Article
Medicine, Research & Experimental
Farkhad Maksudov, Evgenii Kliuchnikov, Daniel Pierson, M. L. Ujwal, Kenneth A. Marx, Arani Chanda, Valeri Barsegov
Summary: This article investigates the structure-function relationships of PMOs, which are therapeutic RNA mimicking molecules. By utilizing various techniques, such as circular dichroism and molecular dynamics simulations, the solution structures of PMOs were determined. The study reveals that PMOs adopt non-canonical, partially helical, and stable folded structures, and exhibit thermodynamic stability and concentration-dependent viscosity properties.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Chemistry, Medicinal
Jesse Vanloon, Thad Harroun, Hongbin Yan
Summary: This study reports the first CD profiles of nucleic acids at submM concentrations, which are relevant to nucleic acid concentrations in cellular cytoplasm and nucleus, providing a new approach for studying nucleic acid conformations under biologically relevant conditions.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Adriana Volna, Martin Bartas, Vaclav Karlicky, Jakub Nezval, Kristyna Kundratova, Petr Pecinka, Vladimir Spunda, Jiri Cerven
Summary: A stable G-quadruplex has been identified in the gene RPB1, encoding for RNA polymerase II, and is highly evolutionarily conserved among plants. A new hypothesis suggests the interaction of G-quadruplexes with UV light in plants to potentially form an additional layer of regulatory network.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Chakkarai Sathyaseelan, Vinothini Vijayakumar, Thenmalarchelvi Rathinavelan
Summary: XGBoost and nnet algorithms were utilized to predict diverse secondary structures of nucleic acids, showing similar prediction accuracy of approximately 85% to 87%. Both algorithms can be employed for predicting hybrid nucleic acid topologies in the future.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
Jony Castangna, Fausto Martelli, Kirk E. Jordan, Jason Crain
Summary: A strategy using embedded quantum oscillators has been introduced to predict material properties with remarkable accuracy, efficiently implemented on high-performance computing platforms to significantly increase the scale of accessible problems. This approach has enabled simulations of the largest system yet using molecular dynamics with electronically-derived forces.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Review
Spectroscopy
Krzysztof Karon, Mieczyslaw Lapkowski, Jan Cz Dobrowolski
Summary: The ECD spectroelectrochemical method has mainly been focused on organic and marginally inorganic chiroptical switching, as well as biochemical redox reactions. However, despite its importance, the history of ECD SEC studies is relatively short and has not received widespread attention.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Multidisciplinary
Tom Miclot, Camille Corbier, Alessio Terenzi, Cecilia Hognon, Stephanie Grandemange, Giampaolo Barone, Antonio Monari
Summary: This study demonstrated the crucial role of the stability of G-quadruplex in telomeric DNA in resisting oxidative stress and as an inhibitor of telomerase, an enzyme overexpressed in most cancers associated with oxidative stress. The combined experimental and computational investigation utilized circular dichroism, cellular immunofluorescence assays, and molecular dynamics simulations to identify these roles.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Review
Chemistry, Medicinal
Hikaru Kato
Summary: Natural products exhibit structural diversity, and computational chemistry can be used to determine their chemical structures, which is important in drug discovery research.
JOURNAL OF NATURAL MEDICINES
(2022)
Article
Biochemical Research Methods
Lixia Chen, Mingxia Liu, Sen Yang, Hong Zhao, Xin Yao, Xiangjun Li, Jinghua Meng
Summary: By using computational protocols and environmental simulations, theoretical electronic circular dichroism (ECD) spectra of 19 chiral amino acids were successfully matched with their forms in aqueous solutions. New methods for enantioseparation of these chiral amino acids by capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) were introduced. The combination of ECD with chromatographic separation methods allowed for identification and quantification of enantiomers without the need for a single enantiomer standard.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Multidisciplinary
Chong-Yang Li, Han Xu, Pei-Ming Cheng, Ming-Hao Du, La-Sheng Long, Lan-Sun Zheng, Xiang-Jian Kong
Summary: This study presents the mechanism behind the formation of chiral crystals and explores their chiral expression from micro- to macroscopic levels. The research also reveals the strong magneto-optical response of chiral crystals, highlighting their potential as magneto-optical materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Massimiliano Aschi, Laura Palombi, Andrea Amadei
Summary: The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were successfully modeled using a theoretical-computational method combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations. The method accurately reproduced the experimental spectra and demonstrated its effectiveness in modeling spectral features in complex systems. The strategy involved performing a long timescale MD simulation, extracting relevant conformations, and calculating the ECD spectrum using the PMM approach.
Article
Biochemistry & Molecular Biology
Bilal Ahmad, Asma Achek, Mariya Farooq, Sangdun Choi
Summary: The study presents a computational method for designing peptides targeting the NLRP3 inflammasome, which showed inhibitory effects on IL-1β and IL-18 mediated by NLRP3. Experimental results indicate the potential anti-inflammatory efficacy of these peptides, with one peptide demonstrating high potency in IL-1β inhibition and selectivity towards NLRP3.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Maria Drosou, Georgia Zahariou, Dimitrios A. Pantazis
Summary: The study reveals that the tetramanganese-calcium cluster of the oxygen-evolving complex in photosystem II adopts orientational Jahn-Teller isomeric forms in the resting state, which explains previous spectroscopic observations and establishes the functional role of this isomerism in the catalytic process.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Medicinal
Reed C. Dowling, Gregory T. Carroll, David L. Kirschman, Mark B. Masthay, Angela Mammana
Summary: In this report, we show that CD spectroscopy is a useful tool for detecting changes in DNA caused by UV light irradiation. By using both CD and UV-Vis spectroscopy, we monitor the spectroscopic response of DNA samples exposed to UV light for different durations. We studied four different nucleic acids to understand the impact of sequence on photodegradation, and observed sequence-dependent changes in CD and UV-Vis spectra, with poly (dA)•poly (dT) showing the most rapid changes.
Article
Plant Sciences
Gwi Ja Hwang, Mina Jang, Sangkeun Son, Gil Soo Kim, Byeongsan Lee, Kyung Taek Heo, Geum Jin Kim, Hyukjae Choi, Jae-Seoun Hur, Jun-Pil Jang, Sung-Kyun Ko, Young-Soo Hong, Jong Seog Ahn, Jae-Hyuk Jang
Summary: In this study, a new secondary metabolite, ulleungdolin, was isolated from the co-culture of an actinomycete and a fungus. Ulleundolin exhibited antimigration effect on breast cancer cells.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Chemistry, Physical
Michele Nottoli, Patrizia Mazzeo, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: Hybrid TDDFT/MM approaches are popular for describing electronic transitions of molecules in solution or complex matrices. However, when combined with a polarisable force field, problems may arise. This paper presents a possible solution by introducing a Delta SCF formulation, which is expected to be particularly suitable for accurately describing charge-transfer states.
Review
Chemistry, Medicinal
Matteo Cei, Lorenzo Di Bari, Francesco Zinna
Summary: In this short review, the authors collected the dissymmetry factors associated with the first Cotton effect of the ECD spectrum for 170 [n]-helicenes. They found reasonable correlations between luminescence and absorption, suggesting similarity in the stereochemistry of the ground and emitting excited states for most helicenes. These results can be helpful in rationalizing chiroptical data and designing new helicene structures with desired CPL properties.
Article
Chemistry, Physical
Laura Pedraza-Gonzalez, Leonardo Barneschi, Michal Marszalek, Daniele Padula, Luca De Vico, Massimo Olivucci
Summary: We propose a computational protocol, implemented through a general Python-based driver, for fast and automated screening of hybrid QM/MM models of rhodopsins as fluorescent probes. The protocol is benchmarked using experimentally measured absorption and emission spectra of different rhodopsin variants. We demonstrate that the protocol can reproduce observed trends in fluorescence and select potentially fluorescent rhodopsins, although it has limitations as a black-box tool. The protocol can also be used for mechanistic investigations of fluorescence enhancement effects associated with S1/S2 states or coupling of S0/S1 wave functions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Edoardo Cignoni, Lorenzo Cupellini, Benedetta Mennucci
Summary: We propose a machine learning strategy to calculate the excitonic properties of light harvesting complexes. By combining molecular dynamics simulations with ML prediction of the excitonic Hamiltonian, the proposed model can account for geometric fluctuations and electrostatic interactions. The model is trained on chlorophylls but can extrapolate beyond the training set, and its accuracy is demonstrated through simulations of absorption spectra in different environments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Chemistry, Multidisciplinary
Oliver G. Willis, Francesco Zinna, Lorenzo Di Bari
Summary: In recent years, there has been a resurgence of interest in circularly polarized luminescence (CPL) due to its popularity as a spectroscopic technique and improved accessibility to instruments. New efficient CPL emitters have been developed and various applications have been proposed. Although most examples of CPL are in the visible range, there are limited cases of near infrared (NIR) CPL active complexes. NIR-CPL compounds have potential applications in the telecommunication industry, electronic devices, and bioassays. This review provides an overview of recent developments in NIR-CPL measurements and discusses the chiroptical properties of metal complexes that achieve this capability.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Krzysztof Nowak, Olaf Morawski, Francesco Zinna, Gennaro Pescitelli, Lorenzo Di Bari, Marcin Gorecki, Marek Grzybowski
Summary: Chiral fluorescent macrocycles, consisting of dimethyl 2,5-diaminoterephthalate units, can be easily synthesized from inexpensive building blocks. Depending on the concentration, the reaction mainly produces a paracyclophane-like dimer or a triangular trimer. These macrocycles exhibit fluorescence in solution and the solid state, with red-shifted maxima as the size of the macrocyclic ring decreases. Chirality affects their absorption and emission of circularly polarized light.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Editorial Material
Chemistry, Multidisciplinary
Gianluigi Albano, Francesco Zinna, Andrea Taddeucci, Maria Annunziata M. Capozzi, Gennaro Pescitelli, Angela Punzi, Lorenzo Di Bari, Gianluca M. Farinola
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Manoop Chenchiliyan, Joachim Kuebel, Saik Ann Ooi, Giacomo Salvadori, Benedetta Mennucci, Sebastian Westenhoff, Michal Maj
Summary: Phytochromes are photoreceptor proteins with a bound chromophore that can convert between two forms upon photoexcitation. This study uses isotope-labeling techniques to isolate the vibrational bands of the chromophore and reveals its structure and dynamics through 2D infrared spectroscopy and molecular dynamics simulations. The research provides insights into how point mutations in the protein sequence affect the chromophore's hydrogen-bonding structure and photoisomerization ability.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Shaima Hashem, Giovanni Battista Alteri, Lorenzo Cupellini, Benedetta Mennucci
Summary: We use a combination of microsecond MD simulations and (polarizable) QM/MM calculations of NMR, FTIR, and UV-vis spectra to confirm the structure of the light-activated form of AppA photoreceptor. Our simulations demonstrate that the observed spectral features are directly linked to the tautomer form of glutamine, supporting the PCET mechanism. Furthermore, we observe small but significant structural changes in AppA, which propagate from the flavin binding pocket to the protein surface.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Laura Pedraza-Gonzalez, Edoardo Cignoni, Jacopo D'Ascenzi, Lorenzo Cupellini, Benedetta Mennucci
Summary: In response to varying light conditions, light-harvesting complexes (LHCs) undergo conformational changes to protect the photosynthetic organism from excessive light irradiation. Activation of the non-photochemical quenching (NPQ) mechanism is triggered by the acidification of the thylakoid lumen, resulting in a switch from a light-harvesting state to a quenched state. The pH sensitivity of the complex is driven by protonation of specific residues, and the quenching mechanism is controlled by a charge-transfer process controlled by the protein conformation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Chemistry, Multidisciplinary
Michele Nottoli, Mattia Bondanza, Patrizia Mazzeo, Lorenzo Cupellini, Carles Curutchet, Daniele Loco, Louis Lagardere, Jean-Philip Piquemal, Benedetta Mennucci, Filippo Lipparini
Summary: This article describes the development, implementation, and application of a polarizable QM/MM strategy based on the AMOEBA polarizable force field for calculating molecular properties and performing dynamics of molecular systems embedded in complex matrices. The authors demonstrate that this technology is well-understood and mature, and it can be efficiently implemented using advanced numerical methods and linear scaling techniques. The polarizable QM/AMOEBA approach has a wide range of applications, including predicting spectroscopies and performing multiscale ab initio molecular dynamics simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Education & Educational Research
Maria Antonietta Carpentieri, Gioia Fano, Sandro Jurinovich, Valentina Domenici
Summary: This study aimed to design, optimize, and implement a didactic sequence on light phenomena, including the basic principles of reflection, refraction, interference, diffraction, and light dispersion, as well as ultraviolet-visible spectroscopy and spectroscopic instruments. By investigating the difficult concepts of light phenomena and using inquiry-based learning, interactive STEM laboratory activities, and a historical epistemological teaching method, this study aimed to help high-school students better understand and apply these concepts in analytical chemistry applications.
EDUCATION SCIENCES
(2023)
Article
Chemistry, Medicinal
Gianluigi Albano, Laura Antonella Aronica, Gennaro Pescitelli, Lorenzo Di Bari
Summary: In this study, we synthesized a series of structurally related chiral oligothiophenes with a 1,4-diketo-3,6-diarylpyrrolo[3,4-c]pyrrole (DPP) unit as the central core. These oligothiophenes were functionalized with the same (S)-3,7-dimethyl-1-octyl chains on the nitrogen atoms of lactam moieties, differing only in the number of lateral thiophene units. We evaluated the aggregation modes of these chiral systems through UV-Vis absorption and ECD spectroscopies in solution aggregation conditions and as thin films, highlighting the impact of pi-conjugation length on their chiroptical properties. The study also revealed that the number of thiophene units attached to the DPP core affects both the propensity to aggregation and the helicity of aggregates.
Article
Chemistry, Physical
Vladislav Slama, Lorenzo Cupellini, Vincenzo Mascoli, Nicoletta Liguori, Roberta Croce, Benedetta Mennucci
Summary: This study uncovers the molecular mechanism for the formation and tuning of exciton-CT interactions in Lhca4 through molecular dynamics, multiscale quantum chemical calculations, and spectral simulations. The study shows that the coupling between exciton and CT states is extremely sensitive to tiny variations in the Chl dimer arrangement, explaining both the red-shifted bands and the switch between conformations with blue and red emission observed in single-molecule spectroscopy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Daniele Padula, Alessandro Landi, Giacomo Prampolini
Summary: Recent advances in non-fullerene acceptors have improved the efficiency of organic photovoltaics. This study computationally characterizes the supramolecular structure and electron transfer properties of a promising non-fullerene acceptor and its derivatives. The findings suggest that alkyl side chains primarily impact crystal packing rather than dynamic disorder, leading to improved electron transfer integrals and charge mobilities.