Praveena Gopalan | PSGR KRISHNAMMAL COLLEGE FOR WOMEN (original) (raw)
Papers by Praveena Gopalan
Journal of Chemical Sciences, 2022
The present study explores the conformational dependence of the redox potentials of 1,4-benzoquin... more The present study explores the conformational dependence of the redox potentials of 1,4-benzoquinone (1,4-BQ) molecule employing density functional theory (DFT). The basic 38 conformers of 1,4-BQ (2 chairs, 6 boats, 6 skew-boats, 12 half-chairs, 12 envelopes) were extracted following the IUPAC nomenclature by Berces et al. and were optimized at B3LYP/6-31+G(d), M06-2X/6-31+G(d) and wB97X-D/6-31+G(d) levels of theory. The quantitative analysis was made using the spherical polar coordinates (d, θ, and ϕ) and structural parameters. The electrochemical performance is explored through the calculation of free energies and redox potentials using conductor-like polarizable continuum model (C-PCM). A good correlation is found between the conformers with more negative lowest unoccupied molecular orbital (LUMO) energies and their redox potentials. The results put emphasis on the variation of redox potential with respect to conformational change of 1,4-BQ molecule and the importance of using B3...
This contribution reports on the photosensitizing competence of Sn(IV)tetrakis(4-pyridyl)porphyri... more This contribution reports on the photosensitizing competence of Sn(IV)tetrakis(4-pyridyl)porphyrins (SnTP) for potential applications in dye sensitized solar cell (DSSC). The photosensitization of SnTPs is accounted on the basis of different axial ligands (OH−, Cl−, and H2O) and the pyridine protons. The qualitative information on the photovoltaic performance of the sensitizers is obtained at B3LYP/6-31+G(d) level of theory with LANL2DZ basis set for Sn atom through the calculation of parameters such as free energy change of electron injection (ΔGinject\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta G^{\text{inject}}$$\end{document}) and regeneration (ΔGreg\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepack...
ECS Journal of Solid State Science and Technology
Monatshefte für Chemie - Chemical Monthly
Journal of the Chinese Chemical Society
Zeitschrift für Physikalische Chemie
We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs... more We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs, Guanine-Cytosine (GC), Adenine-Thymine (AT) and Adenine-Uracil (AU) by incorporating N-(2-aminoethyl) glycine units (linked by amide bonds) at the purine and pyrimidine sites of the nucleobases. Density functional theory (DFT) is employed in which B3LYP/6-311++G∗∗ level of theory has been used to optimize all the structures. The peptide attached base pairs are compared with the natural deoxyribose nucleic acid (DNA)/ribonucleic acid (RNA) base pairs and the calculations are carried out in both the gas and solution phases. The structural propensities of the optimized base pairs are analyzed using base pair geometries, hydrogen bond distances and stabilization energies and, compared with the standard reference data. The structural parameters were found to correlate well with the available data. The addition of peptide chain at the back bone of the DNA/RNA base pairs results only with a m...
![Research paper thumbnail of Interaction of metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide – A theoretical study](https://attachments.academia-assets.com/70091416/thumbnails/1.jpg)
](Journal of Molecular Structure: THEOCHEM, 2009
The interaction of monovalent metal ions with cyclo[(1R,3S)-c-Acc-Gly] 3 hexapeptide ((TAG) 3) is... more The interaction of monovalent metal ions with cyclo[(1R,3S)-c-Acc-Gly] 3 hexapeptide ((TAG) 3) is studied using density functional theory calculations. The (TAG) 3 and its Li + , Na + and K + metal ionic complexes are optimized at B3LYP/6-311+G * level of theory. The optimized structure of (TAG) 3 ionic complexes agrees well with the various cyclic peptide cationic complexes that are obtained experimentally. The valence, peptide deformation and Ramachandran angles clearly explain the structural effects in (TAG) 3 upon ionic interaction. The dependability of cavity size towards the size of ions is noted. The molecular electrostatic potential (MEP) map effectively illustrates the weak interaction between metal ion and (TAG) 3 , and further confirms carbonyl oxygens to be the active sites. The binding energy of (TAG) 3 towards metal ion increases as Li + > Na + > K + , which is consistent with the electron density at bond critical points. The significant binding energies and the symmetric nature of (TAG) 3 upon Na + and K + enclosures in turn shows that its nanotubular structures might act as the ion channels of biological interest.
Communications in Theoretical Physics, 2015
ABSTRACT This paper is proposed to understand the interaction of porphyrin layers with diatomic m... more ABSTRACT This paper is proposed to understand the interaction of porphyrin layers with diatomic molecules interacting at their interior regions by applying ab initio and density functional theory (DFT) methods. We have used NO, CO, and O2 diatomic molecules to interact with the porphyrin layers. The most common Fe-centered metalloporphyrin structure with tetra-pyrrlic rings having N4 core is chosen for the study. The optimization of Porphyrin-Porphyrin (PI-PII) and Porphyrin-Diatomic molecule-Porphyrin (PI-AB-PII) (AB = NO, CO, and O2) complexes are performed using HF method. In order to understand the planarity and appropriate stacking size of porphyrins and also to infer the separation of diatomic molecules between porphyrin layers the behavior of PI-AB-PII complexes (where AB = NO, CO, and O2) are analyzed using structural properties and molecular electrostatic potentials (MEP). The MEPs are calculated using hybrid exchange correlation functional B3PW91 of DFT along with 6-31+G* basis set for the PI-PII and PI-AB-PII complexes obtained from HF method.
Soft Materials, 2014
ABSTRACT The transport properties of oxygen in three amino-functionalized cubic polyhedral oligom... more ABSTRACT The transport properties of oxygen in three amino-functionalized cubic polyhedral oligomeric silsesquioxanes (POSS) have been studied using classical molecular dynamics (MD) simulations over a timescale long enough to reach the Fickian regime for diffusion. An amount of O2 corresponding to an applied pressure of 3 bars was inserted into molecular models of hybrid organic/inorganic POSS with the chemical composition (RSiO3/2)8, which differed by the end-groups of their organic pendant chains, that is, R = −(CH2)3−NH−CO−X with X = −C6H4OH, −C6H5 or −C6H11. The oxygen … POSS energies were found to be small with respect to the POSS… POSS interactions. The O2 molecules permeate the organic phase and move through combinations of oscillations within available free volumes in the matrices and occasional jumping events. Gas mobility was more restricted in the system with the salicylic end-group and the largest hydrogen-bond network, whereas it was enhanced in the system with the cyclohexyl end-group. The most energetically-favorable sites for O2 insertion were either in the vicinity of the silica cages or close to the rings of the chain end-groups. On the other hand, the amide and hydroxyls groups engaging in H-bonds were less energetically favorable. This confirms that H-bonding networks are a hindrance for O2 transport in such systems.
Journal of Nanoscience and Nanotechnology, 2007
Since the discovery of CNT by Iijima, Nature 354, 56 (1991). CNT's have surged to the forefront a... more Since the discovery of CNT by Iijima, Nature 354, 56 (1991). CNT's have surged to the forefront as a versatile nanostructured material in nanoelectronic applications. Polypeptides nanotubular structures with tunable properties offer a challenging alternative to CNT. Earlier experimental studies on L-Alanyl-L-Valine (AV) and L-Valyl-L-Alanine (VA) have demonstrated their potential as novel porous materials, which form channel-like structure (Soldatov et al., Angew. Chem. Int. Ed. 43, 6308 (2004)). In the study reported here, DFT calculations on two closely related cyclic dipeptides cyclo[Lalanyl-L-valine] 3 and cyclo[L-valyl-L-alanine] 3 and on their linear correlates, [L-alanyl-L-valine] 3 and [L-valyl-L-alanine] 3 have been performed. This paper presents the general structural and electronic properties of cyclic and linear correlates of the nanotubular oligomeric dipeptides constructs, AV, and VA. We have compared the energy gaps of these cyclic rings and their linear correlates with that of other nanotubular constructs. The calculated HOMO-LUMO gap of these isolated ring structures is significantly larger than CNT's. Further research is required to reduce the band gaps to be comparable to CNT's and other inorganic tubular structures. Polypeptide design promises to be a major tool in engineering desirable band gap for the creation of novel nanostructured polypeptide nanotubes.
Journal of Molecular Structure, 2007
Density functional theory calculations have been carried out to analyze the effect of hydrogen ha... more Density functional theory calculations have been carried out to analyze the effect of hydrogen halides and H 2 O molecule interactions with the three lowest energy isomers the ring, bowl and cage of C 20 fullerene. The single-point energy calculations have also been performed at MP2/6-31+G*//B3LYP/6-31G* level of theory. The complexes (C 20 Á Á ÁH-X and H 2 O, where X = F, Cl, and Br) are bounded by two interactions namely: (i) very weak X-HÁ Á Áp H-bond interactions and (ii) long range van der Waals interactions of H-XÁ Á ÁC type. These interactions produced negligible distortion in the structures and a good correlation between electron density and stabilization energy of the complexes is found. The counterpoise correction to the interaction energies and the study of topology of the electron density for all the complexes have been performed. The charge transfer and the maneuver of resonance interaction in the interacting orbitals have been investigated by natural bond orbital (NBO) approach.
Journal of Molecular Modeling, 2008
The quantum chemical and molecular dynamics studies have been performed to infer the structural c... more The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(gamma-Acc)-alpha-Glycine(Gly)](3) hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation angles applying B3LYP/6-311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-gamma-Acc-Gly](3) hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing the pore of all-cis cyclo[(1R,3S)-gamma-Acc-Gly](3) peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site...water hydrogen bond interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-gamma-Acc-Gly](3) due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of molecules through the pore of all-trans cyclo[(1R,3S)-gamma-Acc-Gly](3) peptide due to the obstruction produced by cyclohexane groups.
Journal of Chemical Sciences, 2005
In this paper, we have introduced the atomic descriptors s(f) k to determine the local reactive s... more In this paper, we have introduced the atomic descriptors s(f) k to determine the local reactive sites of the molecular systems during electrophilic, nucleophilic and radical attacks. The condensed Fukui function and the newly introduced condensed atomic descriptor have been calculated for six different systems, namely glycine, alanine, aniline, BH 2 Cl, trans-FC(O)OF and m-anisidine. The individual atomic charges (gross charge) calculated by the MPA scheme have been used to calculate the condensed Fukui functions (f k) and the newly derived condensed atomic descriptors (sf) α k at B1-DZP level of theory. We carried out the calculation using the "stockholders" charge partitioning technique (i.e., Hirshfeld population scheme). The newly derived quantity gives the same reactive sites as the condensed Fukui functions, and the complexities associated with the negative Fukui functions are removed.
IEEE Transactions on NanoBioscience, 2000
ABSTRACT The quantum mechanics/molecular mechanics ONIOM calculations have been performed to stud... more ABSTRACT The quantum mechanics/molecular mechanics ONIOM calculations have been performed to study the structure and metal-ion binding properties of all-trans cyclo[1R-3S-γ-Acc- Gly]3 hexapeptide nanotube (TAG)3PNT. The intersubunit distances and tube angle of (TAG)3PNT exhibited the sturdy nature of (TAG)3 stacks upon Li+, K+, Mg2+, and Zn2+ enclosure. The calculated dimer binding energies of (TAG)3PNT and its ionic complexes confirm that the building blocks are bound by C=O...H-N hydrogen bond interactions. The binding energy of (TAG)3PNT with ions interacting at the surface cavity exhibit the affinity of ions at the entrance of the channel and the many-body analysis for the ion interacting at the central region substantiates the major contribution of two-body interactions to the total binding energy. In general, the binding energies of (TAG) 3PNT metal ion interacting complexes with well-maintained channel shows α-γ hybrid cyclic peptides as the promising peptidic nanochannels of biological interests.
Journal of Molecular Modeling
Journal of Chemical Sciences, 2022
The present study explores the conformational dependence of the redox potentials of 1,4-benzoquin... more The present study explores the conformational dependence of the redox potentials of 1,4-benzoquinone (1,4-BQ) molecule employing density functional theory (DFT). The basic 38 conformers of 1,4-BQ (2 chairs, 6 boats, 6 skew-boats, 12 half-chairs, 12 envelopes) were extracted following the IUPAC nomenclature by Berces et al. and were optimized at B3LYP/6-31+G(d), M06-2X/6-31+G(d) and wB97X-D/6-31+G(d) levels of theory. The quantitative analysis was made using the spherical polar coordinates (d, θ, and ϕ) and structural parameters. The electrochemical performance is explored through the calculation of free energies and redox potentials using conductor-like polarizable continuum model (C-PCM). A good correlation is found between the conformers with more negative lowest unoccupied molecular orbital (LUMO) energies and their redox potentials. The results put emphasis on the variation of redox potential with respect to conformational change of 1,4-BQ molecule and the importance of using B3...
This contribution reports on the photosensitizing competence of Sn(IV)tetrakis(4-pyridyl)porphyri... more This contribution reports on the photosensitizing competence of Sn(IV)tetrakis(4-pyridyl)porphyrins (SnTP) for potential applications in dye sensitized solar cell (DSSC). The photosensitization of SnTPs is accounted on the basis of different axial ligands (OH−, Cl−, and H2O) and the pyridine protons. The qualitative information on the photovoltaic performance of the sensitizers is obtained at B3LYP/6-31+G(d) level of theory with LANL2DZ basis set for Sn atom through the calculation of parameters such as free energy change of electron injection (ΔGinject\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta G^{\text{inject}}$$\end{document}) and regeneration (ΔGreg\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepack...
ECS Journal of Solid State Science and Technology
Monatshefte für Chemie - Chemical Monthly
Journal of the Chinese Chemical Society
Zeitschrift für Physikalische Chemie
We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs... more We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs, Guanine-Cytosine (GC), Adenine-Thymine (AT) and Adenine-Uracil (AU) by incorporating N-(2-aminoethyl) glycine units (linked by amide bonds) at the purine and pyrimidine sites of the nucleobases. Density functional theory (DFT) is employed in which B3LYP/6-311++G∗∗ level of theory has been used to optimize all the structures. The peptide attached base pairs are compared with the natural deoxyribose nucleic acid (DNA)/ribonucleic acid (RNA) base pairs and the calculations are carried out in both the gas and solution phases. The structural propensities of the optimized base pairs are analyzed using base pair geometries, hydrogen bond distances and stabilization energies and, compared with the standard reference data. The structural parameters were found to correlate well with the available data. The addition of peptide chain at the back bone of the DNA/RNA base pairs results only with a m...
Journal of Molecular Structure: THEOCHEM, 2009
The interaction of monovalent metal ions with cyclo[(1R,3S)-c-Acc-Gly] 3 hexapeptide ((TAG) 3) is... more The interaction of monovalent metal ions with cyclo[(1R,3S)-c-Acc-Gly] 3 hexapeptide ((TAG) 3) is studied using density functional theory calculations. The (TAG) 3 and its Li + , Na + and K + metal ionic complexes are optimized at B3LYP/6-311+G * level of theory. The optimized structure of (TAG) 3 ionic complexes agrees well with the various cyclic peptide cationic complexes that are obtained experimentally. The valence, peptide deformation and Ramachandran angles clearly explain the structural effects in (TAG) 3 upon ionic interaction. The dependability of cavity size towards the size of ions is noted. The molecular electrostatic potential (MEP) map effectively illustrates the weak interaction between metal ion and (TAG) 3 , and further confirms carbonyl oxygens to be the active sites. The binding energy of (TAG) 3 towards metal ion increases as Li + > Na + > K + , which is consistent with the electron density at bond critical points. The significant binding energies and the symmetric nature of (TAG) 3 upon Na + and K + enclosures in turn shows that its nanotubular structures might act as the ion channels of biological interest.
Communications in Theoretical Physics, 2015
ABSTRACT This paper is proposed to understand the interaction of porphyrin layers with diatomic m... more ABSTRACT This paper is proposed to understand the interaction of porphyrin layers with diatomic molecules interacting at their interior regions by applying ab initio and density functional theory (DFT) methods. We have used NO, CO, and O2 diatomic molecules to interact with the porphyrin layers. The most common Fe-centered metalloporphyrin structure with tetra-pyrrlic rings having N4 core is chosen for the study. The optimization of Porphyrin-Porphyrin (PI-PII) and Porphyrin-Diatomic molecule-Porphyrin (PI-AB-PII) (AB = NO, CO, and O2) complexes are performed using HF method. In order to understand the planarity and appropriate stacking size of porphyrins and also to infer the separation of diatomic molecules between porphyrin layers the behavior of PI-AB-PII complexes (where AB = NO, CO, and O2) are analyzed using structural properties and molecular electrostatic potentials (MEP). The MEPs are calculated using hybrid exchange correlation functional B3PW91 of DFT along with 6-31+G* basis set for the PI-PII and PI-AB-PII complexes obtained from HF method.
Soft Materials, 2014
ABSTRACT The transport properties of oxygen in three amino-functionalized cubic polyhedral oligom... more ABSTRACT The transport properties of oxygen in three amino-functionalized cubic polyhedral oligomeric silsesquioxanes (POSS) have been studied using classical molecular dynamics (MD) simulations over a timescale long enough to reach the Fickian regime for diffusion. An amount of O2 corresponding to an applied pressure of 3 bars was inserted into molecular models of hybrid organic/inorganic POSS with the chemical composition (RSiO3/2)8, which differed by the end-groups of their organic pendant chains, that is, R = −(CH2)3−NH−CO−X with X = −C6H4OH, −C6H5 or −C6H11. The oxygen … POSS energies were found to be small with respect to the POSS… POSS interactions. The O2 molecules permeate the organic phase and move through combinations of oscillations within available free volumes in the matrices and occasional jumping events. Gas mobility was more restricted in the system with the salicylic end-group and the largest hydrogen-bond network, whereas it was enhanced in the system with the cyclohexyl end-group. The most energetically-favorable sites for O2 insertion were either in the vicinity of the silica cages or close to the rings of the chain end-groups. On the other hand, the amide and hydroxyls groups engaging in H-bonds were less energetically favorable. This confirms that H-bonding networks are a hindrance for O2 transport in such systems.
Journal of Nanoscience and Nanotechnology, 2007
Since the discovery of CNT by Iijima, Nature 354, 56 (1991). CNT's have surged to the forefront a... more Since the discovery of CNT by Iijima, Nature 354, 56 (1991). CNT's have surged to the forefront as a versatile nanostructured material in nanoelectronic applications. Polypeptides nanotubular structures with tunable properties offer a challenging alternative to CNT. Earlier experimental studies on L-Alanyl-L-Valine (AV) and L-Valyl-L-Alanine (VA) have demonstrated their potential as novel porous materials, which form channel-like structure (Soldatov et al., Angew. Chem. Int. Ed. 43, 6308 (2004)). In the study reported here, DFT calculations on two closely related cyclic dipeptides cyclo[Lalanyl-L-valine] 3 and cyclo[L-valyl-L-alanine] 3 and on their linear correlates, [L-alanyl-L-valine] 3 and [L-valyl-L-alanine] 3 have been performed. This paper presents the general structural and electronic properties of cyclic and linear correlates of the nanotubular oligomeric dipeptides constructs, AV, and VA. We have compared the energy gaps of these cyclic rings and their linear correlates with that of other nanotubular constructs. The calculated HOMO-LUMO gap of these isolated ring structures is significantly larger than CNT's. Further research is required to reduce the band gaps to be comparable to CNT's and other inorganic tubular structures. Polypeptide design promises to be a major tool in engineering desirable band gap for the creation of novel nanostructured polypeptide nanotubes.
Journal of Molecular Structure, 2007
Density functional theory calculations have been carried out to analyze the effect of hydrogen ha... more Density functional theory calculations have been carried out to analyze the effect of hydrogen halides and H 2 O molecule interactions with the three lowest energy isomers the ring, bowl and cage of C 20 fullerene. The single-point energy calculations have also been performed at MP2/6-31+G*//B3LYP/6-31G* level of theory. The complexes (C 20 Á Á ÁH-X and H 2 O, where X = F, Cl, and Br) are bounded by two interactions namely: (i) very weak X-HÁ Á Áp H-bond interactions and (ii) long range van der Waals interactions of H-XÁ Á ÁC type. These interactions produced negligible distortion in the structures and a good correlation between electron density and stabilization energy of the complexes is found. The counterpoise correction to the interaction energies and the study of topology of the electron density for all the complexes have been performed. The charge transfer and the maneuver of resonance interaction in the interacting orbitals have been investigated by natural bond orbital (NBO) approach.
Journal of Molecular Modeling, 2008
The quantum chemical and molecular dynamics studies have been performed to infer the structural c... more The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(gamma-Acc)-alpha-Glycine(Gly)](3) hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation angles applying B3LYP/6-311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-gamma-Acc-Gly](3) hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing the pore of all-cis cyclo[(1R,3S)-gamma-Acc-Gly](3) peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site...water hydrogen bond interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-gamma-Acc-Gly](3) due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of molecules through the pore of all-trans cyclo[(1R,3S)-gamma-Acc-Gly](3) peptide due to the obstruction produced by cyclohexane groups.
Journal of Chemical Sciences, 2005
In this paper, we have introduced the atomic descriptors s(f) k to determine the local reactive s... more In this paper, we have introduced the atomic descriptors s(f) k to determine the local reactive sites of the molecular systems during electrophilic, nucleophilic and radical attacks. The condensed Fukui function and the newly introduced condensed atomic descriptor have been calculated for six different systems, namely glycine, alanine, aniline, BH 2 Cl, trans-FC(O)OF and m-anisidine. The individual atomic charges (gross charge) calculated by the MPA scheme have been used to calculate the condensed Fukui functions (f k) and the newly derived condensed atomic descriptors (sf) α k at B1-DZP level of theory. We carried out the calculation using the "stockholders" charge partitioning technique (i.e., Hirshfeld population scheme). The newly derived quantity gives the same reactive sites as the condensed Fukui functions, and the complexities associated with the negative Fukui functions are removed.
IEEE Transactions on NanoBioscience, 2000
ABSTRACT The quantum mechanics/molecular mechanics ONIOM calculations have been performed to stud... more ABSTRACT The quantum mechanics/molecular mechanics ONIOM calculations have been performed to study the structure and metal-ion binding properties of all-trans cyclo[1R-3S-γ-Acc- Gly]3 hexapeptide nanotube (TAG)3PNT. The intersubunit distances and tube angle of (TAG)3PNT exhibited the sturdy nature of (TAG)3 stacks upon Li+, K+, Mg2+, and Zn2+ enclosure. The calculated dimer binding energies of (TAG)3PNT and its ionic complexes confirm that the building blocks are bound by C=O...H-N hydrogen bond interactions. The binding energy of (TAG)3PNT with ions interacting at the surface cavity exhibit the affinity of ions at the entrance of the channel and the many-body analysis for the ion interacting at the central region substantiates the major contribution of two-body interactions to the total binding energy. In general, the binding energies of (TAG) 3PNT metal ion interacting complexes with well-maintained channel shows α-γ hybrid cyclic peptides as the promising peptidic nanochannels of biological interests.
Journal of Molecular Modeling