Article
Chemistry, Physical
Ramachandren Dushanan, Samantha Weerasinghe, Dhammike P. Dissanayake, Rajendram Senthilinithy
Summary: This study investigated the effect of HDAC inhibitors on the stability of the HDLP enzyme through various analyses, finding that LBH589 and PCI24781 are excellent candidates for further research as HDLP inhibitors.
MOLECULAR SIMULATION
(2022)
Article
Chemistry, Physical
Joseph P. Heindel, Sotiris S. Xantheas
Summary: A protocol for classical and nuclear quantum dynamics is presented, utilizing the many-body expansion (MBE) for generating energies and forces, applied to water clusters using different interaction potentials at various temperatures. Results show that a four-body description of energies and forces is essential for accurate anharmonic vibrational frequencies.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Keisuke Hirata, Ken-ichi Kasai, Gilles Gregoire, Shun-ichi Ishiuchi, Masaaki Fujii
Summary: UV and IR spectra of protonated dopamine and its hydrated clusters were measured, showing different spectral features. Structure and excited state lifetime were determined through calculations, suggesting that water insertion inhibits excited state proton transfer.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
John P. Pederson, Jesse G. McDaniel
Summary: We propose a method that combines density functional theory and quantum mechanics/molecular mechanics to achieve long-range electrostatic embedding. By directly integrating the computed electrostatic potential from a particle-mesh Ewald grid, we are able to accurately evaluate integrals using standard DFT machinery. The benchmarks and evaluations demonstrate the importance of our algorithm in accurately calculating redox potentials in complex solvents such as ionic liquids.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Nuno M. Fortunato, Andreas Taubel, Alberto Marmodoro, Lukas Pfeuffer, Ingo Ophale, Hebert Ebert, Oliver Gutfleisch, Hongbin Zhang
Summary: Magnetic refrigeration is an efficient and eco-friendly alternative to traditional vapor-cooling, but its implementation relies on materials with tailored magnetic and structural properties. This study introduces a high-throughput computational workflow for designing magnetocaloric materials, using density functional theory calculations to screen potential candidates in the MM'X compound family (M/M' = metal, X = main group element). Out of 274 stable compositions, 46 magnetic compounds are found to stabilize in both austenite and martensite phases. By evaluating and comparing the structural phase transition and magnetic ordering temperatures, nine compounds with structural transitions are identified as potential candidates based on the concept of the Curie temperature window. Additionally, the use of doping to tailor magnetostructural coupling and isostructural substitution as a general approach to engineer magnetocaloric materials is suggested.
Article
Chemistry, Multidisciplinary
John H. Hack, James P. Dombrowski, Xinyou Ma, Yaxin Chen, Nicholas H. C. Lewis, William B. Carpenter, Chenghan Li, Gregory A. Voth, Harold H. Kung, Andrei Tokmakoff
Summary: The molecular structure and behavior of water confined in aluminosilicate zeolite pores is essential for understanding zeolite acid chemistry under hydrous conditions. By using a combination of ultrafast two-dimensional infrared spectroscopy and ab initio molecular dynamics, this study was able to characterize the hydrogen-bonding network within highly hydrated zeolite HZSM-5 pores. Results indicated that the excess charge is detached from the zeolite and resides near the more highly coordinated water molecules in the cluster.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Hans Georg Gallmetzer, Thomas S. Hofer
Summary: Optimized link bond parameters for the C-alpha-C-beta bond have been determined and compared to reference data. The results suggest that the optimized parameters are more suitable for QM/MM link bonds compared to a single global setting, and virtually identical parameters were obtained in calculations using different levels of theory. The provided collection of link atoms parameters is valuable for QM/MM studies of biomacromolecules.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Optics
Giorgio Visentin, Alexei A. Buchachenko, Pawel Tecmer
Summary: The precision of photoassociation spectroscopy of the Yb dimer in degenerate gases can improve constraints on short-range gravity-like forces, dependent on the refinement of theoretical knowledge of interatomic potential and interactions. This research provides a flexible and accurate reference for future refinement of constraints on short-range gravity-like forces by ultracold atomic spectroscopy, based on the evaluation of Yb dimer potentials from previous studies.
Article
Chemistry, Physical
Nikolay V. Tkachenko, Pavel Rublev, Pavel A. Dub
Summary: The research on the mechanism of the Noyori-Ikariya asymmetric transfer hydrogenation of ketones has been ongoing for nearly three decades. While the early part of the catalytic cycle involving hydride transfer is well-understood, the later part involving proton transfer remains ambiguous. This study uses various molecular dynamics simulation methods to identify the source of protons in different reagents/solvents, clarifying the roles of the catalyst and reagent/solvent in the reaction.
Article
Chemistry, Physical
Nikolay V. Tkachenko, Pavel Rublev, Pavel A. Dub
Summary: The study of the mechanism of the Noyori-Ikariya asymmetric transfer hydrogenation of ketones has been investigated for nearly three decades. While the early part of the catalytic cycle is well-understood, the later part involving proton transfer is still unclear. This study eliminates the ambiguity by using molecular dynamics simulation methods and reveals that the source of the proton depends on the nature of the reagent/solvent.
Article
Chemistry, Physical
Keisuke Hirata, Ken-Ichi Kasai, Koki Yoshizawa, Gilles Gregoire, Shun-Ichi Ishiuchi, Masaaki Fujii
Summary: This study investigates protonated dopamine water clusters using electronic and vibrational spectroscopy in a cryogenic ion trap. The spectroscopic results are compared and assigned with quantum chemistry calculations performed in different states. The researchers observe a significant hydration effect when dopamine is solvated by three water molecules. The study also reveals conformer selectivity in the 1-3 complex, where the occurrence of an excited state proton transfer reaction depends on the hydrogen bond network formed between dopamine and water molecules.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Leila Shahrokh, Reza Omidyan, Gholamhassan Azimi
Summary: The non-radiative relaxation mechanism of protonated adenine was investigated using quantum chemical computational methods and dynamics simulations. It was found that the out-of-plane deformation of the six-member ring plays a significant role in the deactivation of the excited state to the ground state, which is important for the photostability of protonated DNA/RNA bases.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Benjamin McKinnon, Samuel J. P. Marlton, Jordan Dezalay, Satchin Soorkia, Stephen J. Blanksby, Adam J. Trevitt
Summary: This study investigates the first pi pi* transition for protonated 2-, 3-, and 4-formylpyridine (FPH+) using mass spectrometry coupled with photodissociation action spectroscopy. The findings reveal the photodissociation pathways and product distributions for different ions. While the elimination of CO is thermodynamically preferred, the loss of CH2O also shows kinetic competitiveness. This study is important for understanding the photochemical properties of these ionized compounds.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Summer L. Sherman, Kaitlyn C. Fischer, Etienne Garand
Summary: The influence of methyl side chains on the microsolvated structures of Gly(3)H(+)(H2O)(1-2) and Ala(3)H(+)(H2O)(1-2) clusters was investigated using infrared predissociation spectra. Multiple solvated structures were observed for each cluster, and their relative populations were determined. The results showed that the presence of methyl side chains affects the intramolecular hydrogen bonding even in the presence of solvent molecules.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biophysics
Thomas J. Summers, Qianyi Cheng, Manuel A. Palma, Diem-Trang Pham, Dudley K. Kelso, Charles Edwin Webster, Nathan J. DeYonker
Summary: The lab has developed the RINRUS toolkit to simulate enzyme active sites with interatomic contact network information for rational residue selection and QM-cluster model generation. By computing methyl transfer reactions for 550 models, it was found that even smaller RINRUS-designed models can converge efficiently. RINRUS will be essential for enhancing and automating enzyme model design based on cheminformatics.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Iwen Fu, Yugin Cai, Yingkai Zhang, Nicholas E. Geacintov, Suse Broyde
Article
Chemistry, Multidisciplinary
Cheng Wang, Yingkai Zhang
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2017)
Article
Chemistry, Medicinal
Chen Chen, Xuben Hou, Guohua Wang, Wenyan Pan, Xinying Yang, Yingkai Zhang, Hao Fang
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2017)
Article
Chemistry, Multidisciplinary
David Rooklin, Ashley E. Modell, Haotian Li, Viktoriya Berdan, Paramjit S. Arora, Yingkai Zhang
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Genetics & Heredity
Yuqin Cai, Iwen Fu, Nicholas E. Geacintov, Yingkai Zhang, Suse Broyde
Article
Chemistry, Physical
Linqiong Qiu, Cong Shen, Jianing Song, Yingkai Zhang, John Z. H. Zhang
Article
Chemistry, Medicinal
Hong Mu, Yingkai Zhang, Nicholas E. Geacintov, Suse Broyde
CHEMICAL RESEARCH IN TOXICOLOGY
(2018)
Article
Chemistry, Medicinal
Xuben Hou, David Rooklin, Duxiao Yang, Xiao Liang, Kangshuai Li, Jianing Lu, Cheng Wang, Peng Xiao, Yingkai Zhang, Jin-peng Sun, Hao Fang
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2018)
Article
Multidisciplinary Sciences
Jinping Lei, Gang Sheng, Peter Pak-Hang Cheung, Shenglong Wang, Yu Li, Xin Gao, Yingkai Zhang, Yanli Wang, Xuhui Huang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Kangshuai Li, Xuben Hou, Ruirui Li, Wenxiang Bi, Fan Yang, Xu Chen, Peng Xiao, Tiantian Liu, Tiange Lu, Yuan Zhou, Zhaomei Tian, Yuemao Shen, Yingkai Zhang, Jiangyun Wang, Hao Fang, Jinpeng Sun, Xiao Yu
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Chemistry, Physical
Jianing Lu, Cheng Wang, Yingkai Zhang
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Biochemistry & Molecular Biology
William M. Marsiglia, Joseph Katigbak, Sijin Zheng, Moosa Mohammadi, Yingkai Zhang, Nathaniel J. Traasethl
Article
Chemistry, Physical
Carmen Ka Man Tse, Jun Xu, Liang Xu, Fu Kit Sheong, Shenglong Wang, Hoi Yee Chow, Xin Gao, Xuechen Li, Peter Pak-Hang Cheung, Dong Wang, Yingkai Zhang, Xuhui Huang
Article
Chemistry, Medicinal
Hong Mu, Nicholas E. Geacintov, Jung-Hyun Min, Yingkai Zhang, Suse Broyde
CHEMICAL RESEARCH IN TOXICOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Iwen Fu, Yuqin Cai, Nicholas E. Geacintov, Yingkai Zhang, Suse Broyde