptide correction does not improve the results (3) the addition of the PDDG function to PM3 can noticeably improve the energetics and (4) none of the QM methods can reproduce the experiment better than the classical ff99SB force field. 

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory80... 

Alanine dipeptide, see Fig. 10.30, is a useful model compound in that it contains the basic constituents of a peptide chain. Thus there are sp -sp backbone C-C bond, backbone N-C bonds and side-chain C-C bonds. The torsions about each of these bonds are denoted as F, O and % respectively. The compound in the solid state has been modelled by molecular mechanics using the CHARMM force field [76]. The best results required non-zero force constants for the T and O torsions. Fig. 10.31 compares the experimental spectrum with the calculated one. There is a uniform mismatch in frequencies of 35 cm", but the overall pattern is reproduced. The individual contributions of the methyl groups... 

A well-studied system is alanine dipeptide (AcAlaNHMe). The relative stability of different conformational states in vacuum - and in water were obtained from PMF calculations, °> and again different models and simulation parameters were applied. In a recent study Marrone, Gilson, and McCammon calculated the PMF of alanine dipeptide by using the Pois-son-Boltzmann method with a hydrophobic term and by using explicit water and found comparable results. Fraternali and van Gunsteren studied PMFs of glycine dipeptide in water for two reaction coordinates. Tobias and Brooks used their own technique to calculate the PMF of the central torsional angle... 

Fig. 7.9 Computed distributions of potentitil eneigy tire overlaid for 22 experiments of solvated alanine dipeptide using the given discretization scheme. The distributions are colored by the stepsizE used to generate them from h = 1 fs (blue) to h = 2.8 fs red), where the common black dashed distribution marks the baseline result...

D. J. Tobias and C. L. Brooks,/. Phys. Chem., 96(9), 3864-3870 (1992). Conformational Equilibrium in the Alanine Dipeptide in the Gas Phase and Aqueous Solution A Comparison of Theoretical Results. 

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