Ahmad Raeisi Najafi, Paween Mahinthichaichan, Fraser J. Moss, Ardeschir Vahedi‐Faridi, Walter F. Boron, Emad Tajkhorshid
{"title":"Characterization and Computational Engineering of Structural Elements Controlling Gas Permeability in PIP2 ;1 Aquaporins","authors":"Ahmad Raeisi Najafi, Paween Mahinthichaichan, Fraser J. Moss, Ardeschir Vahedi‐Faridi, Walter F. Boron, Emad Tajkhorshid","doi":"10.1002/jcc.70377","DOIUrl":"https://doi.org/10.1002/jcc.70377","url":null,"abstract":"Aquaporins (AQPs) are classical water channels that also conduct small gas molecules such as and across the membrane. The hydrophobic central pore, located at the fourfold symmetry axis of an AQP tetrameric architecture, has been proposed to constitute the most optimal pathway for gas transport, although monomeric water pores can also contribute somewhat to permeation of less hydrophobic species. Here, we report a comparative molecular dynamics (MD) study of gas permeability in a plant AQP and a mammalian AQP1, taking advantage of complementary computational protocols including flooding simulations, umbrella sampling, and implicit ligand sampling. PIP2;1 AQPs, present in plants, are experimentally reported to have lower gas permeability than AQP1, which is present both in plants and animals. Using the spinach PIP2;1 (SoPIP2;1) and bovine AQP1 (bAQP1) as the models, the study unravels the specific structural features controlling the permeability of the central pore to gases. In SoPIP2;1, residue Trp79, which is highly conserved in the plant PIP2;1 family and lines directly the central pore, forms a major constriction region and the main barrier against gas permeation. Notably, the occluding conformation of the four Trp79 residues from the four monomers is stabilized by another conserved residue, Phe207 in the central pore. Sequence and structural comparisons show that both of these residues are replaced by less bulky residues in AQP1, for example, by Leu56 and Ala179, respectively, in bAQP1. The role of Phe207 residues in hindering gas permeation through SoPIP2;1 is confirmed by in silico alanine substitution, which reveals its effect on the local constriction produced by Trp79 residues. Conversely, by mutating Leu56 to tryptophan and Ala179 to phenylalanine in bAQP1, we engineer the protein to a less permeable gas channel.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"13 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147743821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K. S. V. Anurag, Ashish Kumar Patra, Vikas Dattatraya Ghevade, P. Sai Shankar, Ruchika Bhat, V. Raghavendra, Rahul Maitra, G. Jaiganesh
{"title":"Resource Estimation for VQE on Small Molecules: Impact of Fermion Mappings and Hamiltonian Reductions","authors":"K. S. V. Anurag, Ashish Kumar Patra, Vikas Dattatraya Ghevade, P. Sai Shankar, Ruchika Bhat, V. Raghavendra, Rahul Maitra, G. Jaiganesh","doi":"10.1002/jcc.70379","DOIUrl":"https://doi.org/10.1002/jcc.70379","url":null,"abstract":"Accurate determination of ground-state energies for molecules remains a challenge in quantum chemistry and a cornerstone for progress in fields such as drug discovery and materials design. The Variational Quantum Eigensolver (VQE) represents a leading hybrid quantum-classical paradigm for addressing this challenge; however, its widespread realization is limited by noise and the restricted scalability of current quantum hardware. Achieving efficient simulations on Noisy Intermediate-Scale Quantum (NISQ) devices and forthcoming Fault-Tolerant Application-Scalable Quantum (FASQ) systems demands a detailed understanding of how computational resources scale with molecular complexity and fermion-to-qubit encoding schemes. In this work, resource requirements for VQE implementations employing the Unitary Coupled Cluster Singles and Doubles (UCCSD) ansatz are systematically analyzed. The molecular Hamiltonian is formulated in second quantization and mapped to qubit operators through the Jordan–Wigner (JW), Bravyi–Kitaev (BK), and Parity (Pa) transformations. Hamiltonian reduction strategies, including <span data-altimg=\"/cms/asset/802039db-8dcb-46b8-bace-e6849524bc8c/jcc70379-math-0001.png\"></span><mjx-container ctxtmenu_counter=\"6\" ctxtmenu_oldtabindex=\"1\" jax=\"CHTML\" role=\"application\" sre-explorer- style=\"font-size: 103%; position: relative;\" tabindex=\"0\"><mjx-math aria-hidden=\"true\" location=\"graphic/jcc70379-math-0001.png\"><mjx-semantics><mjx-mrow><mjx-msub data-semantic-children=\"0,1\" data-semantic- data-semantic-role=\"latinletter\" data-semantic-speech=\"normal double struck upper Z 2\" data-semantic-type=\"subscript\"><mjx-mi data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic- data-semantic-parent=\"2\" data-semantic-role=\"latinletter\" data-semantic-type=\"identifier\"><mjx-c></mjx-c></mjx-mi><mjx-script style=\"vertical-align: -0.15em;\"><mjx-mn data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic- data-semantic-parent=\"2\" data-semantic-role=\"integer\" data-semantic-type=\"number\" size=\"s\"><mjx-c></mjx-c></mjx-mn></mjx-script></mjx-msub></mjx-mrow></mjx-semantics></mjx-math><mjx-assistive-mml display=\"inline\" unselectable=\"on\"><math altimg=\"urn:x-wiley:01928651:media:jcc70379:jcc70379-math-0001\" display=\"inline\" location=\"graphic/jcc70379-math-0001.png\" xmlns=\"http://www.w3.org/1998/Math/MathML\"><semantics><mrow><msub data-semantic-=\"\" data-semantic-children=\"0,1\" data-semantic-role=\"latinletter\" data-semantic-speech=\"normal double struck upper Z 2\" data-semantic-type=\"subscript\"><mi data-semantic-=\"\" data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic-parent=\"2\" data-semantic-role=\"latinletter\" data-semantic-type=\"identifier\" mathvariant=\"normal\">ℤ</mi><mn data-semantic-=\"\" data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic-parent=\"2\" data-semantic-role=\"integer\" data-semantic-type=\"number\">2</mn></msub></mrow>$$ {mathr","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"20 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147732057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Omkar Charapale, Sergio Posada-Pérez, Albert Poater, Miquel Solà
{"title":"Does Aromaticity Drive Metal Cation Binding to Nanographenes? Insights Into Regioselectivity and Cation-\u0000 \u0000 \u0000 π\u0000 \u0000 $$ pi $$\u0000 Bonding","authors":"Omkar Charapale, Sergio Posada-Pérez, Albert Poater, Miquel Solà","doi":"10.1002/jcc.70337","DOIUrl":"10.1002/jcc.70337","url":null,"abstract":"<p>Nanographenes, a subclass of polycyclic aromatic hydrocarbons (PAHs), have attracted significant interest due to their unique electronic properties and broad applications in materials science, optoelectronics, energy storage, and organic chemistry. Here we investigate the interactions of alkali and alkaline-earth metal cations (Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup>, Be<sup>2+</sup>, Mg<sup>2+</sup>, Ca<sup>2+</sup>) with five D<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow></mrow>\u0000 <mrow>\u0000 <mn>6</mn>\u0000 <mi>h</mi>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {}_{6h} $$</annotation>\u0000 </semantics></math>-symmetric PAHs/nanographenes ranging from benzene to circumcircumcircumcoronene, aiming to elucidate the roles of aromaticity and topology in governing cation binding. We find that cation binding is strongest at the most aromatic peripheral six-membered rings. Energy decomposition analysis reveals that binding is dominated by orbital interactions rather than electrostatics, with Be<sup>2+</sup> displaying anomalous, strongly covalent character and minimal ionic contribution. We introduce a novel ring-based reactivity descriptor combining the Fukui function and electronic delocalization, which accurately predicts binding energies. In addition, a local topological indicator shows a strong correlation with cation–PAH interactions and enables reliable predictions for graphene. Overall, our results demonstrate that aromaticity alone does not govern cation binding, but its interplay with local reactivity and topology is decisive, providing a unified framework that bridges chemical topology and computational chemistry.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 10","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70337","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147669424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}