Article
Engineering, Environmental
Qing-Yun Jia, Chien-Min Chen, Bao-Zhen Li, Lan Wang
Summary: In this study, a novel engineered bacterium was constructed using a photosynthetic bacteria as a host and expressing metallothionein from a freshwater crab. The bacterium showed higher biosorption capacity and faster sorption rates for Cd and Cu compared to the wild-type. The proportion of intracellular metal uptake in the engineered bacterium increased under different conditions. The functional groups on the cell membrane of the bacterium were more selective in metal biosorption.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Physics, Multidisciplinary
Fangzhou Zhao, Mark E. Turiansky, Audrius Alkauskas, Chris G. Van de Walle
Summary: Trap-assisted Auger-Meitner recombination is highlighted as a dominant nonradiative process in wide-band-gap materials, and a first-principles methodology is presented to determine the rates of this process in semiconductors or insulators due to defects or impurities.
PHYSICAL REVIEW LETTERS
(2023)
Article
Nuclear Science & Technology
Mingliang Wei, Pengbo Zhang, Shengming Zhou, Xing Wang, Guiqiu Wang, Jijun Zhao
Summary: This study investigates the clustering behaviors and stable configurations of vacancies in vanadium through first-principles investigations. The results show that the average formation energies per vacancy decrease with the cluster sizes, and the reduction is larger when an odd-sized Vn cluster forms an even-sized Vn+1 cluster. The stabilities of vacancy clusters increase with the sizes, and the incremental binding energies exhibit fluctuation trends explained by both size characteristics and the terrace-ledge-kink model. The relationship between vacancy formation/incremental binding energy and Wigner-Seitz area is also estimated. Additionally, a machine learning model based on Linear-SVM is established to predict the formation energies of larger vacancy clusters.
NUCLEAR MATERIALS AND ENERGY
(2022)
Article
Multidisciplinary Sciences
Mohammad Bagheri, Hannu-Pekka Komsa
Summary: Raman spectroscopy is a widely-used non-destructive method for characterizing materials and determining their atomic structure and chemical composition. This study presents an optimized workflow for efficiently calculating Raman spectra using existing material databases. The workflow was validated by comparing the calculated spectra with experimental results, and high-throughput calculations were performed for a large number of materials from various classes, resulting in a comprehensive database of Raman spectra that agree well with experiments.
Article
Chemistry, Physical
Huan Tran, Aubrey Toland, Kellie Stellmach, McKinley K. Paul, Will Gutekunst, Rampi Ramprasad
Summary: This study developed a first-principles computational scheme for accurately calculating the enthalpy of ring-opening polymerization (Delta H-ROP). The scheme demonstrated a smaller root-mean-square error compared to conventional approaches when validated on a diverse benchmark set. This development opens up new pathways for building a high-quality database of Delta H-ROP and accelerating the design of depolymerizable polymers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Huan Tran, Aubrey Toland, Kellie Stellmach, McKinley K. Paul, Will Gutekunst, Rampi Ramprasad
Summary: Researchers have developed a first-principles computational scheme to calculate Delta H-ROP for polymer systems, achieving a root-mean-square error of 7 kJ/mol on a benchmark set of 42 ROP polymers. This development paves the way for building a high-quality database of Delta H-ROP for predictive machine-learning models and accelerating the design of depolymerizable polymers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Materials Science, Multidisciplinary
Pengbo Zhang, Mingliang Wei, Yonggang Li, Jijun Zhao, Pengfei Zheng, Jiming Chen
Summary: This study investigated the interactions of solute atoms with self-interstitial atoms/clusters in vanadium using first-principles calculations. The results show that certain solute elements prefer specific configurations with SIAs, but do not alter the relative stability order of SIA clusters. These findings provide valuable data for understanding the influence of solutes on the stability of SIAs/SIA clusters in V alloys under irradiation.
JOURNAL OF NUCLEAR MATERIALS
(2021)
Article
Chemistry, Physical
Rakshanda Dhawan, Vikrant Chaudhary, Tashi Nautiyal, Jeroen van den Brink, Hem C. Kandpal
Summary: Recent progress in the experimental and theoretical study of semiconducting CaAgP has led us to investigate its electrical and thermal transport properties using first-principles calculations. By using a hybrid functional, we find that CaAgP is a semiconducting material with a narrow band gap of approximately 0.15 eV, in agreement with experimental observations. Our results indicate that CaAgP is dynamically stable and has a gapped electronic band structure, making it potentially suitable for thermoelectric applications, particularly when p-doped.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Multidisciplinary Sciences
Rahul Nikhar, Krzysztof Szalewicz
Summary: Developing theoretical frameworks for predicting new polymorphs is valuable. This study presents an ab initio based force-field approach that significantly speeds up crystal structure prediction compared to fully ab initio schemes. The authors have developed an inexpensive and reliable method for molecular crystal structure predictions. The method starts from a two-dimensional graph of the crystal's monomers and utilizes quantum mechanical calculations to develop an accurate force field for crystal prediction. The robustness of this method has been demonstrated by successfully finding the experimental crystal within the top 20 predicted polymorphs for each molecule investigated.
NATURE COMMUNICATIONS
(2022)
Correction
Chemistry, Physical
Peter L. Rodriguez-Kessler, Alvaro Munoz-Castro, Adan R. Rodriguez-Dominguez, Jose Luis Cabellos
Summary: The study investigates the influence of structure on the oxygen reduction reaction by using first-principles calculations on Pt-15 clusters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Materials Science, Multidisciplinary
Banasree Sadhukhan, Anders Bergman, Yaroslav O. Kvashnin, Johan Hellsvik, Anna Delin
Summary: The study finds that low-dimensional magnets are more sensitive to atomic displacement and phonons due to thermal fluctuations. The spin-lattice coupling in the 2D ferromagnet CrI3 is investigated using relativistic first-principles study, and it is found to be significantly larger than in bulk systems. The magnetic interactions depend on both in-plane and out-of-plane motion of atoms, and the magnetic pair interactions change sign for specific atomic displacements.
Article
Materials Science, Multidisciplinary
Aurash Karimi, Michael Auinger
Summary: This study systematically investigates the diffusion of nitrogen in Ferrite and Austenite using a robust multiscale model combining Density Functional Theory and Kinetic Monte Carlo. Quantitative predictions are made for nitrogen diffusion in vacancy-rich iron crystals, providing valuable insights for nitriding manufacturers. The enhanced diffusion models may play a crucial role in improving existing processes and avoiding common manufacturing problems.
Article
Multidisciplinary Sciences
Alex M. Ganose, Junsoo Park, Alireza Faghaninia, Rachel Woods-Robinson, Kristin A. Persson, Anubhav Jain
Summary: The authors developed a computationally efficient method for calculating carrier scattering rates of semiconductors, which shows similar accuracy to state-of-the-art methods but at a much lower computational cost. This approach enables high-throughput computational workflows for accurate screening of carrier mobilities, lifetimes, and thermoelectric power.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Tian Lan, Qi An
Summary: A novel artificial intelligence framework combining deep reinforcement learning techniques with density functional theory simulations has been developed to automate the search and evaluation of complex catalytic reaction networks. Demonstrated on the Haber-Bosch process, the framework shows outstanding capability in discovering complicated reaction paths.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Dan Han, Xiaoheng Yang, Mu Du, Gongming Xin, Jingchao Zhang, Xinyu Wang, Lin Cheng
Summary: This study systematically investigates the thermoelectric properties of different WS2-WSe2 phononic crystals using first-principles calculations. It is found that the SL1 monolayer has the highest ZT value, at least twice as high as those of the WS2 and WSe2 monolayers; additionally, the PCH2 structure exhibits the best thermoelectric performance with significantly higher ZT values compared to the SL1 monolayer.
Article
Pharmacology & Pharmacy
Rukmankesh Mehra, Kasper P. Kepp
Summary: The study identifies four potential binding sites for pyridopyrazine-1,6-dione GSMs in the substrate-bound gamma-secretase structure, with site 4 showing significant correlation between binding affinity and activity data. Charged protonated GSMs may have higher affinities due to pi-cation interaction with the polar residue Tyr115 of PS1-NTF. Compound pIC(50) values are largely determined by molecular size, hydrophobicity, and polarizability. These findings suggest a primary modulator binding site in gamma-secretase, and highlight the importance of drug size, hydrophobicity, and polarizability in modulating enzyme-substrate interactions.
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Budheswar Dehury, Kasper P. Kepp
Summary: The protease complex gamma-secretase, with four subunits including APH-1 and PS, plays a key role in cleaving transmembrane substrates like Notch and beta-amyloid precursor to generate amyloid-beta, central to Alzheimer's disease. Variations in the subunits APH1-A, APH1-B, PS1, and PS2 could impact A beta production and the effectiveness of gamma-secretase drugs. The structural model of APH-1B suggests similarities with APH-1A but differences in water accessibility that may be relevant to the protein's existence in two forms and their specific function and location.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Octav Caldararu, Tom L. Blundell, Kasper P. Kepp
Summary: The study analyzed the structural sensitivity of stability prediction methods for proteins and found that the methods can be grouped into two categories with varying sensitivity. Accuracy correlates with precision for mutation-type-balanced data sets, highlighting the importance of balance in mutation types. Machine-learning methods may underestimate the significance of protein structure compared to side-chain-sensitive methods.
BMC BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Rukmankesh Mehra, Kasper Planeta Kepp
Summary: This article discusses how computational science has led to a causative model of familial Alzheimer's disease by integrating new cryo-electron microscopy structures and biochemical and clinical data. The model is based on conformational states of the membrane protease gamma-secretase, explaining the Aβ(42)/Aβ(40) ratio and the impact of mutations. It suggests that drugs targeting longer, pathogenic Aβ peptides should stabilize the compact state to reverse the disease progression.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Kasper Planeta Kepp
Summary: Despite the well-documented role of zinc in inflammation and immunity, the underlying chemistry of zinc in relation to specific proteins and pathways of the immune system has been relatively overlooked. This review provides an overview of key proteins structures, zinc coordination chemistry, and potential mechanisms involved in zinc-based immunity, highlighting areas for future chemical and biological research.
Article
Chemistry, Multidisciplinary
Kristoffer T. Baek, Kasper P. Kepp
Summary: Accurate prediction of protein stability changes upon mutation is crucial for various fields and was achieved through the development of two simple yet high-performing models. By addressing biases in training data, the models showed good performance and interpretability across different pathologies.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Rukmankesh Mehra, Kasper P. Kepp
Summary: The study highlights the importance of the S-protein of SARS-CoV-2 in virus evolution and the structural characteristics that facilitate analysis of virus function and evolution. It recommends considering structural heterogeneity and using averages of high-quality protein structures when analyzing structure-function relationships. Chemical tendencies of prominent S-protein mutations and their potential relationship with human ACE2 adaptation were discussed.
ACS INFECTIOUS DISEASES
(2022)
Article
Clinical Neurology
Robert David Henderson, Kasper Planeta Kepp, Andrew Eisen
Summary: Amyotrophic lateral sclerosis and frontotemporal dementia are neurodegenerative diseases with complex cellular pathology. The paper emphasizes the importance of evolution in the development of higher cortical function and the impact of factors related to increased lifespan on neuronal function.
FRONTIERS IN NEUROLOGY
(2022)
Article
Chemistry, Medicinal
Kristoffer T. Bask, Kasper P. Kepp
Summary: This study evaluated the performance of AlphaFold2 (AF2), a protein structure prediction tool, in describing the solvent exposure of human proteins. The results showed that AF2 performed well for monomer proteins but had worse performance for multimers. Challenges related to specific groups of residues were identified. Overall, AF2 demonstrated excellent performance in predicting the solvent exposure of human proteins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biophysics
Rukmankesh Mehra, Kasper P. Kepp
Summary: This study investigates the precision of computational estimates for protein stability changes due to mutations. While single mutation results are uninformative, structure-averaged differences can yield significant results. Functionally important natural mutations have a smaller stability impact compared to other mutations.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2022)
Article
Cell Biology
Kristoffer T. Baek, Rukmankesh Mehra, Kasper P. Kepp
Summary: The stability of SARS-CoV-2 S-protein fold is related to its expression levels and ACE2 binding effects. Computational analysis shows significant correlations between stability changes and experimental expression, as well as weaker correlations with ACE2 binding effects. This suggests that functional properties of the SARS-CoV-2 S-protein mutants are determined by a few simple features.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Public, Environmental & Occupational Health
Kasper P. Kepp, Jonas Bjork, Vasilis Kontis, Robbie M. Parks, Kristoffer T. Baek, Louise Emilsson, Tea Lallukka
Summary: This study critically reviewed different estimates of all-cause excess mortality in the five Nordic countries during the COVID-19 pandemic. The analysis suggests that the Institute for Health Metrics and Evaluation model substantially overestimates excess mortality in Finland, Denmark, and possibly Sweden. The findings highlight the heterogeneity and uncertainty in estimates of excess mortality and emphasize the need for cautious interpretation.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2022)
Review
Clinical Neurology
Kasper P. Kepp, Nikolaos K. Robakis, Poul F. Hoilund-Carlsen, Stefano L. Sensi, Bryce Vissel
Summary: Results from recent clinical trials of anti-amyloid antibodies for Alzheimer's disease have challenged the amyloid cascade hypothesis and indicated a more complex etiology. The treatments have shown no or uncertain clinical effect on cognition, suggesting that amyloid may play a minor role in the disease. Multiple pathogenic factors may contribute to Alzheimer's disease, and evolving multi-factor disease models may lead to more effective treatment strategies.
Article
Biochemical Research Methods
Shivani Thakur, Rajaneesh Kumar Verma, Kasper Planeta Kepp, Rukmankesh Mehra
Summary: Computational structure-based screening of S-protein mutations can help rationalize virus function and aid in early detection of concerning variants. Results show that major variants maintain ACE2 affinity better than random mutations, and the impact of Omicron mutations on binding affinity is modest compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Public, Environmental & Occupational Health
Kasper P. Kepp, Jonas Bjork, Louise Emilsson, Tea Lallukka
Summary: The study focuses on the COVID-19 pandemic in the Nordic countries and investigates the age and sex-specific mortality patterns. It found that Denmark had the highest death rates before and during the pandemic, while Sweden experienced the largest mortality increase in 2020. Overall, 2021 was a year of low mortality for all Nordic countries.
SSM-POPULATION HEALTH
(2023)
Article
Chemistry, Inorganic & Nuclear
Vaibhav Bedi, Dipendu Mandal, Zahid Hussain, Shi-Ming Chen, Yile Wu, Zheng-Wang Qu, Stefan Grimme, Douglas W. Stephan
Summary: The reaction of (tBuO(2)CN)(2) with 9-BBN leads to the formation of a bicyclic heterocyclic compound, while its reactions with BF3 or [Et3Si][B(C6F5)(4)] result in the isolation of different compounds. Computational studies reveal that the steric and electronic properties of the Lewis acid are important in the formation of one of the compounds.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Chisa Itoh, Haruka Yoshino, Taku Kitayama, Wataru Kosaka, Hitoshi Miyasaka
Summary: A new synthetic route for constructing functional paddlewheel diruthenium(II,II) complexes was developed, utilizing Schiff base condensation reactions. The attached Schiff base groups significantly affected the electronic states of the resulting complexes, as revealed by cyclic voltammetry and DFT calculations.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Danrui Ni, Haozhe Wang, Xianghan Xu, Weiwei Xie, Robert J. Cava
Summary: A layered rhombohedral polymorph of indium(iii) triiodide is synthesized at high pressure and temperature. It has an orange color, which is different from ambient pressure InI3, which has a monoclinic molecular structure and a light-yellow color.
DALTON TRANSACTIONS
(2024)
Review
Chemistry, Inorganic & Nuclear
Juan Carlos Perez-Sanchez, Raquel P. Herrera, M. Concepcion Gimeno
Summary: Gold(II) complexes have been less utilized in catalysis compared to their gold(I) and gold(III) counterparts. However, gold(II) complexes offer potential in homo-coupling and cross-coupling reactions, as they are more easily accessible through simplified oxidation and reduction processes. Gold(II) exhibits characteristics of both soft acid gold(I) and hard acid gold(III). This review explores the unique reactivity and potential applications of gold(II) species, highlighting their significance in catalytic transformations.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Nighat Yousuf, Yanping Ma, Qaiser Mahmood, Wenjuan Zhang, Yizhou Wang, Hassan Saeed, Wen-Hua Sun
Summary: In this study, a series of structurally rigid cyclooctyl-fused iminopyridine iron complexes were synthesized and used with methylaluminoxane for isoprene polymerization. The extent of steric hindrance of the ligand framework was found to significantly affect catalytic performance, with less hindrance leading to better activity and stability.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Chenghao Song, Huiwei Du, Menglei Xu, Jie Yang, Xinyu Zhang, Jungan Wang, Yuanfang Zhang, Chengjun Gu, Rui Li, Tao Hong, Jingji Zhang, Jiangying Wang, Yongchun Ye
Summary: This study improves the performance of perovskite solar cells by using a dual-hole transport layer strategy. This strategy enhances the charge transfer efficiency of the transport layer, reduces charge recombination, and improves the quality of the perovskite film layer. Ultimately, the stability of the device is enhanced.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Mahender Singh, Aakash Yadav, Ranjit Singh, Chullikkattil P. Pradeep
Summary: A new aryl selenonium polyoxometalate hybrid was developed and compared with an aryl sulfonium polyoxometalate hybrid in terms of their photocatalytic properties. It was found that the aryl selenonium hybrid exhibited better catalytic performance, which could be attributed to the larger atomic radii of selenium stabilizing the photogenerated electron-hole pair more efficiently. Additionally, the generation of elemental selenium through cleavage of C-Se bonds during catalysis was observed.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Yuhan Xie, Boyu Dong, Xuemin Wang, Siyuan Wang, Jinxi Chen, Yongbing Lou
Summary: This study successfully fabricated visible-light-responsive three-dimensional core-shell CoSe2/ZnIn2S4 heterostructures and achieved attractive activity in photocatalytic hydrogen evolution. The presence of CoSe2 improved light absorption and accelerated charge transfer kinetics. The strong interaction between CoSe2 and ZnIn2S4 reduced charge recombination, further enhancing photocatalytic activity for hydrogen evolution.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Andre L. de O. Batista, Joao Marcos T. Palheta, Mauricio J. Piotrowski, Celso R. C. Rego, Diego Guedes-Sobrinho, Alexandre C. Dias
Summary: This study presents a simulation protocol that provides a solid foundation for exploring two-dimensional materials. Using the TiBr2 2H monolayer as an example, the study reveals its promising properties for optoelectronic and valleytronic applications, including its stability, spin-orbit coupling effects, and optical helicity selection rule.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Jiang Jiang, Zi-Wei Li, Zhi-Zhuan Zhang, Bin Tan, Zhao-Feng Wu, Xiao-Ying Huang
Summary: In this work, two metal organic frameworks (MOFs) containing {Cu2I2} clusters, Eu-CuI-INA and Sr-K-CuI-INA, were synthesized and characterized. Both materials have a three-dimensional structure with {Cu2I2} clusters coordinated by INA(-) ligands and Eu3+ or Sr2+ ions. The Sr-K-CuI-INA material exhibited sensitive fluorescence sensing behaviors towards cysteine and nitro-bearing molecules, showing potential applications in bio and explosive molecule sensing. This work provides a good reference for designing fluorescent MOF probes containing CuI molecules.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Zhiya Lin, Jiasheng Wu, Qianwen Ye, Yulong Chen, Hai Jia, Xiaohui Huang, Shaoming Ying
Summary: Na-ion batteries (NIBs) have attracted great interest as a potential technology for grid-scale energy storage due to the wide distribution, low cost, and environmental friendliness of sodium resources. However, their implementation is hindered by low rate capability and cycling stability caused by the large ionic size of Na+. In this study, a three-dimensional nanoarchitectured coral-like CoSe2@N-doped carbon (CL-CoSe2@NC) was synthesized, and it exhibited improved sodium storage properties with better electrode kinetics and a stable SEI film.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Ya-Qiong Zhang, Yu Zhang, Guoping Zeng, Rong-Zhen Liao, Man Li
Summary: The mechanism and selectivity of CO2 reduction under visible light were investigated using density functional calculations. The results showed that a tetradentate PNNP-type Iridium(III) complex exhibited high activity and selectivity in the reaction.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Sanyukta Ghosh, Shubhanth Jain, Soumya Ranjan Mishra, Gerda Rogl, Peter Rogl, Ernst Bauer, B. S. Murty, A. Govindaraj, Ramesh Chandra Mallik
Summary: In this study, reduced graphene oxide (rGO) was uniformly dispersed in the In0.5Co4Sb12 bulk material by ultrasonication, which effectively reduced the lattice thermal conductivity and improved the thermoelectric efficiency.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Mika Takeuchi, Yutaka Amao
Summary: This study developed an effective visible-light driven system for fumaric acid production using renewable resources such as biomass derivatives, providing an alternative to the current petroleum-based synthesis methods.
DALTON TRANSACTIONS
(2024)
Article
Chemistry, Inorganic & Nuclear
Juan Jian, Meiting Wang, Zhuo Wang, Jingwen Meng, Yuqin Yang, Limin Chang
Summary: Developing low-cost and self-supported bifunctional catalysts is crucial for highly efficient water splitting devices. In this study, nano-NiFe2O4 was directly grown onto iron foil surface and Sn4+ was introduced into the NiFe2O4. The resulting Sn-NiFe2O4/IF showed low overpotentials and high current densities during oxygen evolution reaction (OER) and hydrogen evolution reaction (HER), making it a promising catalyst for large-scale hydrogen production.
DALTON TRANSACTIONS
(2024)