Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

Gong, Xiaoli; Zhou, Zhengyu; Du, Da‐Ming; Dong, Xiu-li; Liu, Shuzhen

doi:10.1002/qua.20471

Cited by 12 publications

(13 citation statements)

References 29 publications

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“…According to the work of Gong et al, 14 the most stable conformer should be the structure N5 whereas from the calculations of Jarmelo et al 4 N5 and N6 conformers are almost degenerate, the energy gap between them being 0.7 kJ/mol. Although a detailed discussion of the conformations of serine is not the aim of this paper, some interesting features regarding their relative stabilities should be highlighted.…”

Section: Resultsmentioning

confidence: 95%

“…1 Serine is a good model for studying peptide structures. Recently, Gong et al 14 have carried out an exhaustive investigation on the interaction of serine with water, exploring the specific solvation of all the reactive sites of the aminoacid. 11,12 One important characteristic of this molecule is the possibility of forming strong hydrogen bonds (HBs) between its HB-donor and HB-acceptor groups, which play an important role as far as the relative stability of its conformers is concerned.…”

Section: Introductionmentioning

confidence: 99%

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Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

2010

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The association of Ca 2+ and Cu 2+ to serine was investigated by means of B3LYP DFT calculations. The [serine-M] 2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine-M] 2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca 2+ and serine is essentially electrostatic, that between Cu 2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu 2+ than Ca 2+ binding energies. More importantly, the interaction with Cu 2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca 2+ . The main consequence is that in Cu 2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine-Cu] 2+ complexes. This is not the case for Ca 2+ complexes. Thus, [serine-Ca] 2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu 2+ should deprotonate spontaneously and therefore only [(serine-H)-Cu] + monocations should be experimentally accessible. Résumé :On étudié l'association des cations Ca 2+ et Cu 2+ avec la serine en utilisant la théorie de la fonctionnelle de la densité, B3LYP. Pour l'ion [sérine-M] 2+ (M = Ca, Cu), comme c'est le cas pour la sérine neutre, les surfaces d'énergie potentielle comportent un grand nombre de conformères dans lesquels on peut observer une réorganisation drastique de la densité électronique de la sérine. Ces changements conduisent à des changements significatifs dans le nombre et la force des liaisons hydrogènes intramoléculaires par rapport à celles qui existent dans les tautomères neutres de la sérine. Dans quelques cas, il se produit un transfert de proton du groupe OH de l'acide carboxylique vers le groupe amino et, en conséquence, un certain nombre des complexes les plus stables de l'ion [sérine-M] 2+ peuvent être considérés comme étant le résultat de l'interaction de la forme zwitterionique de la sérine avec l'ion métallique doublement chargé. Alors que l'interaction entre la Ca 2+ et la sérine est essentiellement électrostatique, celle entre le Cu 2+ et la sérine comporte un caractère covalent non négligeable qui est le reflet de densités électroniques plus grandes aux points critiques de liaison entre les deux systèmes en interaction ainsi que des énergies de liaisons beaucoup ...

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Section: Resultsmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

2010

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“…Gong X et al, have also inferred the same. 15 Blue shift in υ C−H is reflected along with contraction of C-H bond length in complexes involving C-H as HB donor. The decrease in C-H bond length ranges between 0.001-0.005 Å and the stretching frequency shifts for this bond lie in the range +5.89 to +52.05 cm −1 and +8.93 to +52.58 cm −1 for serinewater and serine-HP complexes under study.…”

Section: 2b Geometries and Vibrational Frequenciesmentioning

confidence: 99%

“…The direct study of these interactions is extremely difficult due to the complexity of the protein macromolecule. 12,13 The nature of hydrogen bonding between water and serine [14][15][16] can explain the role of water in various bioprocesses wherein making and breaking of HBs is important.…”

Section: Introductionmentioning

confidence: 99%

Quantum chemical study of hydrogen-bonded complexes of serine with water and $$\hbox {H}_{2}\hbox {O}_{2}$$ H 2 O 2

Chopra

Kaur

2018

J Chem Sci

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The hydrogen bonded complexes of serine with water and with H 2 O 2 (HP) have been completely investigated in the present study using second-order Møller-Plesset perturbation theory (MP2) and density functional theory (DFT) in order to determine their geometries, stabilization energies, vibrational frequencies and electronic characteristics. The stabilization energies (E BSSE) span a range of −2.76 to −12.46 kcal/mol for 1:1 serine-water complexes and −4.54 to −12.73 kcal/mol for 1:1 serine-HP complexes. The E BSSE values suggest that serine-HP complexes are more stable than serine-water complexes. For all the structures, complex formation results in elongation of N-H, O-H bonds and shortening of C-H bonds thereby showing the red-shift and blue-shift for the respective bonds. The structural, vibrational and electronic features are in accordance with the fact that HP is a better proton donor and water a better proton acceptor. The excellent relationship is obtained for the variation of E BSSE values with the sum of the ρ values and the sum of laplacian at the BCPs for the HBs. The E (2) values are also in concordance with the calculated E BSSE values.

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“…Vibrational spectroscopy is one of the most useful experimental tools for study of the H‐bonded clusters, so the information on calculated harmonic vibrational frequencies can be useful. And the elucidation of reaction mechanisms via vibrational mode analysis gets more and more attentions from our laboratory 25–29. Table IV gives the B3LYP/6‐311++G( d , p ) values for vibrational frequencies intensities of selected vibrational modes in the eight complexes and monomers, the change of frequencies of the eight compared with the monomers can also be available in Table IV.…”

Section: Resultsmentioning

confidence: 99%

Density functional theory study of the interaction between formamide and uracil

Duan

et al. 2006

Int J of Quantum Chemistry

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ABSTRACT:The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6-31G to 6-311ϩϩG(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven-membered rings; the others are eight-membered rings. The eight-membered ring is preferred over the seven-membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported.

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Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

Cited by 12 publications

References 29 publications

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

Quantum chemical study of hydrogen-bonded complexes of serine with water and $$\hbox {H}_{2}\hbox {O}_{2}$$ H 2 O 2

Density functional theory study of the interaction between formamide and uracil

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Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

Cited by 12 publications

References 29 publications

Serine–Ca2+versus serine–Cu2+complexes — A theoretical perspective

Serine–Ca2+versus serine–Cu2+complexes — A theoretical perspective

Quantum chemical study of hydrogen-bonded complexes of serine with water and $$\hbox {H}_{2}\hbox {O}_{2}$$ H 2 O 2

Density functional theory study of the interaction between formamide and uracil

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Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective