ACS Physical Chemistry AuPub Date : 2024-07-15DOI: 10.1021/acsphyschemau.4c0003910.1021/acsphyschemau.4c00039
Kaito Miyamoto*,
{"title":"Tailor-Made Design of Three-Dimensional Batteries Using a Simple, Accurate Geometry Optimization Scheme","authors":"Kaito Miyamoto*, ","doi":"10.1021/acsphyschemau.4c0003910.1021/acsphyschemau.4c00039","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00039https://doi.org/10.1021/acsphyschemau.4c00039","url":null,"abstract":"<p >In the rapidly evolving Internet of Things (IoT) society, the demand for microbatteries with high areal energy density is surging. As a promising strategy to enhance areal energy density, three-dimensional (3D) batteries have attracted attention. The feature of 3D batteries is the decoupling of the electrode thickness from the ion-transport distance through the modification of the spatial arrangement of the positive and negative electrodes beyond the conventional parallel plates configuration. This allows for the accommodation of a larger amount of active materials without increasing internal resistance. However, identifying the optimal 3D geometry is a complex task, as it depends on printable materials, the resolution of the fabrication equipment, as well as battery usage, which constitutes a multiobjective optimization problem. To overcome this challenge, we propose a novel approach to determine the optimal 3D microbattery geometry. Our innovative method involves a 3D battery optimization system, which integrates an automatic geometry generator with a quick and accurate performance simulator. This approach allows, for the first time, the discovery of material- and discharge-current-dependent optimal geometries. We successfully apply this optimization scheme to two standard electrode pairs (LiFePO<sub>4</sub>/Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> and LiNi<sub>0.5</sub>Mn<sub>0.3</sub>Co<sub>0.2</sub>O<sub>2</sub>/graphite), demonstrating a significant increase in energy density (30%–40% greater than the current state-of-the-art geometry), particularly under high current conditions. These findings underscore the importance of tailor-made batteries for diverse IoT applications and showcase the potential of our approach in realizing such designs.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 5","pages":"546–554 546–554"},"PeriodicalIF":3.7,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318291","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":"Ratiometric Chemosensors That Are Capable of Quantifying Hydrostatic Pressure Stimulus: A Case of Porphyrin Tweezers","authors":"Seiya Ono, Tomokazu Kinoshita, Hiroshi Iwasaki, Yoshitane Imai and Gaku Fukuhara*, ","doi":"10.1021/acsphyschemau.4c0002510.1021/acsphyschemau.4c00025","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00025https://doi.org/10.1021/acsphyschemau.4c00025","url":null,"abstract":"<p >Investigating chemosensors that are capable of quantifying pressure in solution, particularly hydrostatic pressure, which is one of the mechanical forces, is an attractive challenge in chemistry from the viewpoint of “mechano”-science. Herein, we report the investigation of chiral porphyrin tweezers, <b>Por-Cy</b> and <b>Por-DPhEt</b>, comprising different flexible linkers; <b>Por-Cy</b> and <b>Por-DPhEt</b> displayed distinct ratiometric signaling by using the higher excited S<sub>2</sub> state with a standard excited S<sub>1</sub> level. A novel operative mechanism using the S<sub>1</sub>/S<sub>2</sub> fluorescence ratio was revealed using hydrostatic pressure-ultraviolet/visible (UV/vis), fluorescence/excitation, circular dichroism spectroscopy, and lifetime measurements, which can be further controlled by the open-closed conformational change inherent in the tweezer skeleton. Furthermore, the fluorescent chiral tweezers exhibited a promising |<i>g</i><sub>lum</sub>| of 2.9 × 10<sup>–3</sup>, indicating that they are potential candidates for sensory applications in chiral environments. This study provides opportunities for the development of smart pressure-responsive chemosensors.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 5","pages":"510–521 510–521"},"PeriodicalIF":3.7,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318290","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}
ACS Physical Chemistry AuPub Date : 2024-07-11DOI: 10.1021/acsphyschemau.4c0004410.1021/acsphyschemau.4c00044
Avery B. Dalton, Lisa M. Wingen and Sergey A. Nizkorodov*,
{"title":"Isomeric Identification of the Nitroindole Chromophore in Indole + NO3 Organic Aerosol","authors":"Avery B. Dalton, Lisa M. Wingen and Sergey A. Nizkorodov*, ","doi":"10.1021/acsphyschemau.4c0004410.1021/acsphyschemau.4c00044","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00044https://doi.org/10.1021/acsphyschemau.4c00044","url":null,"abstract":"<p >Oxidation of indole by nitrate radical (NO<sub>3</sub>) was previously proposed to form nitroindole, largely responsible for the brown color of indole secondary organic aerosol (SOA). As there are seven known nitroindole isomers, we used chromatographic separation to show that a single nitroindole isomer is produced in the indole + NO<sub>3</sub> reaction and definitively assigned it to 3-nitroindole by comparison with chromatograms of nitroindole standards. Mass spectra of aerosolized 3-nitroindole particles were recorded with an aerosol mass spectrometer and directly compared to mass spectra of SOA from smog chamber oxidation of indole by NO<sub>3</sub> in order to help identify peaks unique to nitroindole (<i>m</i>/<i>z</i> 162, 132, and 116). Quantum chemical calculations were done to determine the energetics of hypothesized indole + NO<sub>3</sub> intermediates and products. The combination of these data suggests a mechanism, wherein a hydrogen atom is first abstracted from the N–H bond in indole, followed by isomerization to a carbon-centered radical in the 3-position and followed by addition of NO<sub>2</sub>. Alternative mechanisms involving a direct abstraction of a H atom from a C–H bond or a NO<sub>3</sub> addition to the ring are predicted to be energetically unfavorable from large barriers for the initial reaction steps.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 5","pages":"568–574 568–574"},"PeriodicalIF":3.7,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318289","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}
Avery B. Dalton, Lisa M. Wingen, Sergey A. Nizkorodov
{"title":"Isomeric Identification of the Nitroindole Chromophore in Indole + NO3 Organic Aerosol","authors":"Avery B. Dalton, Lisa M. Wingen, Sergey A. Nizkorodov","doi":"10.1021/acsphyschemau.4c00044","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00044","url":null,"abstract":"Oxidation of indole by nitrate radical (NO<sub>3</sub>) was previously proposed to form nitroindole, largely responsible for the brown color of indole secondary organic aerosol (SOA). As there are seven known nitroindole isomers, we used chromatographic separation to show that a single nitroindole isomer is produced in the indole + NO<sub>3</sub> reaction and definitively assigned it to 3-nitroindole by comparison with chromatograms of nitroindole standards. Mass spectra of aerosolized 3-nitroindole particles were recorded with an aerosol mass spectrometer and directly compared to mass spectra of SOA from smog chamber oxidation of indole by NO<sub>3</sub> in order to help identify peaks unique to nitroindole (<i>m</i>/<i>z</i> 162, 132, and 116). Quantum chemical calculations were done to determine the energetics of hypothesized indole + NO<sub>3</sub> intermediates and products. The combination of these data suggests a mechanism, wherein a hydrogen atom is first abstracted from the N–H bond in indole, followed by isomerization to a carbon-centered radical in the 3-position and followed by addition of NO<sub>2</sub>. Alternative mechanisms involving a direct abstraction of a H atom from a C–H bond or a NO<sub>3</sub> addition to the ring are predicted to be energetically unfavorable from large barriers for the initial reaction steps.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141614222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stewart F. Parker, Peter J. Baker, Robert McGreevy
{"title":"A Vision for the Future of Neutron Scattering and Muon Spectroscopy in the 2050s","authors":"Stewart F. Parker, Peter J. Baker, Robert McGreevy","doi":"10.1021/acsphyschemau.4c00026","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00026","url":null,"abstract":"Neutron scattering and muon spectroscopy are techniques that use subatomic particles to understand materials across a wide range of energy (μeV to tens of eV), length (Å to cm) and time (attosecond to hour) scales. The methods are widely used to study condensed phase materials in areas that span physics, chemistry, biology, engineering and cultural heritage. In this Perspective we consider three questions: (i) will neutron scattering and muon spectroscopy still be needed in the 2050s? (ii) What might the technology to produce neutron and muon beams look like in the 2050s? (iii) What will be the applications in the 2050s? Overall, the neutron/muon ecosystem in the 2050s will have less capacity than now, but greater capability because of the somewhat higher power sources, better instrumentation and data analysis.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"125 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141586551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2024-07-10DOI: 10.1021/acsphyschemau.4c0002610.1021/acsphyschemau.4c00026
Stewart F. Parker*, Peter J. Baker and Robert McGreevy,
{"title":"A Vision for the Future of Neutron Scattering and Muon Spectroscopy in the 2050s","authors":"Stewart F. Parker*, Peter J. Baker and Robert McGreevy, ","doi":"10.1021/acsphyschemau.4c0002610.1021/acsphyschemau.4c00026","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00026https://doi.org/10.1021/acsphyschemau.4c00026","url":null,"abstract":"<p >Neutron scattering and muon spectroscopy are techniques that use subatomic particles to understand materials across a wide range of energy (μeV to tens of eV), length (Å to cm) and time (attosecond to hour) scales. The methods are widely used to study condensed phase materials in areas that span physics, chemistry, biology, engineering and cultural heritage. In this Perspective we consider three questions: (i) will neutron scattering and muon spectroscopy still be needed in the 2050s? (ii) What might the technology to produce neutron and muon beams look like in the 2050s? (iii) What will be the applications in the 2050s? Overall, the neutron/muon ecosystem in the 2050s will have less capacity than now, but greater capability because of the somewhat higher power sources, better instrumentation and data analysis.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 5","pages":"439–452 439–452"},"PeriodicalIF":3.7,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318288","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}
Jonathan B. Eastwood, Barbara Procacci, Sabina Gurung, Jason M. Lynam, Neil T. Hunt
{"title":"Understanding the Vibrational Structure and Ultrafast Dynamics of the Metal Carbonyl Precatalyst [Mn(ppy)(CO)4]","authors":"Jonathan B. Eastwood, Barbara Procacci, Sabina Gurung, Jason M. Lynam, Neil T. Hunt","doi":"10.1021/acsphyschemau.4c00037","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00037","url":null,"abstract":"The solution phase structure, vibrational spectroscopy, and ultrafast relaxation dynamics of the precatalyst species [Mn(ppy)(CO)<sub>4</sub>] (<b>1</b>) in solution have been investigated using ultrafast two-dimensional infrared (2D-IR) spectroscopy. By comparing 2D-IR data with the results of anharmonic density functional theory (DFT) calculations, we establish an excellent agreement between measured and predicted inter-mode couplings of the carbonyl stretching vibrational modes of <b>1</b> that relates to the atomic displacements of axial and equatorial ligands in the modes and the nature of the molecular orbitals involved in M–CO bonding. Measurements of IR pump–probe spectra and 2D-IR spectra as a function of waiting time reveal the presence of ultrafast (few ps) intramolecular vibrational energy redistribution between carbonyl stretching modes prior to vibrational relaxation. The vibrational relaxation times of the CO-stretching modes of <b>1</b> are found to be relatively solvent-insensitive, suggestive of limited solvent–solute interactions in the ground electronic state. Overall, these data provide a detailed picture of the complex potential energy surface, bonding and vibrational dynamics of <b>1</b>, establishing a fundamental basis for the next steps in understanding and modulating precatalyst behavior.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141568731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2024-07-09DOI: 10.1021/acsphyschemau.4c0003710.1021/acsphyschemau.4c00037
Jonathan B. Eastwood, Barbara Procacci, Sabina Gurung, Jason M. Lynam* and Neil T. Hunt*,
{"title":"Understanding the Vibrational Structure and Ultrafast Dynamics of the Metal Carbonyl Precatalyst [Mn(ppy)(CO)4]","authors":"Jonathan B. Eastwood, Barbara Procacci, Sabina Gurung, Jason M. Lynam* and Neil T. Hunt*, ","doi":"10.1021/acsphyschemau.4c0003710.1021/acsphyschemau.4c00037","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00037https://doi.org/10.1021/acsphyschemau.4c00037","url":null,"abstract":"<p >The solution phase structure, vibrational spectroscopy, and ultrafast relaxation dynamics of the precatalyst species [Mn(ppy)(CO)<sub>4</sub>] (<b>1</b>) in solution have been investigated using ultrafast two-dimensional infrared (2D-IR) spectroscopy. By comparing 2D-IR data with the results of anharmonic density functional theory (DFT) calculations, we establish an excellent agreement between measured and predicted inter-mode couplings of the carbonyl stretching vibrational modes of <b>1</b> that relates to the atomic displacements of axial and equatorial ligands in the modes and the nature of the molecular orbitals involved in M–CO bonding. Measurements of IR pump–probe spectra and 2D-IR spectra as a function of waiting time reveal the presence of ultrafast (few ps) intramolecular vibrational energy redistribution between carbonyl stretching modes prior to vibrational relaxation. The vibrational relaxation times of the CO-stretching modes of <b>1</b> are found to be relatively solvent-insensitive, suggestive of limited solvent–solute interactions in the ground electronic state. Overall, these data provide a detailed picture of the complex potential energy surface, bonding and vibrational dynamics of <b>1</b>, establishing a fundamental basis for the next steps in understanding and modulating precatalyst behavior.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 5","pages":"536–545 536–545"},"PeriodicalIF":3.7,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318364","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}
Swati N. Rahane, Ganesh K. Rahane, Animesh Mandal, Yogesh Jadhav, Akshat Godha, Avinash Rokade, Shruti Shah, Yogesh Hase, Ashish Waghmare, Nilesh G. Saykar, Anurag Roy, Kranti N. Salgaonkar, Deepak Dubal, Surendra K. Makineni, Nelson Y. Dzade, Sandesh R. Jadkar, Sachin R. Rondiya
{"title":"Lead-Free Cs2AgBiCl6 Double Perovskite: Experimental and Theoretical Insights into the Self-Trapping for Optoelectronic Applications","authors":"Swati N. Rahane, Ganesh K. Rahane, Animesh Mandal, Yogesh Jadhav, Akshat Godha, Avinash Rokade, Shruti Shah, Yogesh Hase, Ashish Waghmare, Nilesh G. Saykar, Anurag Roy, Kranti N. Salgaonkar, Deepak Dubal, Surendra K. Makineni, Nelson Y. Dzade, Sandesh R. Jadkar, Sachin R. Rondiya","doi":"10.1021/acsphyschemau.4c00008","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00008","url":null,"abstract":"Lead-free double perovskites (DPs) will emerge as viable and environmentally safe substitutes for Pb-halide perovskites, demonstrating stability and nontoxicity if their optoelectronic property is greatly improved. Doping has been experimentally validated as a powerful tool for enhancing optoelectronic properties and concurrently reducing the defect state density in DP materials. Fundamental understanding of the optical properties of DPs, particularly the self-trapped exciton (STEs) dynamics, plays a critical role in a range of optoelectronic applications. Our study investigates how Fe doping influences the structural and optical properties of Cs<sub>2</sub>AgBiCl<sub>6</sub> DPs by understanding their STEs dynamics, which is currently lacking in the literature. A combined experimental–computational approach is employed to investigate the optoelectronic properties of pure and doped Cs<sub>2</sub>AgBiCl<sub>6</sub> (Fe–Cs<sub>2</sub>AgBiCl<sub>6</sub>) perovskites. Successful incorporation of Fe<sup>3+</sup> ions is confirmed by X-ray diffraction and Raman spectroscopy. Moreover, the Fe–Cs<sub>2</sub>AgBiCl<sub>6</sub> DPs exhibit strong absorption from below 400 nm up to 700 nm, indicating sub-band gap state transitions originating from surface defects. Photoluminescence (PL) analysis demonstrates a significant enhancement in the PL intensity, attributed to an increased radiative recombination rate and higher STE density. The radiative kinetics and average lifetime are investigated by the time-resolved PL (TRPL) method; in addition, temperature-dependent PL measurements provide valuable insights into activation energy and exciton–phonon coupling strength. Our findings will not only deepen our understanding of charge carrier dynamics associated with STEs but also pave the way for the design of some promising perovskite materials for use in optoelectronics and photocatalysis.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS Physical Chemistry AuPub Date : 2024-07-05DOI: 10.1021/acsphyschemau.4c0000610.1021/acsphyschemau.4c00006
Md. Shahadat Hossain, Md. Siddik Alom, Mohammad Salauddin Kader, Mohammed Akhter Hossain and Mohammad A. Halim*,
{"title":"Structure-Guided Antiviral Peptides Identification Targeting the HIV-1 Integrase","authors":"Md. Shahadat Hossain, Md. Siddik Alom, Mohammad Salauddin Kader, Mohammed Akhter Hossain and Mohammad A. Halim*, ","doi":"10.1021/acsphyschemau.4c0000610.1021/acsphyschemau.4c00006","DOIUrl":"https://doi.org/10.1021/acsphyschemau.4c00006https://doi.org/10.1021/acsphyschemau.4c00006","url":null,"abstract":"<p >HIV-1 integrase (IN), a major protein in the HIV life cycle responsible for integrating viral cDNA into the host DNA, represents a promising drug target. Small peptides have emerged as antiviral therapeutics for HIV because of their facile synthesis, highly selective nature, and fewer side effects. However, selecting the best candidates from a vast pool of peptides is a daunting task. In this study, multistep virtual screening was employed to identify potential peptides from a list of 280 HIV inhibitory peptides. Initially, 80 peptides were selected based on their minimum inhibitory concentrations (MIC). Then, molecular docking was performed to evaluate their binding scores compared to HIP000 and HIP00N which are experimentally validated HIV-1 integrase binding peptides that were used as a positive and negative control, respectively. The top-scoring docked complexes, namely, IN-HIP1113, IN-HIP1140, IN-HIP1142, IN-HIP678, IN-HIP776, and IN-HIP777, were subjected to initial 500 ns molecular dynamics (MD) simulations. Subsequently, HIP776, HIP777, and HIP1142 were selected for an in-depth mechanistic study of peptide interactions, with multiple simulations conducted for each complex spanning one microsecond. Independent simulations of the peptides, along with comparisons to the bound state, were performed to elucidate the conformational dynamics of the peptides. These peptides exhibit strong interactions with specific residues, as revealed by snapshot interaction analysis. Notably, LYS159, LYS156, VAL150, and GLU69 residues are prominently involved in these interactions. Additionally, residue-based binding free energy (BFE) calculations highlight the significance of HIS67, GLN148, GLN146, and SER147 residues within the binding pocket. Furthermore, the structure–activity relationship (SAR) analysis demonstrated that aromatic amino acids and the overall volume of peptides are the two major contributors to the docking scores. The best peptides will be validated experimentally by incorporating SAR properties, aiming to develop them as therapeutic agents and structural models for future peptide-based HIV-1 drug design, addressing the urgent need for effective HIV treatments.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"4 5","pages":"464–475 464–475"},"PeriodicalIF":3.7,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.4c00006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318362","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}