A theoretical study on hydration of alanine zwitterions

Sagarik, Kritsana; Dokmaisrijan, Supaporn

doi:10.1016/j.theochem.2004.10.091

Cited by 25 publications

(44 citation statements)

References 49 publications

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“…Due to the fact that the mobility of water molecules depends on the transition energy barriers, which could be estimated from the average potential energy landscapes, the AWPD, WWPD and AW-WWPD maps were examined in details. Various cross section plots of the average potential energy landscapes were generated by taking vertical slices along predefined profile lines, through the surfaces of the AW-WWPD maps, as well as the AWPD and WWPD maps [16]. In the present study, the cross section plots computed from the longitudinal profile lines could be associated with the transition energy barriers to water exchange within, as well as between, the H-bond networks (bE aq L À).…”

Section: R=xmentioning

confidence: 99%

“…In the present study, the AW-WWPD maps represent the average potential energy landscapes of the H-bond networks of water. They were computed by combination of the AWPD and WWPD maps [16]. Only the negative interaction energies were displayed in the AWPD, WWPD and AW-WWPD maps.…”

Section: R=xmentioning

confidence: 99%

“…These remarks partly formed the basis of our previous theoretical investigations on alanine zwitterion in aqueous solutions ([Alaz] aq ) [16], in which the detail structures and energetic of the H-bond networks of water in the first hydration shell of Alaz were derived from MD simulations. In Ref.…”

Section: Introductionmentioning

confidence: 97%

“…In Ref. [16], the three-dimensional structures of the H-bond networks of water were analyzed and visualized using various probability distribution (PD) maps, such as the oxygen (PDO) and hydrogen probability distribution (PDH) maps, as well as the average solute-solvent (AWPD) and solvent -solvent interaction energy probability distribution (WWPD) maps. The structures of the average potential energy landscapes were employed to describe the dynamic behavior of water molecules in the first hydration shell of the functional groups of Alaz.…”

Section: Introductionmentioning

confidence: 99%

“…It was concluded in Ref. [16] that a complete picture of molecular hydration could be obtained only when explicit water molecules, together with their hydration dynamics in the first hydration shell, are considered in the model calculations.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Structures and stability of salt-bridge in aqueous solution

Sagarik¹,

Chaiyapongs²

2005

Biophysical Chemistry

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Section: R=xmentioning

confidence: 99%

Section: R=xmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structures and stability of salt-bridge in aqueous solution

Sagarik¹,

Chaiyapongs²

2005

Biophysical Chemistry

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Glycine Dimers: Structure, Stability, and Medium Effects

Friant-Michel

Ruiz‐López

2010

ChemPhysChem

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We report a study on different ionization states and conformations of the bimolecular (Gly)(2) system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug-cc-pVTZ and B3LYP/6-311+G(2df,2p) methods on B3LYP/6-31+G(d,p) optimized structures (some single-point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion-zwitterion or neutral-zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (-4 kcal mol(-1)). Thus, according to our results, zwitterion-zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α-glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion-zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.

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Proton dissociation and transfer in hydrated phosphoric acid clusters

Suwannakham

Chaiwongwattana

Sagarik

2015

Int J of Quantum Chemistry

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The dynamics and mechanisms of proton dissociation and transfer in hydrated phosphoric acid (H3PO4) clusters under excess proton conditions were studied based on the concept of presolvation using the H3PO4–H3O+–nH2O complexes (n = 1–3) as the model systems and ab initio calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the RIMP2/TZVP level as model calculations. The static results showed that the smallest, most stable intermediate complex for proton dissociation (n = 1) is formed in a low local‐dielectric constant environment (e.g., ε = 1), whereas proton transfer from the first to the second hydration shell is driven by fluctuations in the number of water molecules in a high local‐dielectric constant environment (e.g., ε = 78) through the Zundel complex in a linear H‐bond chain (n = 3). The two‐dimensional potential energy surfaces (2D‐PES) of the intermediate complex (n = 1) suggested three characteristic vibrational and 1H NMR frequencies associated with a proton moving on the oscillatory shuttling and structural diffusion paths, which can be used to monitor the dynamics of proton dissociation in the H‐bond clusters. The BOMD simulations over the temperature range of 298–430 K validated the proposed proton dissociation and transfer mechanisms by showing that good agreement between the theoretical and experimental data can be achieved with the proposed rate‐determining processes. The theoretical results suggest the roles played by the polar solvent and iterate that insights into the dynamics and mechanisms of proton transfer in the protonated H‐bond clusters can be obtained from intermediate complexes provided that an appropriate presolvation model is selected and that all of the important rate‐determining processes are included in the model calculations. © 2015 Wiley Periodicals, Inc.

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A theoretical study on hydration of alanine zwitterions

Cited by 25 publications

References 49 publications

Structures and stability of salt-bridge in aqueous solution

Structures and stability of salt-bridge in aqueous solution

Glycine Dimers: Structure, Stability, and Medium Effects

Proton dissociation and transfer in hydrated phosphoric acid clusters

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