title: Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes.
abstract: The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.
authors.affiliation: College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China. Electronic address: ckc1117@iccas.ac.cn.
authors.forename: Kaicong
authors.initials: K
authors.lastname: Cai
authors.affiliation: College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
authors.forename: Fenfen
authors.initials: F
authors.lastname: Du
authors.affiliation: College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
authors.forename: Jia
authors.initials: J
authors.lastname: Liu
authors.affiliation: College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Su
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000577:Amides / Q000737:chemistry; D002623:Chemistry Techniques, Analytical; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012996:Solutions; D012997:Solvents / Q000737:chemistry*; D014732:Vibration
chemical_list: D000577:Amides; D010455:Peptides; D011506:Proteins; D012996:Solutions; D012997:Solvents; D000409:Alanine
keywords: Ab initio calculations; Alanine dipeptide; Amide I mode; Molecular dynamic simulations; Solvation effect; Vibrational spectroscopy