Article
Multidisciplinary Sciences
Manuel Cordova, Martins Balodis, Bruno Simoes de Almeida, Michele Ceriotti, Lyndon Emsley
Summary: This study successfully demonstrates probabilistic chemical shift assignment of organic crystals using a combination of machine learning model and statistical analysis, enabling scientists to assign shifts directly from the structure. The correct assignment was found in over 80% of cases among experimental and predicted shifts.
Article
Chemistry, Multidisciplinary
Martins Balodis, Manuel Cordova, Albert Hofstetter, Graeme M. Day, Lyndon Emsley
Summary: The determination of the three-dimensional atomic-level structure of powdered solids is an important goal in current chemistry. This study successfully determined the crystal structures of ampicillin, piroxicam, cocaine, and two polymorphs of the drug molecule AZD8329 using machine-learned isotropic chemical shifts generated on-the-fly to guide a Monte Carlo-based structure determination process.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Nigel John Clayden
Summary: NMR chemical shifts play a role in determining protein structure by NMR methods by depending on the local conformation. NMR chemical shielding calculations show that the C alpha H inequivalence in cyclosarcosyls can be rationalized with an appropriate electronic model and basis set. For cyclotetrasarcosyl, although there are significant distant non-bonded effects of a peptide group, the majority of the large inequivalence (>2 ppm) is due to the local conformation between adjacent sarcosine.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Automation & Control Systems
Tomas R. Cotos-Yanez, Ana Perez-Gonzalez, Beatriz Iglesias, Luis Munoz
Summary: The article presents an improved statistical approach for estimating the conformational composition of small molecules with low standard error and good p-values.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Chemistry, Multidisciplinary
Ziyue Yang, Maghesree Chakraborty, Andrew D. White
Summary: The study utilizes graph neural networks (GNNs) for NMR chemical shift prediction, accurately capturing important chemical shift phenomena such as hydrogen bonding-induced downfield shift and shifts of organic molecules. These GNN models do not require feature engineering, only data training, yet are as accurate as previous empirical protein NMR models.
Article
Chemistry, Physical
Themistoklis Venianakis, Alexandra Primikyri, Eleni Alexandri, George Papamokos, Ioannis P. Gerothanassis
Summary: Low-energy conformers of alpha-linolenic acid, eicosapentaenoic acid, and docosahexaenoic acid in the liquid state have been studied using NMR and density functional theory calculations. A critical discussion on issues related to chemical shifts, signal attribution, and electron shielding was presented. The data demonstrate that folding effects of the chain do not result in unusually strong electron shielding.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Nanoscience & Nanotechnology
Michael Kathan, Stefano Crespi, Niklas O. Thiel, Daniel L. Stares, Denis Morsa, John de Boer, Gianni Pacella, Tobias van den Enk, Piermichele Kobauri, Giuseppe Portale, Christoph A. Schalley, Ben L. Feringa
Summary: In this study, researchers reported a light-fuelled small-molecule ratchet capable of driving a coupled chemical equilibrium energetically uphill. By bridging imine macrocycles with a molecular motor, the machine can adopt different topologies, allowing for the coupling of continuous mechanical motion with a chemical transformation.
NATURE NANOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Youngkyu Park, Mark E. Davis
Summary: Chemical shifts from the 11B nuclear magnetic resonance (NMR) spectra of crystalline borosilicate minerals with tetrahedrally coordinated boron atoms (B) correlate linearly with the local geometric parameters related to B-O-T angles obtained from single-crystal X-ray diffraction. These correlations are similar to the well-known correlations of 29Si and 27Al NMR chemical shifts with structural features of silicates and aluminosilicates, respectively. The use of 11B NMR chemical shifts can provide insights into the local geometry of tetrahedrally coordinated B and help establish B ordering in crystalline borosilicates.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
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, Physical
Manuel Cordova, Edgar A. Engel, Artur Stefaniuk, Federico Paruzzo, Albert Hofstetter, Michele Ceriotti, Lyndon Emsley
Summary: Nuclear magnetic resonance (NMR) chemical shifts provide information about the atomic environments in solid materials, but accurately predicting these shifts is computationally expensive. ShiftML is a machine-learning model that can rapidly predict chemical shifts with the same accuracy as density functional theory (DFT) calculations, reducing the computational cost by over four orders of magnitude.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Multidisciplinary Sciences
Jingzhen Du, John A. Seed, Victoria E. J. Berryman, Nikolas Kaltsoyannis, Ralph W. Adams, Daniel Lee, Stephen T. Liddle
Summary: Determining the covalency of early actinide chemical bonding is a fundamentally important challenge. In this study, N-15 nuclear magnetic resonance spectroscopy is used to investigate a terminal uranium-nitride, revealing exceptional NMR properties and covalency that redefine N-15 NMR parameter space and our understanding of actinide chemical bonding.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Laura Abella, Adam Philips, Jochen Autschbach
Summary: The behavior of the sodium anion has been found to interact strongly with its chemical environment, isolating the core from the surroundings and appearing as a free ion in NMR experiments.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Jonas C. Ott, Elizaveta A. Suturina, Ilya Kuprov, Joscha Nehrkorn, Alexander Schnegg, Markus Enders, Lutz H. Gade
Summary: In this study, experimental observations of P-31 and H-1 NMR resonances shifted by over 10 000 ppm in a square planar ferrous complex were reported. The influence of magnetic anisotropy and zero-field splitting on paramagnetic shift and relaxation enhancement was investigated using various techniques, and spin dynamics simulations showed the possibility of observing NMR signals of directly metal-bonded atoms even with relatively slow electron spin relaxation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Manuel Cordova, Lyndon Emsley
Summary: The determination of the molecular solid structure using NMR crystallography relies on generating a comprehensive set of candidate crystal structures and comparing computed chemical shifts with experimental values. However, exploring the polymorph landscape of molecular solids requires a significant computational power, leading to a bottleneck in candidate crystal generation. This study constructs three-dimensional interaction maps using a crystal structure database with associated chemical shifts to identify structural constraints for accelerating crystal structure prediction protocols, without requiring DFT-level chemical shift computations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Jinhuan Zhang, Clara Nassrin Kriebel, Zheng Wan, Man Shi, Clemens Glaubitz, Xiao He
Summary: In this study, an accurate and cost-effective method was developed to calculate the chemical shifts of membrane proteins. It was found that considering environmental factors can improve the accuracy of the predicted chemical shifts. Furthermore, the proposed method outperformed most empirical models in predicting the chemical shifts of key ligands and non-standard residues.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Juan M. R. Albano, Julio C. Facelli, Marta B. Ferraro, Monica Pickholz
JOURNAL OF MOLECULAR MODELING
(2019)
Article
Biochemistry & Molecular Biology
Juan M. R. Albano, Gabriel E. Jara, M. Laura Fernandez, Julio C. Facelli, Marta B. Ferraro, Monica Pickholz
JOURNAL OF MEMBRANE BIOLOGY
(2019)
Article
Computer Science, Interdisciplinary Applications
Yulan Wang, Bernard Li, Ramkiran Gouripeddi, Julio C. Facelli
Summary: The emergence of SARS-CoV-2 has led to the need for optimal community responses, with modeling being a key tool to develop effective strategies. Utilizing agent-based techniques and human activity data can help in predicting infection rates more accurately.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2021)
Article
Oncology
Lisa Anne Cannon-Albright, Craig Carl Teerlink, Jeff Stevens, Franklin W. Huang, Csilla Sipeky, Johanna Schleutker, Rolando Hernandez, Julio Facelli, Neeraj Agarwal, Donald L. Trump
Summary: This study utilized a predisposition candidate gene identification strategy to identify 152 bladder cancer predisposition candidate variants in affected bladder cancer relative pairs from high-risk pedigrees, with one variant in ERF significantly associated with bladder cancer risk in an independent population, suggesting it may be a predisposition gene for bladder and prostate cancer.
Article
Oncology
Craig C. Teerlink, Jeff Stevens, Rolando Hernandez, Julio C. Facelli, Lisa A. Cannon-Albright
Summary: A rare intronic variant of the CELF4 gene was significantly associated with colorectal cancer (CRC) risk and shown to segregate within a high-risk pedigree. This provides further support for the role of this variant in CRC risk.
CANCER EPIDEMIOLOGY
(2021)
Article
Endocrinology & Metabolism
Sejal Mistry, Ramkiran Gouripeddi, Vandana Raman, Julio C. Facelli
Summary: This study developed a data-driven model to stratify the risk of type 1 diabetes onset based on the characteristics of islet autoantibody development, including timing, type, and titre. The results showed that the titre of islet autoantibodies varied with age and modulated the risk for type 1 diabetes onset.
Article
Multidisciplinary Sciences
Sejal Mistry, Ramkiran Gouripeddi, Candace M. Reno, Samir Abdelrahman, Simon J. Fisher, Julio C. Facelli
Summary: Distinct patterns of electrocardiogram heartbeats were identified that correlated with different glycemic levels, diabetes status, and mortality. Some patterns were specific to hypoglycemia conditions, while others were specific to severe hypoglycemia conditions and exhibited arrhythmogenic waveforms.
Article
Oncology
Lisa A. Cannon-Albright, Jeff Stevens, Julio C. Facelli, Craig C. Teerlink, Kristina Allen-Brady, Neeraj Agarwal
Summary: This study identified a rare variant in the LRBA gene that is significantly associated with prostate cancer risk. The variant was shared among 51 affected cousin pairs who died from the disease. Further analysis showed the variant to be present in multiple pedigrees. These findings provide candidate genes and mutation sites for further research on the genetic risk of prostate cancer.
Article
Immunology
Sejal Mistry, Ramkiran Gouripeddi, Julio C. Facelli
Summary: We developed an in-silico pipeline to evaluate molecular mimicry in the etiology of type 1 diabetes, and identified potential high-impact molecular mimics. These findings provide valuable insights for further research and prevention efforts related to type 1 diabetes.
JOURNAL OF AUTOIMMUNITY
(2023)
Article
Chemistry, Physical
Damian A. Grillo, Juan M. R. Albano, Rufino E. Valladares T., Esteban E. Mocskos, Julio C. Facelli, Monica Pickholz, Marta B. Ferraro
Summary: In this study, a new methodology was implemented to investigate the structural and mechanical properties of systems with spherical and planar symmetries using Molecular Dynamics simulations. The methodology was applied to a drug delivery system based on polymersomes, with prilocaine as the chosen model drug. The results showed that the structural properties of the polymersome membrane could be obtained from bilayer simulations, but the mechanical aspects were better understood through simulations of the entire polymersomes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Computer Science, Information Systems
Janette Vazquez, Julio C. Facelli
Summary: The use of machine learning and artificial intelligence in medicine has gained attention, but little is known about how to use Conformal Predictions to assess the accuracy of individual predictions in clinical applications. A comprehensive search found that Conformal Predictions can provide important insights into the accuracy of individual predictions in clinical applications. However, most studies have been performed in isolation without input from practicing clinicians, and important socio-technical considerations have not been taken into account.
JOURNAL OF HEALTHCARE INFORMATICS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Rolando Hernandez, Julio C. Facelli
Summary: By comparing predicted structure-derived properties from wild type and mutated proteins using protein structure prediction methods, diverse structural changes were revealed, providing a new research avenue for understanding the impact of protein mutations on health.
Article
Medical Informatics
Mohammad Amin Mond, Olivia R. Liu Sheng, Guilherme Del Fiol, Julio C. Facelli, Bruce E. Bray, Samir Abdelrahman
JMIR MEDICAL INFORMATICS
(2020)
Proceedings Paper
Engineering, Biomedical
Ramkiran Gouripeddi, Le-Thuy Tran, Randy Madsen, Tanvi Gangadhar, Peter Mo, Nicole Burnett, Ryan Butcher, Katherine Sward, Julio Facelli
2019 IEEE EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL & HEALTH INFORMATICS (BHI)
(2019)
Article
Endocrinology & Metabolism
Yu Kuei Lin, Danielle Groat, Owen Chan, Man Hung, Anu Sharma, Michael W. Varner, Ramkiran Gouripeddi, Julio C. Facelli, Simon J. Fisher
JOURNAL OF THE ENDOCRINE SOCIETY
(2020)
