Article
Plant Sciences
Sonja L. Knowles, Christopher D. Roberts, Mario Augustinovic, Laura Flores-Bocanegra, Huzefa A. Raja, Kimberly N. Heath-Borrero, Joanna E. Burdette, Joseph O. Falkinham, Cedric J. Pearce, Nicholas H. Oberlies
Summary: Four new bislactones were isolated from cultures of two fungal strains and identified as Clonostachys spp. based on molecular data. These compounds showed antimicrobial activities, with compounds 1 and 4 being the most potent against Staphylococcus aureus.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Chemistry, Multidisciplinary
Xuanyu Chen, Xiaomin Deng, Xingxing Han, Yinmei Liang, Zhiping Meng, Rui Liu, Wenqiang Su, Huaxu Zhu, Tingming Fu
Summary: This study investigated the inhibitory effects of silybin diastereomers on HEWL fibril formation and demonstrated that silybin B had a more significant inhibitory effect than silybin A, particularly at high concentrations. The research provides insights into screening amyloid inhibitors from natural products and suggests silybin B as a promising candidate for further development as an amyloid inhibitor.
Article
Plant Sciences
Tae Hyun Lee, Song Lim Ham, Da Yeong Lee, Ju Ryeong Lee, Jonghwan Kim, Chung Sub Kim
Summary: In this study, the structures of balsamisides A-D were reassigned as 2,3-dihydro-3-hydroxyfuran instead of an epoxide using computational methods. Two new biflavonoidal glycosides were also characterized. Moreover, a rapid determination method for biflavonoid classes was formulated based on diagnostic 13C NMR chemical shift values.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Chemistry, Physical
Rosa M. Claramunt, Concepcion Lopez, Dionisia Sanz, Jose Elguero, Ibon Alkorta
Summary: This research paper presents a structural study of albendazole, focusing on the conformational properties of its amino and imino tautomers. Experimental measurements and computational calculations help to understand the complex issues in the structure of albendazole and explain some of the disorder phenomena.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
Jiri Czernek, Jiri Brus
Summary: The liquid state NMR chemical shift of protons is a commonly used parameter to characterize host-guest complexes. The theoretical counterpart of this parameter, H-1 NMR chemical shielding affected by the solvent (H-1 CS), can provide valuable insights into spatial arrangements of supramolecular systems. Computational analysis can reliably predict H-1 CS values for challenging cases, such as aggregation of aromatic and antiaromatic molecules in solution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Organic
Kota Inose, Shizuya Tanaka, Kazuaki Tanaka, Masaru Hashimoto
Summary: Density functional theory (DFT) calculations demonstrate both effectiveness and limitations in determining the structures of complex and conformationally flexible natural products. Validation of structures can be achieved using NMR chemical shifts, coupling constants, and ECD spectra. Combining different computational methods can improve accuracy in verifying complex structures.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Andrea Defant, Ines Mancini
Summary: In this study, NMR DFT calculations were used to predict the 1H and 13C NMR chemical shifts of twelve polyarsenical analogs and compared with experimental data. The best computational approaches for predicting chemical shifts and coupling constants were identified. These findings make NMR spectroscopy more appealing for structural elucidation.
Review
Biochemistry & Molecular Biology
Anna Helena Mazurek, Lukasz Szeleszczuk, Dariusz Maciej Pisklak
Summary: This review discusses the combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations, highlighting the advantages of this approach over computations optimized at 0 K. The article serves as a convenient overview of various applied parameters and examples of previously studied systems. Analyzing published works, it is concluded that incorporating fast, small-amplitude motions through aiMD noticeably enhances the accuracy of NMR parameters calculations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ilya G. Shenderovich, Gleb S. Denisov
Summary: Enriched cyanide anions have potential as NMR probes for non-covalent interactions, but hydrogen cyanide is toxic. Analyzing the effect of hydrogen bonding on NMR properties of cyanide anions can help characterize the geometry of complexes.
Article
Biochemistry & Molecular Biology
Kevin Ritter, Nikolaus Jork, Anne-Sophie Unmuessig, Maja Koehn, Henning J. J. Jessen
Summary: Inositol phosphates, a family of highly charged messenger molecules, have diverse functions in cellular processes. The phosphorylation patterns result in a vast array of compounds. This study presents a method using NMR measurements for enantiomer assignment, enabling the differentiation of enantiomers. The method was applied to various inositol phosphates and will aid in the assignment of biologically relevant isomers.
Article
Chemistry, Physical
Guilherme Colherinhas, Valdemir Ludwig, Zelia M. da Costa Ludwig
Summary: In this study, we investigated the structural solute-solvent, electrical, and magnetic properties of xanthine derivatives (caffeine, paraxanthine, and theophylline), taking into account the polarization effects in water. Atomistic computer simulations, including Classical Monte Carlo Simulations and Quantum Mechanics (S-QM/MM), were performed. The efficiency of different DFT exchange and correlation functionals (B3LYP, CAM-B3LYP, BHandHLYP, and PBE1PBE) was compared using additional DFT calculations for the chemical shielding of xanthine molecules in the liquid environment. The hydrogen bonds between the solute and solvent, as well as their contribution to the NMR spectrum, were analyzed. Supramolecular models for xanthine-water solutions were evaluated to determine their ability to describe the magnetic signatures of carbon and hydrogen atoms.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Leonardo B. A. Oliveira, Wesley B. Cardoso, Guilherme Colherinhas
Summary: This study combines quantum calculations with molecular dynamics simulations to investigate the polarization effects on different amino acids structures, resulting in findings that are in full agreement with experimental results, thus validating the reliability of the approach.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Organic
Antonio de la Hoz, Ibon Alkorta, Jose Elguero
Summary: This study investigated the reaction of hydrazines with alpha, beta-unsaturated carbonyl compounds to produce 2-pyrazolines, identifying several products and establishing some reaction paths through the evolution of H-1 and C-13 NMR spectra with time. Theoretical calculations on energies and chemical shifts played a key role in confirming the structure of some products, while IRCs were necessary to discover unexpected intermediates.
Review
Chemistry, Organic
Ryszard B. Nazarski
Summary: Computational NMR spectroscopy, with reliable DFT coupling constants and chemical shifts, plays an essential role in validating or revising chemical structures. However, incorrect assignments may occur, especially for natural products, and should be approached with caution.
TETRAHEDRON LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Themistoklis Venianakis, Christina Oikonomaki, Michael G. Siskos, Alexandra Primikyri, Ioannis P. Gerothanassis
Summary: The DFT study of H-1 NMR chemical shifts for various conjugated trienyl compounds demonstrated its effectiveness in predicting chemical shifts accurately and identifying geometric isomers reliably. The approach is powerful for addressing issues related to resonance assignments and structure elucidation in solution.
Review
Chemistry, Medicinal
Marcus W. H. Wang, Jonathan M. Goodman, Timothy E. H. Allen
Summary: Machine learning has become prominent in predictive toxicology, with support vector machines, random forest, and decision trees being the dominant methods. Challenges include the characteristics of the data and exploring areas for improvement.
CHEMICAL RESEARCH IN TOXICOLOGY
(2021)
Correction
Environmental Sciences
Kamel Mansouri, Agnes Karmaus, Jeremy Fitzpatrick, Grace Patlewicz, Prachi Pradeep, Domenico Alberga, Nathalie Alepee, Timothy E. H. Allen, Dave Allen, Vinicius M. Alves, Carolina H. Andrade, Tyler R. Auernhammer, Davide Ballabio, Shannon Bell, Emilio Benfenati, Sudin Bhattacharya, Joyce V. Bastos, Stephen Boyd, J. B. Brown, Stephen J. Capuzzi, Yaroslav Chushak, Heather Ciallella, Alex M. Clark, Viviana Consonni, Pankaj R. Daga, Sean Ekins, Sherif Farag, Maxim Fedorov, Denis Fourches, Domenico Gadaleta, Feng Gao, Jeffery M. Gearhart, Garett Goh, Jonathan M. Goodman, Francesca Grisoni, Christopher M. Grulke, Thomas Hartung, Matthew Hirn, Pavel Karpov, Alexandru Korotcov, Giovanna J. Lavado, Michael Lawless, Xinhao Li, Thomas Luechtefeld, Filippo Lunghini, Giuseppe F. Mangiatordi, Gilles Marcou, Dan Marsh, Todd Martin, Andrea Mauri, Eugene N. Muratov, Glenn J. Myatt, Dac-Trung Nguyen, Orazio Nicolotti, Reine Note, Paritosh Pande, Amanda K. Parks, Tyler Peryea, Ahsan Polash, Robert Rallo, Alessandra Roncaglioni, Craig Rowlands, Patricia Ruiz, Daniel Russo, Ahmed Sayed, Risa Sayre, Timothy Sheils, Charles Siegel, Arthur C. Silva, Anton Simeonov, Sergey Sosnin, Noel Southall, Judy Strickland, Yun Tang, Brian Teppen, Igor V. Tetko, Dennis Thomas, Valery Tkachenko, Roberto Todeschini, Cosimo Toma, Ignacio Tripodi, Daniela Trisciuzzi, Alexander Tropsha, Alexandre Varnek, Kristijan Vukovic, Zhongyu Wang, Liguo Wang, Katrina M. Waters, Andrew J. Wedlake, Sanjeeva J. Wijeyesakere, Dan Wilson, Zijun Xiao, Hongbin Yang, Gergely Zahoranszky-Kohalmi, Alexey V. Zakharov, Fagen F. Zhang, Zhen Zhang, Tongan Zhao, Hao Zhu, Kimberley M. Zorn, Warren Casey, Nicole C. Kleinstreuer
ENVIRONMENTAL HEALTH PERSPECTIVES
(2021)
Article
Chemistry, Multidisciplinary
Jonathan M. Goodman, Igor Pletnev, Paul Thiessen, Evan Bolton, Stephen R. Heller
Summary: The software for the IUPAC Chemical Identifier, InChI, is highly reliable and has been upgraded to version 1.06 with significant new features including support for pseudo-element atoms and improved description of polymers. Research results show that the accuracy of version 1.05 was 99.996% and version 1.06 represents a step closer to perfection, with few applications needing changes as a result of the upgrade.
JOURNAL OF CHEMINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Daniel S. Wigh, Jonathan M. Goodman, Alexei A. Lapkin
Summary: Interdisciplinary work in chemistry is becoming increasingly important due to advancements in computing, machine learning, and artificial intelligence. Understanding the representation of molecules in a machine-readable format is crucial for computational chemistry. This article introduces different representations of molecules and highlights three significant ones. Researchers often share their work on platforms like GitHub, but discussions on computation time and domain of applicability are often overlooked. The authors propose questions for further consideration to make chemical VAEs more accessible.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Jonathan M. Goodman, Gerd Blanke, Hans Kraut
Summary: RInChI is a canonical identifier widely used for reactions in databases. It can handle large collections of reactions and link information from diverse sources. Studies demonstrate its usefulness in analyzing billion-scale molecular data in the SAVI database, with the simplified form of Web-RInChIKey providing enough information for effective differentiation. RInChI exhibits different properties from Reaction SMILES, and both approaches offer valuable and distinct information.
PURE AND APPLIED CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Christopher J. Swain, Jeremy G. Frey, Jonathan M. Goodman
Summary: In November 2020, the Royal Society of Chemistry's Chemical Information and Computer Applications interest group held a five-day conference on Open Chemical Science, focusing on open data, open access publishing, and various open-source tools for chemistry. This online event was highly popular and attracted attendees from 45 different countries. The workshops, in particular, were well-received and led to a year-long series of further workshops.
PURE AND APPLIED CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Mathew M. Simpson, Ching Ching Lam, Jonathan M. Goodman, Shankar Balasubramanian
Summary: The epigenetic modification 5-methylcytosine is crucial for development, cell specific gene expression, and disease states. However, the selective chemical modification of 5-methylcytosine is currently challenging. In this study, we present a xanthone-photosensitized process that introduces a 4-pyridine modification at the methyl group of 5-methylcytosine. This reaction mechanism involves single electron oxidation and deprotonation to generate the methyl group radical, followed by cross coupling to install the 4-pyridine label.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Daniel S. Wigh, Matthieu Tissot, Patrick Pasau, Jonathan M. Goodman, Alexei A. Lapkin
Summary: Computational reaction prediction is a widely used task in chemistry, and in this work, an algorithm for predicting the rate of protodeboronation of boronic acids is presented. The algorithm is based on a mechanistic model derived from kinetic studies and is validated using cross-validation techniques. The algorithm shows promise in assisting chemists in reactions involving boronic acids.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Jonathan Lam, Richard J. Lewis, Jonathan M. Goodman
Summary: Vibrational circular dichroism (VCD) spectroscopy provides data for determining absolute configuration, but interpretation is challenging. We have validated a method, the Cai dot factor, using a database of VCD data for 30 pairs of organic compounds. Analysis shows that this method is reliable and efficient for absolute configuration determination, even with imperfect spectra. Most molecules tested have high confidence scores and correct assignments.
JOURNAL OF CHEMINFORMATICS
(2023)
Correction
Chemistry, Organic
Ching Ching Lam, Jonathan M. Goodman
Summary: In this paper, the authors provide computational insights on the origin of enantioselectivity in reactions with diarylprolinol silyl ether catalysts via a radical pathway. This study is of significant importance for understanding the mechanism of organic catalytic reactions and developing efficient chiral catalysts.
ORGANIC CHEMISTRY FRONTIERS
(2022)
Article
Chemistry, Organic
Ching Ching Lam, Jonathan M. Goodman
Summary: The study reveals that the effect of catalyst variation on the selectivity reaction can be explained by conformational changes and structural deformations.
ORGANIC CHEMISTRY FRONTIERS
(2022)
Article
Chemistry, Multidisciplinary
Sanha Lee, Kristaps Ermanis, Jonathan M. Goodman
Summary: The use of machine learning in computational chemistry has seen significant progress, with the ability to predict molecular properties accurately and cost-effectively using large molecular databases.
Article
Chemistry, Multidisciplinary
Alexander Howarth, Jonathan M. Goodman
Summary: DP5 probability is a new method for quantifying molecular uncertainty. It can rapidly differentiate between structure proposals using C-13 NMR spectra and prevent incorrect structures from being published and reassigned.
Meeting Abstract
Toxicology
T. E. H. Allen, A. J. Wedlake, M. N. Grayson, A. M. Middleton, M. Folia, M. Baltazar, P. Piechota, E. Gelzinyte, J. M. Goodman, P. J. Russell, P. Kukic, S. Gutsell
TOXICOLOGY LETTERS
(2021)
Review
Chemistry, Organic
Guillermo Caballero-Garcia, Jonathan M. Goodman
Summary: N-Triflylphosphoramides (NTPA) have emerged as popular catalysts for enantioselective transformations due to their stronger Bronsted acid properties compared to phosphoric acids (PA). This review categorizes NTPA-catalyzed reactions based on the enantio-determining step and highlights their use in total synthesis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
