Formation of hydrogen-bonded dimers of uracil and amino acids: Cysteine, lysine and phenylalanine. A density functional theory study

Troitiño, D.; Bailey, Lorna E.; Peral, F.

doi:10.1016/j.theochem.2006.05.034

Cited by 18 publications

(18 citation statements)

References 46 publications

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“…DFT has been accepted by the ab initio quantum chemistry community as a cost-effective approach for the computation of molecular structures, vibrational frequencies, and energies of chemical reactions. Recently, DFT has been used widely to study H-bond interactions [13][14][15][16]. Generally, the formation of H-bond can be estimated by the structural parameters (e.g.…”

Section: Introductionmentioning

confidence: 99%

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

Huang

Dai

2010

Struct Chem

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The (CH 3 OH) n (n = 2-8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OHÁÁÁO H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH 3 OH) n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH 3 OH) n (n = 4-8) clusters are remarkably stronger than those in (CH 3 OH) n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH 3 OH) n (n = 6-8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (q b ) and the HÁÁÁO bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.Keywords The quantum theory of atoms in molecule (QTAIM) Á Natural bond orbital (NBO) Á Density functional theory (DFT) Á Hydrogen bond Á Methanol clusters

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Section: Introductionmentioning

confidence: 99%

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

Huang

Dai

2010

Struct Chem

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“…However, for the case of amino acids, it is needed to get a clue which might lead to the specification of association scheme, i.e., number of association sites and type of association. In recent years, there have been many advances in the research on association behaviors of amino acids by using the molecular simulation method such as Monte Carlo (MC) or molecular dynamics (MD) techniques [32][33][34][35]. Tunon et al [32] reported that 2.8 water molecules are bound to a nitrogen atom of zwitterionic form of glycine and 2.3 water molecules also are bound to the oxygen atoms of zwitterion.…”

Section: Thermodynamic Backgroundmentioning

confidence: 99%

“…Chang et al [33] reported that hydration numbers range from 3.2 to 3.4 for the ammonium H of zwitterion and from 5.7 to 5.9 for the carboxylate O over several amino acids like glycine, serine, threonine, tyrosine, etc. Besides, Rossi et al [34] and Troitino et al [35] elucidated the occurrence of self-association (hydrogen bond) between the ammonium H of zwitterion and the carboxylate O, through the molecular dynamic simulations. Apart from these molecular simulation studies, recently, Cameretti and Sadowski [29] assumed that each of NH 2 and COOH groups in amino acid has two proton donor sites and two acceptor sites, respectively.…”

Section: Thermodynamic Backgroundmentioning

confidence: 99%

Study on the activity coefficients and solubilities of amino acids in aqueous solutions with perturbed-chain statistical associating fluid theory

Lee

Kim

2010

Korean J. Chem. Eng.

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Perturbed-chain statistical associating fluid theory (PC-SAFT) was applied for modeling the thermodynamic properties of aqueous amino acid solutions. To account for the association phenomena of amino acids occurring in the aqueous solution, the zwitterionic forms of amino acids are assumed to be associating species with proton donor and acceptor sites. Also, in order to reduce the number of adjustable parameters of PC-SAFT equation of state (EoS) for amino acids from five to three, it is assumed that segment numbers of amino acids are linearly related with the molecular weight of amino acids, and the association volume parameters of amino acids can be set to a fixed value. Thus, 3-parameters of PC-SAFT EoS for amino acids were estimated by simultaneously fitting the activity coefficients of amino acid and densities data in the aqueous amino acid solutions. The PC-SAFT EoS with estimated 3-parameters of amino acid is found to well describe activity coefficients of amino acid and densities of the aqueous amino acid solutions. Also, this equation was used for predicting solubilities of amino acids as well as the water activities and osmotic coefficients in the aqueous amino acid solutions. The predicted values of these properties are in good agreement with the experimental data.

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“…Recently, density functional theory (DFT) has been used widely to study hydrogen bonding interactions [5][6][7][8]. The structure parameters are the principal criteria of the existence of H-bond and can be calculated by DFT.…”

Section: Introductionmentioning

confidence: 99%

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

Huang

Dai

2010

Struct Chem

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The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311??G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine-propanoic acid (Cys-Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra-and inter-molecular H-bonds have been found in Cys-Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of CysProp complexes. The strongest H-bonds (O2H A ÁÁÁO1 B and O2H A ÁÁÁO1 B ) exist in the most stable Cys-Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (q) of BCP and H-bond length as well as the Fock matrix element (F ij ) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.

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Formation of hydrogen-bonded dimers of uracil and amino acids: Cysteine, lysine and phenylalanine. A density functional theory study

Cited by 18 publications

References 46 publications

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

Study on the activity coefficients and solubilities of amino acids in aqueous solutions with perturbed-chain statistical associating fluid theory

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

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