Article
Chemistry, Multidisciplinary
Lin Cheng, Ping Tian, Honghong Duan, Qingfang Li, Xiaowen Song, Anyang Li, Liping Cao
Summary: In this study, a chiral adaptive recognition (CAR) method with sequence specificity for aromatic dipeptides was reported using an achiral tetraphenylethene-based octacationic cage as a molecular receptor and chiroptical sensor. The receptor selectively binds and dimerizes aromatic dipeptides, forming host-guest complexes with high binding affinity. The CAR method also enables the recognition of tetrapeptides, polypeptides, and proteins containing tryptophan or phenylalanine residues with characteristic circular dichroism (CD) responses.
Article
Multidisciplinary Sciences
Alaa F. Nahhas, Alrayan F. Nahhas, Thomas J. Webster
Summary: This study demonstrates the potential of synthesized dipeptides to inhibit Src kinase activity and shows their promising anticancer ability. However, further research is required to enhance their cell membrane permeability.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Chemistry, Physical
Huafeng Xu, Timothy Palpant, Cody Weinberger, David E. Shaw
Summary: A key step in the emergence of human pandemic influenza strains is the switch of viral glycoprotein HA's binding preference from avian to human receptors. Molecular dynamics simulations revealed diverse receptor conformations and predicted mutations that increased HA affinity for human receptors.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Koki Yoshizawa, Keisuke Hirata, Shun-Ichi Ishiuchi, Masaaki Fujii, Anne Zehnacker
Summary: This study investigates the two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr) using IR photodissociation spectroscopy and quantum chemical calculations. It is found that these diastereomers have similar structures with one folded ring over the DKP ring and the other extended in a trans geometry, forming a strong OH···π interaction. The neutral cyclo(LTyr-LTyr) dipeptide only exhibits a stacked geometry under supersonic expansion conditions, which is not observed in cyclo(LTyr-DTyr). In the protonated form, the strength of the OH···π interaction differs between the two diastereomers, resulting in significant differences in the nu(OH+) and protonated amide nu(NH) frequencies.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Ahmed Mohamed, Sean C. Edington, Maxim Secor, James R. Breton, Sharon Hammes-Schiffer, Mark A. Johnson
Summary: Cryogenic ion vibrational spectra are used to characterize the intrinsic spectroscopic responses of D2-tagged cyanobenzoate derivatives. The location of the -CO2- headgroup on the ring and its interaction with divalent metal ions are analyzed. The ortho isomer shows a unique tridentate binding motif and different spectral responses upon metal ion complexation. Electronic structure calculations provide insights into the origins of these spectroscopic features and their implications for metal binding in chemical and biological systems.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Cell Biology
Yanting Yin, Xiang Feng, Hongjun Yu, Allison Fay, Amanda Kovach, Michael S. Glickman, Huilin Li
Summary: This study uses cryo-EM analysis to investigate the Mtb CIpB-DnaK bi-chaperone system in the presence of ATP gamma S and a protein substrate. The authors identified different conformations of CIpB and crucial loops connecting various domains, proposing a model for the synergistic actions of protein disaggregation and refolding by this bi-chaperone system.
Article
Chemistry, Multidisciplinary
Swapna Debnath, S. R. Vignesh, Priyadarshi Satpati, Sunanda Chatterjee
Summary: We attempted to construct isolated alpha gamma non-helical C-12 beta-turn mimics by introducing differentially dimethyl substituted gamma amino acid residues at the (i+2) position of the peptide. The solution conformation was studied using NMR and CD spectroscopy. Peptides containing gamma(3,3) and gamma(4,4) residues successfully adopted the desired structure, while peptides containing gamma(2,2) residues failed. This difference in stereochemical ability was attributed to the position of the di-substitution along the peptide backbone.
Article
Multidisciplinary Sciences
Titli Sarkar, Camille R. Reaux, Jianxiong Li, Vijay V. Raghavan, Wu Xu
Summary: We have developed an alignment-free computational method based on Triangular Spatial Relationship (TSR) for protein structural comparison and motif identification and discovery. With two datasets, we demonstrate the potential applications of the method in protein clustering, identification and discovery of metal ion binding sites, and understanding the effect of amino acid grouping on protein 3D structural relationships.
Article
Chemistry, Inorganic & Nuclear
Garrett C. McKeown Wessler, Tianlin Wang, Volker Blum, David B. Mitzi
Summary: This study analyzes the relationship between different structures and members of the composition family, focusing on the structure formation and optoelectronic properties of quaternary chalcogenide semiconductors, providing a foundation for further research on this class of materials.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Yi Yao, Dorothea Golze, Patrick Rinke, Volker Blum, Yosuke Kanai
Summary: We present an accurate computational approach to calculate absolute K-edge core electron excitation energies as measured by X-ray absorption spectroscopy. The method is based on the Bethe-Salpeter equation and GW quasiparticle energies, and takes into account various numerical approximations and basis sets. The results show excellent agreement with experimental data, demonstrating the high accuracy of the method.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Mark Steger, Svenja M. Janke, Peter C. Sercel, Bryon W. Larson, Haipeng Lu, Xixi Qin, Victor Wen-zhe Yu, Volker Blum, Jeffrey L. Blackburn
Summary: In this study, a comprehensive approach combining experimental and theoretical methods is used to investigate the optical properties and anisotropy of two-dimensional metal-halide perovskites. The research reveals the fundamental physical parameters that shape the electronic structure of these materials and demonstrates a strong correlation between structure and induced optical anisotropy.
Article
Chemistry, Physical
Niara E. Wright, Xixi Qin, Junwei Xu, Leah L. Kelly, Steven P. Harvey, Michael F. Toney, Volker Blum, Adrienne D. Stiff-Roberts
Summary: This study focuses on the control of band gap in mixed-halide 2D hybrid organic-inorganic perovskites. The research demonstrates that mixed-halide perovskites are not simple random alloys and exhibit distinct ordering preferences. Understanding and tuning these preferences are essential for manipulating the properties of these materials.
CHEMISTRY OF MATERIALS
(2022)
Article
Chemistry, Physical
Jianhang Xu, Ruiyi Zhou, Zhen Tao, Christopher Malbon, Volker Blum, Sharon Hammes-Schiffer, Yosuke Kanai
Summary: The paper presents a strategy to implement the nuclear-electronic orbital (NEO) method for periodic electronic structure calculations, with a focus on multicomponent density functional theory. The NEO-DFT method is implemented using a combination of analytical and numerical integration techniques, as well as a resolution of the identity scheme. Proof-of-concept applications are provided to demonstrate the impact of quantized protons on the physical properties of extended systems.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Correction
Chemistry, Physical
B. Hourahine, B. Aradi, V. Blum, F. Bonafe, A. Buccheri, C. Camacho, C. Cevallos, M. Y. Deshaye, T. Dumitrica, A. Dominguez, S. Ehlert, M. Elstner, T. van der Heide, J. Hermann, S. Irle, J. Jakowski, J. J. Kranz, C. Koehler, T. Kowalczyk, T. Kubar, I. S. Lee, V. Lutsker, R. J. Maurer, S. K. Min, I. Mitchell, C. Negre, T. A. Niehaus, A. M. N. Niklasson, A. J. Page, A. Pecchia, G. Penazzi, M. P. Persson, J. Rezac, C. G. Sanchez, M. Sternberg, M. Stohr, F. Stuckenberg, A. Tkatchenko, V. W. -Z. Yu, T. Frauenheim
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Xiaojuan Hu, Maja-Olivia Lenz-Himmer, Carsten Baldauf
Summary: This study presents a dataset of amino-methylated and acetylated dipeptides of 20 proteinogenic amino acids, including their possible side chain protonation states and interactions with selected divalent cations. The data was generated through first-principles calculations and is suitable for force field parameterization and other applications. The metadata has been formalized in an ontology to make the data accessible across domains and machines.
Article
Chemistry, Physical
Eric T. Chang, Gabrielle Koknat, Garrett C. McKeown Wessler, Yi Yao, Volker Blum, David B. Mitzi
Summary: Recently, researchers have discovered the potential of bournonite (CuPbSbS3) as a ferroelectric photovoltaic (PV) material with a band gap of 1.3 eV. Studies have shown successful thin-film processing of bournonite, achieving a power conversion efficiency of 2.65% for a bournonite-based PV device. In this study, the solid-state synthesis of selenium-alloyed bournonite, CuPbSb(S1-xSex)3, was investigated across the entire range of x (0.0 <= x <= 1.0), and phase purity was reported for 0.0 <= x <= 0.5. Characterization of the samples revealed a decrease in band gap from 1.25 eV at x = 0.0 to 1.06 eV at x = 0.5.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Physical
Ryan Pederson, John Kozlowski, Ruyi Song, Jackson Beall, Martin Ganahl, Markus Hauru, Adam G. M. Lewis, Yi Yao, Shrestha Basu Mallick, Volker Blum, Guifre Vidal
Summary: We demonstrate the use of Google's cloud-based Tensor Processing Units (TPUs) to accelerate and scale up conventional (cubic scaling) density functional theory (DFT) calculations. By utilizing 512 TPU cores, we achieved the largest ever DFT computation, involving 247848 orbitals and a cluster of 10327 water molecules with 103270 electrons. Our work opens up new possibilities for accessible and systematic use of conventional DFT calculations at unprecedented scales, free from any system-specific constraints.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Annalise E. Maughan, Gabrielle Koknat, Peter C. Sercel, Manoj K. Jana, Roman Brunecky, David B. Mitzi, Joseph J. Berry, Volker Blum, Matthew C. Beard
Summary: In this study, a series of chiral antimony and bismuth halide materials were investigated, and the impact of chiral symmetry breaking on the inorganic sublattice was studied, leading to a unique spin texture. The chiral spin-splitting of inorganic states was revealed using density functional theory and a multiband effective mass theory. Additionally, broad red photoluminescence was observed in these compounds.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Yi Xie, Jack Morgenstein, Benjamin G. G. Bobay, Ruyi Song, Naidel A. M. S. Caturello, Peter C. C. Sercel, Volker Blum, David B. B. Mitzi
Summary: Cation mixing in 2D HOIP structures is an important factor for modifying organic templating effects and tailoring inorganic structures. In this study, a chiral-chiral mixed-cation system is demonstrated, where a small amount of chiral cation S-2-MeBA can be doped into S-BrMBA(2)PbI4 to modulate the structural symmetry. The concentration of S-2-MeBA determines the structural change from higher symmetry state (C2) to the lowest symmetry state (P1). Atomic occupancy analysis suggests that a specific S-BrMBA cation site is preferentially substituted by S-2-MeBA. The chiral cation doping system provides a material design strategy for enhancing emergent properties sensitive to symmetry breaking.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Materials Science, Multidisciplinary
Vikram Gavini, Stefano Baroni, Volker Blum, David R. Bowler, Alexander Buccheri, James R. Chelikowsky, Sambit Das, William Dawson, Pietro Delugas, Mehmet Dogan, Claudia Draxl, Giulia Galli, Luigi Genovese, Paolo Giannozzi, Matteo Giantomassi, Xavier Gonze, Marco Govoni, Francois Gygi, Andris Gulans, John M. Herbert, Sebastian Kokott, Thomas D. Kuehne, Kai-Hsin Liou, Tsuyoshi Miyazaki, Phani Motamarri, Ayako Nakata, John E. Pask, Christian Plessl, Laura E. Ratcliff, Ryan M. Richard, Mariana Rossi, Robert Schade, Matthias Scheffler, Ole Schutt, Phanish Suryanarayana, Marc Torrent, Lionel Truflandier, Theresa L. Windus, Qimen Xu, Victor W-Z Yu, D. Perez
Summary: Electronic structure calculations provide important insights into physical and chemical properties of various systems, and they are crucial in fields like materials science and computational chemistry. As we enter the exascale era, there are new opportunities and challenges in terms of simulation capabilities and efficient use of new architectures. This roadmap discusses the current status, development priorities, and plans of 14 electronic structure codes in tackling these challenges and leveraging the benefits of exascale computing.
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING
(2023)
Article
Materials Science, Multidisciplinary
Ruyi Song, Chi Liu, Yosuke Kanai, David B. Mitzi, Volker Blum
Summary: This study investigates twelve layered hybrid organic-inorganic perovskites by first-principles density functional theory (DFT), revealing tunability of band gap, quantum well type, and spin-dependent energy band properties. A refined structure is identified for (NMA)(2)PbCl4 and a new, lower-energy structure is suggested for (AMA)(2)PbCl4. The DFT based search methodology is applied to predict the likely structures for the six unknown compounds. The computed energy levels reveal tunable type I quantum well alignments and potential for spin-dependent transport properties and tunable chiroptical applications.
PHYSICAL REVIEW MATERIALS
(2023)
Review
Chemistry, Multidisciplinary
Rayan Chakraborty, Volker Blum
Summary: In the past decade, research on hybrid perovskites has made significant progress, but there are still material design challenges to be addressed. The dispersed nature of the data requires the establishment of material property databases for systematic research. Additionally, the importance of information related to different material attributes and properties is emphasized when using machine learning tools to solve problems.
TRENDS IN CHEMISTRY
(2023)
Article
Chemistry, Physical
Yi Yao, Dorothea Golze, Patrick Rinke, Volker Blum, Yosuke Kanai
Summary: This article presents an accurate computational approach to calculate absolute K-edge core electron excitation energies using numeric atom-centered orbitals (NAOs). The method is validated by comparing the results with experimental data and demonstrates excellent agreement.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)