ACS Physical Chemistry Au最新文献

{"title":"Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair","authors":"Chi H. Mak*,&nbsp;","doi":"10.1021/acsphyschemau.3c00058","DOIUrl":"10.1021/acsphyschemau.3c00058","url":null,"abstract":"<p >Base pairing complementarity is central to DNA function. G·C and A·T pair specificity is thought to originate from the different number of hydrogen bonds the pairs make. Quantifying how many hydrogen bonds exist can be difficult because water molecules in the surrounding can make up for or disrupt direct hydrogen bonds, and the hydration structures around A·T and G·C pairs on duplex DNA are distinct. Large-scale computer simulations have been used here to create a detailed map for the hydration structure on A·T and G·C base pairs in water. The contributions of specific hydration waters to the free energy of each of the hydrogen bonds in the A·T and G·C pairs were computed. Using the equilibrium fractions of hydrated versus unhydrated states from the hydration profiles, the impact of specific bound waters on each hydrogen bond can be uniquely quantified using a thermodynamic construction. The findings suggest that hydration water in the minor groove of an A·T pair can provide up to about 2 kcal/mol of free energy advantage, effectively making up for the missing third hydrogen bond in the A·T pair compared to G·C, rendering the intrinsic thermodynamic stability of the A·T pair almost synonymous with G·C.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 2","pages":"180–190"},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139551978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harvesting Chemical Understanding with Machine Learning and Quantum Computers","authors":"Shubin Liu*,&nbsp;","doi":"10.1021/acsphyschemau.3c00067","DOIUrl":"10.1021/acsphyschemau.3c00067","url":null,"abstract":"<p >It is tenable to argue that nobody can predict the future with certainty, yet one can learn from the past and make informed projections for the years ahead. In this Perspective, we overview the status of how theory and computation can be exploited to obtain chemical understanding from wave function theory and density functional theory, and then outlook the likely impact of machine learning (ML) and quantum computers (QC) to appreciate traditional chemical concepts in decades to come. It is maintained that the development and maturation of ML and QC methods in theoretical and computational chemistry represent two paradigm shifts about how the Schrödinger equation can be solved. New chemical understanding can be harnessed in these two new paradigms by making respective use of ML features and QC qubits. Before that happens, however, we still have hurdles to face and obstacles to overcome in both ML and QC arenas. Possible pathways to tackle these challenges are proposed. We anticipate that hierarchical modeling, in contrast to multiscale modeling, will emerge and thrive, becoming the workhorse of <i>in silico</i> simulations in the next few decades.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 2","pages":"135–142"},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139500855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the Membrane Binding Process of a Disordered Protein: Dynamic Interplay of Anionic Lipids and the Polybasic Region","authors":"Azadeh Alavizargar*,&nbsp;Maximilian Gass,&nbsp;Michael P. Krahn and Andreas Heuer,&nbsp;","doi":"10.1021/acsphyschemau.3c00051","DOIUrl":"10.1021/acsphyschemau.3c00051","url":null,"abstract":"<p >Intrinsically disordered regions of proteins are responsible for many biological processes such as in the case of liver kinase B1 (LKB1)─a serine/threonine kinase relevant for cell proliferation and cell polarity. LKB1 becomes fully activated upon recruitment to the plasma membrane by binding of its disordered C-terminal polybasic motif consisting of eight lysines/arginines to phospholipids. Here, we present extensive molecular dynamics (MD) simulations of the polybasic motif interacting with a model membrane composed of 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleyl phosphatidic acid (PA) and cell culture experiments. Protein–membrane binding effects are due to the electrostatic interactions between the polybasic amino acids and PAs. For significant binding, the first three lysines turn out to be dispensable, which was also recapitulated in cell culture using transfected GFP-LKB1 variants. LKB1–membrane binding results in nonmonotonous changes in the structure of the protein as well as the membrane, in particular, accumulation of PAs and reduced thickness at the protein–membrane contact area. The protein–lipid binding turns out to be highly dynamic due to an interplay of PA–PA repulsion and protein–PA attraction. The thermodynamics of this interplay is captured by a statistical fluctuation model, which allows the estimation of both energies. Quantification of the significance of each polar amino acid in the polybasic provides detailed insights into the molecular mechanism of protein–membrane binding of LKB1. These results can likely be transferred to other proteins, which interact by intrinsically disordered polybasic regions with anionic membranes.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 2","pages":"167–179"},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139500849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular CO2 Storage: State of a Single-Molecule Gas","authors":"Yoshifumi Hashikawa*,&nbsp;Shumpei Sadai and Yasujiro Murata*,&nbsp;","doi":"10.1021/acsphyschemau.3c00068","DOIUrl":"10.1021/acsphyschemau.3c00068","url":null,"abstract":"<p >CO₂ evolution is one of the urgent global issues; meanwhile, understanding of sorptive/dynamic behavior is crucial to create next-generation encapsulant materials with stable sorbent processes. Herein, we showcase molecular CO₂ storage constructed by a [60]fullerenol nanopocket. The CO₂ density reaches 2.401 g/cm³ within the nanopore, showing strong intramolecular interactions, which induce nanoconfinement effects such as forbidden translation, restricted rotation, and perturbed vibration of CO₂. We also disclosed an equation of state for a molecular CO₂ gas, revealing a very low pressure of 3.14 rPa (1 rPa = 10^–27 Pa) generated by the rotation/vibration at 300 K. Curiously enough, the CO₂ capture enabled to modulate an external property of the encapulant material itself, i.e., association of the [60]fullerenol via intercage hydrogen-bonding.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 2","pages":"143–147"},"PeriodicalIF":0.0,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139501241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Magnetoelectrocatalysis: Evidence from the Hydrogen Evolution Reaction","authors":"Krysti L. Knoche Gupta,&nbsp;Heung Chan Lee and Johna Leddy*,&nbsp;","doi":"10.1021/acsphyschemau.3c00039","DOIUrl":"10.1021/acsphyschemau.3c00039","url":null,"abstract":"<p >Hydrogen evolution reaction (HER) rates are higher where magnetic gradients are established at electrode surfaces. In comparison of literature data for metals with comparable work functions, we note 1000× higher rates for paramagnetic metals than diamagnetic metals. With unpaired electron spins, paramagnetic and ferromagnetic metals establish interfacial magnetic gradients. At diamagnetic electrodes, gradients are induced by addition of magnetized microparticles. Onset of hydrogen evolution for magnetized γ-Fe₂O₃ microparticles in Nafion on diamagnetic glassy carbon electrodes is lower by 190 mV (−18 kJ mol^–1) relative to demagnetized microparticles. Chemically the same as demagnetized particles, the physical distinction of magnetic field and gradient at magnetized microparticles increases electron transfer rate. For magnetized Fe₃O₄ microparticles, the onset is lower by 280 mV (−27 kJ mol^–1). Paramagnetic platinum electrodes are unaffected by addition of magnetized microparticles. Magnetoelectrocatalysis is established by magnetic gradients.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 2","pages":"148–159"},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139082884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electron Transfer at Molecule–Metal Interfaces under Floquet Engineering: Rate Constant and Floquet Marcus Theory","authors":"Yu Wang,&nbsp; and ,&nbsp;Wenjie Dou*,&nbsp;","doi":"10.1021/acsphyschemau.3c00049","DOIUrl":"10.1021/acsphyschemau.3c00049","url":null,"abstract":"<p >Electron transfer (ET) at molecule–metal or molecule–semiconductor interfaces is a fundamental reaction that underlies all electrochemical processes and substrate-mediated surface photochemistry. In this study, we show that ET rates near a metal surface can be significantly manipulated by periodic driving (e.g., Floquet engineering). We employ the Floquet surface hopping and Floquet electronic friction algorithms developed previously to calculate the ET rates near the metal surface as a function of driving amplitudes and driving frequencies. We find that ET rates have a turnover effect when the driving frequencies increase. A Floquet Marcus theory is further formulated to analyze such a turnover effect. We then benchmark the Floquet Marcus theory against Floquet surface hopping and Floquet electronic friction methods, indicating that the Floquet Marcus theory works in the strong nonadiabatic regimes but fails in the weak nonadiabatic regimes. We hope these theoretical tools will be useful to study ET rates in the plasmonic cavity and plasmon-assisted photocatalysis.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 2","pages":"160–166"},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00049","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Vision for the Future of Astrochemistry in the Interstellar Medium by 2050","authors":"Ryan C. Fortenberry*,&nbsp;","doi":"10.1021/acsphyschemau.3c00043","DOIUrl":"10.1021/acsphyschemau.3c00043","url":null,"abstract":"<p >By 2050, many, but not nearly all, unattributed astronomical spectral features will be conclusively linked to molecular carriers (as opposed to nearly none today in the visible and IR); amino acids will have been observed remotely beyond our solar system; the largest observatories ever constructed on the surface of the Earth or launched beyond it will be operational; high-throughput computation either from brute force or machine learning will provide unprecedented amounts of reference spectral and chemical reaction data; and the chemical fingerprints of the universe delivered by those of us who call ourselves astrochemists will provide astrophysicists with unprecedented resolution for determining how the stars evolve, planets form, and molecules that lead to life originate. Astrochemistry is a relatively young field, but with the entire universe as its playground, the discipline promises to persist as long as telescopic observations are made that require reference data and complementary chemical modeling. While the recent commissionings of the <i>James Webb Space Telescope</i> and Atacama Large Millimeter Array are ushering in the second “golden age” of astrochemistry (with the first being the radio telescopic boom period of the 1970s), this current period of discovery should facilitate unprecedented advances within the next 25 years. Astrochemistry forces the asking of hard questions beyond the physical conditions of our “pale blue dot”, and such questions require creative solutions that are influential beyond astrophysics. By 2050, more creative solutions will have been provided, but even more will be needed to answer the continuing question of our astrochemical ignorance.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 1","pages":"31–39"},"PeriodicalIF":0.0,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138589420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of Corrosion Inhibition of Mild Steel in 0.5 M H2SO4 with Lachancea fermentati Inhibitor Extracted from Rotten Grapefruits (Vitis vinifera): Adsorption, Thermodynamic, Electrochemical, and Quantum Chemical Studies","authors":"Baluchamy Tamilselvi,&nbsp;Durvas Seshian Bhuvaneshwari*,&nbsp;Periyakaruppan Karuppasamy*,&nbsp;Sethuramasamy Padmavathy,&nbsp;Santhosh Nikhil,&nbsp;Surendra Boppanahalli Siddegowda and H C Ananda Murthy*,&nbsp;","doi":"10.1021/acsphyschemau.3c00055","DOIUrl":"10.1021/acsphyschemau.3c00055","url":null,"abstract":"<p >Corrosion inhibition of mild steel (MS) was studied using <i>Lachancea fermentati</i> isolate in 0.5 M H₂SO₄, which was isolated from rotten grapes (<i>Vitis vinifera</i>) via biofilm formation. Biofilm over the MS surface was asserted by employing FT-IR and FE-SEM with EDXS, electrochemical impedance spectroscopy (EIS), AFM, and DFT-ESP techniques. The weight loss experiments and temperature studies supported the physical adsorption behavior of the corrosion inhibitors. The maximum inhibition efficiency (IE) value (90%) was observed at 293 K for 9 × 10⁶ cfu/mL of <i>Lachancea fermentati</i> isolate. The adsorption of <i>Lachancea fermentati</i> isolate on the surface of MS confirms Langmuir’s adsorption isotherm model, and the −Δ<i>G</i> values indicate the spontaneous adsorption of inhibitor over the MS surface. Electrochemical studies, such as potentiodynamic polarization (PDP) and EIS were carried out to investigate the charge transfer (CT) reaction of the <i>Lachancea fermentati</i> isolate. Tafel polarization curves reveal that the <i>Lachancea fermentati</i> isolate acts as a mixed type of inhibitor. The Nyquist plots (EIS) indicate the increase in charge transfer resistance (<i>R</i>_ct) and decrease of double-layer capacitance (<i>C</i>_dl) values when increasing the concentration of <i>Lachancea fermentati</i> isolate. The spectral studies, such as UV–vis and FT-IR, confirm the formation of a complex between MS and the <i>Lachancea fermentati</i> isolate inhibitor. The formation of biofilm on the MS surface was confirmed by FE-SEM, EDXS, and XPS analysis. The proposed bioinhibitor shows great potential for the corrosion inhibition of mild steel in acid media.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 1","pages":"67–84"},"PeriodicalIF":0.0,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00055","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138581297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patterns Lead the Way to Far-from-Equilibrium Materials","authors":"Pamela Knoll*,&nbsp;Bin Ouyang* and Oliver Steinbock*,&nbsp;","doi":"10.1021/acsphyschemau.3c00050","DOIUrl":"10.1021/acsphyschemau.3c00050","url":null,"abstract":"<p >The universe is a complex fabric of repeating patterns that unfold their beauty in system-specific diversity. The periodic table, crystallography, and the genetic code are classic examples that illustrate how even a small number of rules generate a vast range of shapes and structures. Today, we are on the brink of an AI-driven revolution that will reveal an unprecedented number of novel patterns, many of which will escape human intuition and expertise. We suggest that in the second half of the 21st century, the challenge for Physical Chemistry will be to guide and interpret these advances in the broader context of physical sciences and materials-related engineering. If we succeed in this role, Physical Chemistry will be able to extend to new horizons. In this article, we will discuss examples that strike us as particularly promising, specifically the discovery of high-entropy and far-from-equilibrium materials as well as applications to origins-of-life research and the search for life on other planets.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 1","pages":"19–30"},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Follow Your Heart","authors":"Tianruo Shen*,&nbsp;","doi":"10.1021/acsphyschemau.3c00034","DOIUrl":"https://doi.org/10.1021/acsphyschemau.3c00034","url":null,"abstract":"","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 6","pages":"477"},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138301467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}