Pub Date : 2026-05-22DOI: 10.1007/s12039-026-02520-z
Oscar Xavier Guerrero-Gutiérrez, Ashley Acosta-García, Alberto Vela
{"title":"Correction to: PyCRDFT: A Python package to evaluate chemical reactivity descriptors within conceptual DFT","authors":"Oscar Xavier Guerrero-Gutiérrez, Ashley Acosta-García, Alberto Vela","doi":"10.1007/s12039-026-02520-z","DOIUrl":"10.1007/s12039-026-02520-z","url":null,"abstract":"","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"138 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148009545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-22DOI: 10.1007/s12039-026-02534-7
Samidh Ghosh, Pradipta Dey, Debashree Ghosh
The cyanobacteriochromes are characterized by chromophores that are akin to phytochromes, but with a much larger variability in their spectral characteristics. In this study, we aim to unearth the reason for this increased variability in their spectral features. We employ a combination of high-level quantum mechanical and molecular mechanical calculations for this purpose. Quite surprisingly, we observe that instead of the electrostatic effect, it is predominantly the cavity effect of the protein that brings about a structural change of the chromophore, leading to a spectral shift. We also attempt to decipher the individual contribution of the amino acid residues near the cavity, which interact significantly with the chromophore. Understanding the subtle details will help these photoreceptor proteins to emerge as a promising source of optogenetic tools in near future.
Graphical abstract
In this work we have elucidated the spectral tuning mechanism in a cyanobacteriochrome. The blue shift of absorption spectra is governed by the structural effect of the protein rather than the electrostatic effect. We have proposed a general protocol to calculate this spectral shift using hybrid QM/MM approaches in photoreceptors.
The alternative text for this image may have been generated using AI.
{"title":"Spectral tuning in cyanobacteriochrome","authors":"Samidh Ghosh, Pradipta Dey, Debashree Ghosh","doi":"10.1007/s12039-026-02534-7","DOIUrl":"10.1007/s12039-026-02534-7","url":null,"abstract":"<div><p>The cyanobacteriochromes are characterized by chromophores that are akin to phytochromes, but with a much larger variability in their spectral characteristics. In this study, we aim to unearth the reason for this increased variability in their spectral features. We employ a combination of high-level quantum mechanical and molecular mechanical calculations for this purpose. Quite surprisingly, we observe that instead of the electrostatic effect, it is predominantly the cavity effect of the protein that brings about a structural change of the chromophore, leading to a spectral shift. We also attempt to decipher the individual contribution of the amino acid residues near the cavity, which interact significantly with the chromophore. Understanding the subtle details will help these photoreceptor proteins to emerge as a promising source of optogenetic tools in near future.</p><h3>Graphical abstract</h3><p>In this work we have elucidated the spectral tuning mechanism in a cyanobacteriochrome. The blue shift of absorption spectra is governed by the structural effect of the protein rather than the electrostatic effect. We have proposed a general protocol to calculate this spectral shift using hybrid QM/MM approaches in photoreceptors.\u0000</p><div><figure><div><div><picture><source><img></source></picture><span>The alternative text for this image may have been generated using AI.</span></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"138 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148009542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-22DOI: 10.1007/s12039-026-02530-x
Shashank Sahu, Amresh Kumar, Elangannan Arunan
Though hydrogen bonding has been discussed for over a century now, no hydrogen bonding potential has been proposed yet. In recent years, Shahi and Arunan [Phys. Chem. Chem. Phys.16(42), 22935–22952 (2014)] and Hays et al. [Nature Chem14(7), 811–815 (2022)] reported results that suggested that HNC has stronger intermolecular interaction than HCN, though both have nearly identical dipole moment. Theoretical estimation on charges indicated that the H in HNC has a higher charge than that in HCN. This suggested that the HCN/HNC interaction could be charge-dipole and the potential could show r−2 dependence. We examined the potential energy curves of HCN/HNC complexes with HB acceptors, including HF, HCN, HNC, C2H4, C2H2, and Ar through MP2/(full)/aug-cc-PVTZ level of calculations. The initial three acceptors possess significant dipole moments, the subsequent two exhibit a quadrupole moment, and the last acceptor, Ar, features a spherical electron cloud on average. Depending on the acceptor, the interactions could vary as charge-dipole, charge-quadrupole, and charge-induced dipole. Our results show that the attractive part of the potentials do vary as r−n as expected for these interactions, though all of them have a geometry that could be characterized as hydrogen bonded. This work confirms that hydrogen bonding cannot be attributed to any single physical force.
Graphical Abstract
Hydrogen bond potential energy curve for the HF⋯HCN and C2H2⋯HCN complexes show 1/r2 and 1/r3 dependence as expected for chargedipole and charge-quadrupole interactions. This shows that the common description of hydrogen bonding as dipole-dipole interaction is inaccurate
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{"title":"Hydrogen bond potentials for some HCN and HNC complexes","authors":"Shashank Sahu, Amresh Kumar, Elangannan Arunan","doi":"10.1007/s12039-026-02530-x","DOIUrl":"10.1007/s12039-026-02530-x","url":null,"abstract":"<div><p>Though hydrogen bonding has been discussed for over a century now, no hydrogen bonding potential has been proposed yet. In recent years, Shahi and Arunan [<i>Phys. Chem. Chem. Phys.</i> <b>16</b>(42), 22935–22952 (2014)] and Hays <i>et al.</i> [<i>Nature Chem</i> <b>14</b>(7), 811–815 (2022)] reported results that suggested that HNC has stronger intermolecular interaction than HCN, though both have nearly identical dipole moment. Theoretical estimation on charges indicated that the H in HNC has a higher charge than that in HCN. This suggested that the HCN/HNC interaction could be charge-dipole and the potential could show <i>r</i><sup><i>−2</i></sup> dependence. We examined the potential energy curves of HCN/HNC complexes with HB acceptors, including HF, HCN, HNC, C<sub>2</sub>H<sub>4</sub>, C<sub>2</sub>H<sub>2</sub>, and Ar through MP2/(full)/aug-cc-PVTZ level of calculations. The initial three acceptors possess significant dipole moments, the subsequent two exhibit a quadrupole moment, and the last acceptor, Ar, features a spherical electron cloud on average. Depending on the acceptor, the interactions could vary as charge-dipole, charge-quadrupole, and charge-induced dipole. Our results show that the attractive part of the potentials do vary as r<sup>−n</sup> as expected for these interactions, though all of them have a geometry that could be characterized as hydrogen bonded. This work confirms that hydrogen bonding cannot be attributed to any single physical force.</p><h3>Graphical Abstract</h3><p>Hydrogen bond potential energy curve for the HF⋯HCN and C2H2⋯HCN complexes show 1/r<sup>2</sup> and 1/r<sup>3</sup> dependence as expected for chargedipole and charge-quadrupole interactions. This shows that the common description of hydrogen bonding as dipole-dipole interaction is inaccurate</p><div><figure><div><div><picture><source><img></source></picture><span>The alternative text for this image may have been generated using AI.</span></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"138 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148009543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-22DOI: 10.1007/s12039-026-02518-7
Sushanta Dattagupta
An exact analysis of the evolution of the density operator from an arbitrary initial state is presented for an anharmonic Morse potential. The evolution is decoherent due to a quantum environment modeled as an infinite set of bosonic excitations. The treatment clearly brings out the effect of anharmonicity on the decoherence time beyond the harmonic limit.
Graphical Abstract
An exact analysis of the evolution of the density operator from an arbitrary initial state is presented for an anharmonic Morse potential. The evolution is decoherent because of the presence of a quantum environment that is viewed as a collection of an infinite set of bosonic excitations. The treatment clearly brings out the effect of anharmonicity on the decoherence time beyond the harmonic limit.
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{"title":"Vibrational dephasing of a Morse oscillator","authors":"Sushanta Dattagupta","doi":"10.1007/s12039-026-02518-7","DOIUrl":"10.1007/s12039-026-02518-7","url":null,"abstract":"<div><p>An exact analysis of the evolution of the density operator from an arbitrary initial state is presented for an anharmonic Morse potential. The evolution is decoherent due to a quantum environment modeled as an infinite set of bosonic excitations. The treatment clearly brings out the effect of anharmonicity on the decoherence time beyond the harmonic limit.</p><h3>Graphical Abstract</h3><p>An exact analysis of the evolution of the density operator from an arbitrary initial state is presented for an anharmonic Morse potential. The evolution is decoherent because of the presence of a quantum environment that is viewed as a collection of an infinite set of bosonic excitations. The treatment clearly brings out the effect of anharmonicity on the decoherence time beyond the harmonic limit.</p><div><figure><div><div><picture><source><img></source></picture><span>The alternative text for this image may have been generated using AI.</span></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"138 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148009628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To investigate the role of stereochemistry in supramolecular assembly, we constructed a supramolecular system incorporating crown ether derivatives bearing chiral centers. Supramolecular systems were constructed in [Ni(dmit)2]− salts by 4-aminopyridinium (4-ApyH+) and chiral crown ether isomers: trans-anti-trans-dicyclohexano[18]crown-6 (tat-DCH18C6) or trans-syn-trans-dicyclohexano[18]crown-6 (tst-DCH18C6). Racemic crystals of (4-ApyH+)(tat-DCH18C6)[Ni(dmit)2]− (1) and (4-ApyH+)(tst-DCH18C6)[Ni(dmit)2]− (2) have one-dimensional (1D) supramolecular chains via N–H···O hydrogen bonds between 4-ApyH+ and crown ether derivatives, but the stereochemistry of the crown ether derivatives affects the geometric structure of the supramolecular 1D chain. Crystal 1 adopted space group Pnc2, with the supramolecular cations arranged in a zigzag 1D manner. Crystal 2 had space group P-1, with a linear 1D chain of supramolecular cation. Disorder was observed in the 4-ApyH+ cations in both structures, suggesting the presence of molecular space allowing dynamic behaviour. Temperature dependence of the molar magnetic susceptibility in both crystals showed antiferromagnetic interaction between [Ni(dmit)2]− anions. The subtle stereochemical differences in the crown ether suggest controllability of the supramolecular assembly pattern, the space available for the molecular motion of the cation, and the strength of magnetic interactions mediated by the arrangement of the magnetic anion. This provides a foundation for designing novel functional molecular materials with coupling between dynamic properties and electronic functions.
Graphical abstract
Chiral crown ether stereochemistry directs supramolecular assembly, resulting in zigzag and linear cation chains. This control regulates cationic dynamic space and modulates antiferromagnetic interactions, expecting a link between structure, dynamics, and electronic functions.
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{"title":"Stereochemical regulation of cationic order in supramolecular ionic crystals","authors":"Kiyonori Takahashi, Daiki Watanabe, Yu Ohshima, Hiroyasu Sato, Kazuya Kubo, Shin-Ichiro Noro, Takayoshi Nakamura","doi":"10.1007/s12039-026-02523-w","DOIUrl":"10.1007/s12039-026-02523-w","url":null,"abstract":"<div><p>To investigate the role of stereochemistry in supramolecular assembly, we constructed a supramolecular system incorporating crown ether derivatives bearing chiral centers. Supramolecular systems were constructed in [Ni(dmit)<sub>2</sub>]<sup>−</sup> salts by 4-aminopyridinium (4-ApyH<sup>+</sup>) and chiral crown ether isomers: <i>trans-anti-trans</i>-dicyclohexano[18]crown-6 (<i>tat</i>-DCH18C6) or <i>trans-syn-trans</i>-dicyclohexano[18]crown-6 (<i>tst</i>-DCH18C6). Racemic crystals of (4-ApyH<sup>+</sup>)(<i>tat</i>-DCH18C6)[Ni(dmit)<sub>2</sub>]<sup>−</sup> (<b>1</b>) and (4-ApyH<sup>+</sup>)(<i>tst</i>-DCH18C6)[Ni(dmit)<sub>2</sub>]<sup>−</sup> (<b>2</b>) have one-dimensional (1D) supramolecular chains via N–H···O hydrogen bonds between 4-ApyH<sup>+</sup> and crown ether derivatives, but the stereochemistry of the crown ether derivatives affects the geometric structure of the supramolecular 1D chain. Crystal <b>1</b> adopted space group <i>Pnc</i>2, with the supramolecular cations arranged in a zigzag 1D manner. Crystal <b>2</b> had space group <i>P</i>-1, with a linear 1D chain of supramolecular cation. Disorder was observed in the 4-ApyH<sup>+</sup> cations in both structures, suggesting the presence of molecular space allowing dynamic behaviour. Temperature dependence of the molar magnetic susceptibility in both crystals showed antiferromagnetic interaction between [Ni(dmit)<sub>2</sub>]<sup>−</sup> anions. The subtle stereochemical differences in the crown ether suggest controllability of the supramolecular assembly pattern, the space available for the molecular motion of the cation, and the strength of magnetic interactions mediated by the arrangement of the magnetic anion. This provides a foundation for designing novel functional molecular materials with coupling between dynamic properties and electronic functions.</p><h3>Graphical abstract</h3><p>Chiral crown ether stereochemistry directs supramolecular assembly, resulting in zigzag and linear cation chains. This control regulates cationic dynamic space and modulates antiferromagnetic interactions, expecting a link between structure, dynamics, and electronic functions.\u0000</p><div><figure><div><div><picture><source><img></source></picture><span>The alternative text for this image may have been generated using AI.</span></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"138 2","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148009544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-05-18DOI: 10.1007/s12039-026-02525-8
Akhil Gorre, Harilal, Shuvra Singha, Tushar Jana
Ionic liquids (ILs) have received considerable attention in the development of high temperature proton exchange membrane (HT-PEM) because of their unique ability to help in achieving high conductivity at higher temperature though the issues associated with leaching of ILs at higher temperatures yet to be resolved. In order to overcome this disadvantage, herein, we report the development of cross-linked HT-PEMs designed from phenyl substituted pyridine bridged oxy-polybenzimidazole (Ph-PyOPBI) and cross-linkable polymeric ionic liquid (cPIL). The cross-linking between Ph-PyOPBI and cPIL significantly improved the phosphoric acid (PA) uptake and proton conductivity of the resulting HT-PEMs. The cross-linked membranes were prepared with 10%, 20%, 30%, 40% of cPIL with respect to Ph-PyOPBI polymer weight and their HT-PEM properties were studied. All the four cross-linked membranes were found to be completely stable in 85% PA while the pristine Ph-PyOPBI membrane was stable only up to 75% PA. The reason for such remarkable stability of cross-linked Ph-PyOPBI in high acid concentration is due to the cross-linking interactions with the cPIL. The membrane containing 10% cPIL exhibited a proton conductivity of 0.053 S cm–1 at 160 °C which is higher than the pristine Ph-PyOPBI membrane (0.015 S cm–1 at 160 °C).
Graphical abstract
Proton Exchange Membrane (PEM) with improved properties for the use in high-temperature PEM fuel cell has been developed by cross-linking the pyridine-bridged polybenzimidazole chains through a cross-linkable polymeric ionic liquid.