Quantum mechanical investigations on the role of C-terminal residue in influencing the structural features of dipeptides containing N-terminal proline

Das, Gunajyoti; Mandal, Shilpi

doi:10.1016/j.jmgm.2013.12.009

Cited by 6 publications

(8 citation statements)

References 54 publications

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“…These results are consistent with the previous theoretical observations and serve as the indication of increased stability of the reaction species in the aqueous phase. 39 The predicted total dipole moments of LPA B , LPA C , and their metal complexes at the B3LYP and BHandHLYP levels are collected in Table 1. The tetrahedral Zn 2+ complexes exhibit much larger μ values (up to 11.94 D in the aqueous phase and 8.24 D in the gas phase) than the square-planar Ni 2+ and Cu 2+ complexes (0.10 to 0.79 D for the solvated systems and 0.35 to 1.25 D in vacuum).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…The total energies of the reaction species were corrected for zero point vibrational energy (ZPVE) using the empirical factor 0.9877. 38,39 The vibrational frequencies below 1800 cm −1 were scaled with 1.01, and for those above 1800 cm −1 a correction factor of 0.9679 was used. 38,39 Previous studies have shown that the hybrid B3LYP model performs well in describing the interactions of the aromatic amino acids with various metal cations.…”

Section: ■ Theoretical Backgroundmentioning

confidence: 99%

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Experimental and Quantum Chemical Modeling Studies of the Interactions of l-Phenylalanine with Divalent Transition Metal Cations

Mandal

Das

Askari

2014

J. Chem. Inf. Model.

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Encoded by the UUU and UUC codons of the genetic code, L-phenylalanine (LPA) serves as an important precursor for tyrosine and various other compounds that are necessary to support life on earth. Here, we report the synthesis (both in solid and solvent phases) and characterization of the Ni(2+), Cu(2+), and Zn(2+) complexes of LPA by several analytical, spectral, thermal, and electrochemical techniques. The results reveal that the products formed by following the two synthetic approaches are the same, and the metal ions bind to the LPA molecules in a 1:2 molar ratio (M(+2)/LPA). Complementary geometries of the metal complexes are modeled involving the most predominant LPA conformers predicted at the MP2/6-311++G(d,p) level. The gaseous and aqueous phase interaction enthalpies and free energies; theoretical IR and UV-vis spectra; HOMO-LUMO energy gaps; dipole moments; Wiberg bond indices as well as the partial atomic charges in LPA and its metallic complexes are calculated and evaluated using B3LYP/6-311++G(d,p) as the main computational method. This study also incorporates analyses on the efficacy of the DFT-D2 level in describing dispersion contributions, performance of the BHandHLYP functional for the open-shell Cu(2+)-LPA system, and relative metal binding affinities of the singlet versus triplet states of the Ni(2+)-LPA complex. Metal-π interactions established via the aromatic side chain of LPA add to the thermodynamic stability of the complexes, whereas metal coordination induces considerable intrinsic structural rearrangements in the molecular geometry of LPA. The LPA binding affinity order of the three Lewis acids investigated emerges as Cu(2+) > Ni(2+) > Zn(2+), paralleling the Irving-Williams series. The illustrative evidence offered by the present work suggests that the B3LYP/6-311++G(d,p) level in combination with an empirical dispersion-correction term performs well in describing the vibrational frequencies and cation-π interactions, which are undoubtedly of immense significance for natural sciences.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: ■ Theoretical Backgroundmentioning

confidence: 99%

Experimental and Quantum Chemical Modeling Studies of the Interactions of l-Phenylalanine with Divalent Transition Metal Cations

Mandal

Das

Askari

2014

J. Chem. Inf. Model.

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“…Earlier theoretical studies on the conformational propensities about the Ramachandran dihedrals − ψ and Φ (Figure ) for alanine dipeptide (AD) have revealed that the conformers C7 eq (ψ = 90.1° and Φ = −86.3°) and C5 (ψ = 143.8° and Φ = −156.4°) are the predominant species in gas and nonpolar solvent phases . However, in a polar solvent the conformers C5, α R (ψ = −32.1° and Φ = −70.5°) and β (ψ = 142.1° and Φ = −64.0°) emerge as the dominant species with a relative stability order of C5 > α R > β; where the AD conformers differ in thermodynamic stability within a narrow range.…”

Section: Results and Discussionmentioning

confidence: 99%

“…Interactions of the water molecules with proteins via intermolecular H-bonds are crucial in affording the biologically active three-dimensional structures of proteins, and study of the interactions of water molecules with peptide moieties has been the subject of intense investigation. , The intermolecular H-bonds present in w Ni(GlyGly) 2 are depicted in Figure along with their intermolecular H-bond distances. As presented in Supporting Information, Table S5, interactions of explicit water molecules with the amide planes of Ni(GlyGly) 2 result in elongation of the exposed polar C 4 O 4 and N 3 –H 3 bonds up to 0.006 Å and shortening of the embedded N 3 –C 4 bond by a maximum value of 0.013 Å.…”

Section: Results and Discussionmentioning

confidence: 99%

Metalation of Glycylglycine: An Experimental Study Performed in Tandem with Theoretical Calculations

et al. 2015

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Interactions of the Ni 2+ , Cu 2+ , and Zn 2+ ions with the simplest dipeptide glycylglycine (GlyGly) are explored using various experimental and computational techniques. Solid and aqueous phase syntheses of the metalated GlyGly complexes (by solid-state grinding and by coprecipitation respectively) lead to the same products, as confirmed by physicochemical and spectral properties which indicate metal-coordination through the −NH 2 and −CO 2 − groups of the dipeptide. Phase-diagram and kinetic studies of the solid-phase reaction between GlyGly and copper acetate suggest that complexation occurs in 1:2 (metal/ligand) stoichiometry via a facile kinetic pathway (a barrier of only 22.22 kJ/mol). The right-handed α-helical conformer of GlyGly is considered in DFT modeling studies in gas and aqueous phases elucidating the effects of metalation and solvation upon structural, electronic, and vibrational properties of the complexes. The complexes are found to follow the stability order Cu 2+ > Ni 2+ > Zn 2+ corroborating the Irving-Williams series. The Ni(GlyGly) 2 complex is predicted to exist in its low-spin state. Hydration effects on structural aspects of the complexes are also investigated computationally. The BHandHLYP/6-311++G(d,p) level describes the Cu(GlyGly) 2 complex more efficiently than the B3LYP/6-311++G(d,p) level (which, however, better predicts the vibrational spectra of the systems). Absorption titration experiments with calf thymus DNA together with in silico docking and molecular mechanical studies reveal that these metal−dipeptide complexes are DNA minor-groove binders primarily through Hbonding interactions, yielding a DNA-binding affinity order of Ni 2+ > Zn 2+ > Cu 2+ .

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“…In addition, proline has a side chain in the form of a pyrrolidine ring that connects with its amine group. The structure tends to be rigid and less flexible, this may be interesting to study and observe the effect on the geometric changes of its dipeptides products (Das & Mandal, 2014;El Guerdaoui et al, 2014;Ramaniah et al, 2011;Santos et al, 2014).…”

Section: Figure 1 Concerted Reaction Pathwaymentioning

confidence: 99%

Ab-Initio Computational Study : The Activation Energy Changes and Steric Effects In Peptide Synthesis Of Ac-AA-NH2 and Ac-AP-NH2

Pratiwi

Cahyono

Siahaan

2021

Molekul

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Ab-Initio computational method can be used for simulating reaction mechanisms, such as concerted reaction mechanism on peptide synthesis. The concerted reaction is one of many possible pathways on how peptide can be synthesized. The purpose of this study are probing the concerted reaction mechanism and comparing the steric effect to the reaction, given by different side-chain of alanine (A) and proline (P). Two dipeptides formed from alanine and proline were computed at HF-SCF/6-31G** theory level: Ac-AA-NH2 and Ac-AP-NH2. The res.lts show the activation energy of Ac-AA-NH2 and Ac-AP-NH2 forming via concerted pathway are 167.541 kJ/mol and 161.044 kJ/mol, respectively. The steric difference in side-chain affects the dihedral angle of the structure, and also gives difference to the entropy value of reaction.

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Quantum mechanical investigations on the role of C-terminal residue in influencing the structural features of dipeptides containing N-terminal proline

Cited by 6 publications

References 54 publications

Experimental and Quantum Chemical Modeling Studies of the Interactions of l-Phenylalanine with Divalent Transition Metal Cations

Experimental and Quantum Chemical Modeling Studies of the Interactions of l-Phenylalanine with Divalent Transition Metal Cations

Metalation of Glycylglycine: An Experimental Study Performed in Tandem with Theoretical Calculations

Ab-Initio Computational Study : The Activation Energy Changes and Steric Effects In Peptide Synthesis Of Ac-AA-NH2 and Ac-AP-NH2

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