Article
Chemistry, Multidisciplinary
G. George, O. A. Stasyuk, M. Sola, A. J. Stasyuk
Summary: Belt-shaped aromatic compounds are among the most attractive classes of radial pi-conjugated nanocarbon molecules. We propose rules for their design with improved electron-donating properties.
Article
Biochemistry & Molecular Biology
Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner
Summary: The tetrel bond between 1,2-benzisothiazol-3-one-2-TF3-1,1-dioxide (T = C, Si) and pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO2, CN, F, CH3, OH, OCH3, NH2, and Li) was investigated using quantum chemical methods. The Si-O tetrel bond is strong, with interaction energies reaching a maximum of nearly 70 kcal/mol, while the C-O tetrel bond is weaker, with interaction energies between 2.0 and 2.6 kcal/mol. The presence of an electron-withdrawing substituent weakens the tetrel bond, while an electron-donating group strengthens it. The SiF3 group transfers approximately halfway between the acid's nitrogen and the base's oxygen without the assistance of cooperative effects from a third entity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Anthi Chrysafoudi, Sayan Maity, Ulrich Kleinekathoefer, Vangelis Daskalakis
Summary: Diatoms play a significant role in producing oxygen on Earth due to their exceptional light-harvesting properties, while their efficient adaptation to fluctuating light conditions is critical for photoprotection. A computational study reveals a pH-dependent adaptation at the molecular level in diatoms, with conformational changes in the FCP protein leading to a significant change in exciton transfer rate. A common photoprotective strategy between diatoms and higher plants is identified and discussed based on the interaction between FCP and LHCX proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Giovanni Spinelli, George H. Morritt, Michele Pavone, Michael R. Probert, Paul G. Waddel, Tomas Edvinsson, Ana Belen Munoz-Garcia, Marina Freitag
Summary: Two coordination complexes were synthesized by combining different metal centers with dithiolene complexes [M(mnt)(2)](2-) and a copper(II) coordination complex [Cu(Stetra)]. The Cu-Cu variant exhibited semiconductor behavior with a conductivity of approximately 2.5 x 10(-8) S cm(-1), whereas the Ni-Cu variant showed no observable conductivity. Computational studies revealed that Cu-Cu had lower reorganization energy losses, resulting in a lower barrier to the charge transfer process, which explains its higher conductivity.
ACS APPLIED ENERGY MATERIALS
(2023)
Article
Chemistry, Physical
Giovanni Spinelli, George H. Morritt, Michele Pavone, Michael R. Probert, Paul G. Waddel, Tomas Edvinsson, Ana Belen Munoz-Garcia, Marina Freitag
Summary: Two coordination complexes were synthesized by combining the dithiolene complexes [M(mnt)2]2- (mnt = maleonitriledithiolate; M = Ni2+ or Cu2+) as anion with the copper(II) coordination complex [Cu(Stetra)] (Stetra = 6,6 '- bis(4,5-dihydrothiazol-2-yl)-2,2 '-bipyri-dine) as cation. The variation of metal centers led to a significant change in conductivity, with the Cu2+ variant (Cu-Cu) displaying semiconductor behavior, while the Ni2+ variant (Ni-Cu) showed no observable conductivity. Computational studies revealed that Cu-Cu exhibited minimized reorganization energy losses and a lower barrier to the charge transfer process, resulting in higher conductivity.
ACS APPLIED ENERGY MATERIALS
(2023)
Article
Chemistry, Physical
Asem Alenaizan
Summary: In this article, a simple approach is proposed to reduce the basis set requirement for accurate computation of interaction energies of bimolecular noncovalent complexes. The approach utilizes a distributed multipole expansion to assess the significance of basis functions at each atom. By moderately truncating the basis sets, computational cost is reduced without sacrificing accuracy. The approach proves to be successful for wavefunction-based methods and density functional theory approximation using the Dunning, Karlsruhe, and Jensen basis sets.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Renato Pereira Orenha, Saulo Samuel Pereira Furtado, Giovanni Finoto Caramori, Mauricio Jeomar Piotrowski, Alvaro Munoz-Castro, Renato Luis Tame Parreira
Summary: Anions are important in biological processes and chemical production. Compounds with halogen bond donors enhanced by hydrogen bonds have been studied regarding their interaction with anions. The presence of -NO2 groups enhance non-covalent bonds with Cl-. The improvement from a mono to double HBeXB system enhances anion recognition.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Sebastien Designolle, Roope Uola, Kimmo Luoma, Nicolas Brunner
Summary: The coherence of a set of quantum systems can be characterized in a basis-independent way using the concept of set coherence, with measures that have operational meaning in discrimination games and capture the advantage offered by a given set over incoherent ones. This notion of set coherence is also connected to resource-theoretic approaches developed for quantum systems.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Inorganic & Nuclear
Arun Kumar, Samya Banerjee, Nishant Sharma, Mohd Nazish, Nico Graw, Regine Herbst-Irmer, Dietmar Stalke, Upakarasamy Lourderaj, Herbert W. Roesky
Summary: Amidinate compounds with stabilized aluminium(II) and gallium(II) elements were synthesized by prepared their precursors, and insights into their bonding were gained through the study.
DALTON TRANSACTIONS
(2022)
Article
Chemistry, Multidisciplinary
Ruihong Duan, Guangchao Han, Ling-Bo Qu, Yuanping Yi
Summary: Organic solar cells have seen rapid development in recent years, with power conversion efficiencies exceeding 18% thanks to the emergence of small-molecule acceptors with acceptor-donor-acceptor structures. Research shows that fused A-D-A acceptors have smaller reorganization energies for electronic transitions, reducing voltage and current losses, while longer donor unit lengths help reduce charge recombination. Designing and optimizing large fused A-D-A acceptors could further improve organic photovoltaic performance.
MATERIALS CHEMISTRY FRONTIERS
(2021)
Article
Chemistry, Inorganic & Nuclear
Christopher Hossack, Folasade Abdul, Christopher Cahill, Claire Besson
Summary: We synthesized and characterized 11 novel lanthanide complexes with the asymmetrically functionalized trispyrazolylborate ligand 4-nitrotrispyrazolylborate, 4-NO(2)Tp(-). Photophysical analysis revealed that the intra-ligand charge transfer transitions of the nitro-substituted ligands played a dominant role in sensitizing Ln(3+) emission. Additionally, one of the complexes, [Nd(4-NO(2)Tp)(3)], displayed single-molecule magnet properties attributed to the addition of the nitro group and subsequent rigidification of the molecular structure.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Multidisciplinary
Yaya Zhi, Qiang Guo, Jingchen Xie, Jie Hu, Shan Xi Tian
Summary: This study identifies a mechanism for the production of molecular oxygen in carbon dioxide-rich planetary atmospheres, which could contribute to our understanding of astrochemical reactions and the origin of life on Earth.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
William R. Roberts, Thomas N. Rohrabaugh, Ryan M. O'Donnell
Summary: The ARL Spectral Fitting application is a free and transparent method for analyzing and processing spectral data, offering unique attributes compared to other commercial or academic software. FCLSA provides valuable insight into the relationship between ground and excited states of photoluminescent species through a two-mode equation model.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Multidisciplinary
Qingyun Wan, Masanori Wakizaka, Nobuto Funakoshi, Yongbing Shen, Chi-Ming Che, Masahiro Yamashita
Summary: Constructing heterostructures based on molecular conductors or molecular magnets is important, and this study demonstrates the fabrication of molecular heterostructures composed of (TTF)(2)M(pdms)(2) through a controlled electrocrystallization process. The magnetic and single-molecule magnet properties of the heterostructures were characterized and compared to the parent (TTF)(2)Co(pdms)(2) complex, providing a new methodology for creating molecule-based magnetic heterostructures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Samantha I. Johnson, James D. Blakemore, Bruce S. Brunschwig, Nathan S. Lewis, Harry B. Gray, William A. Goddard, Petter Persson
Summary: The attachment of 2,2'-bipyrdine (bpy) moieties to planar silicon surfaces was investigated, revealing that adventitious chlorine atoms in the organic linker backbone caused instability at very negative potentials. Computational studies showed that structures with fluorine substituents were more stable, while fully non-halogenated structures exhibited the highest stability. Immobilizing a hydrogen-evolving molecular catalyst on a silicon cluster showed that reductively stable linkers enabled robust attachment of catalysts with behavior similar to that in homogeneous solution.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Jan Rezac
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2019)
Article
Chemistry, Physical
Saltuk M. Eyrilmez, Cemal Kopruluoglu, Jan Rezac, Pavel Hobza
Article
Chemistry, Medicinal
Kristian Kriz, Jan Rezac
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
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. 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. Stoehr, F. Stuckenberg, A. Tkatchenko, V. W. -z. Yu, T. Frauenheim
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Jan Rezac
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Review
Chemistry, Multidisciplinary
Adam Pecina, Saltuk M. Eyrilmez, Cemal Kopruluoglu, Vijay Madhav Miriyala, Martin Lepsik, Jindrich Fanfrlik, Jan Rezac, Pavel Hobza
Article
Chemistry, Physical
Jan Rezac
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Editorial Material
Chemistry, Multidisciplinary
Adam Pecina, Saltuk M. Eyrilmez, Cemal Koepruelueoglu, Vijay Madhav Miriyala, Martin Lepsik, Jindrich Fanfrlik, Jan Rezac, Pavel Hobza
Article
Chemistry, Physical
Kristian Kriz, Martin Novacek, Jan Rezac
Summary: The study investigates repulsive contacts in molecular complexes and emphasizes the importance of repulsive part in computational methods. The results show that double-hybrid functionals perform the best, while GFN2-xTB stands out among semiempirical methods. By analyzing the source of error, the study successfully corrects the most serious uncorrected issues encountered in practical calculations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Chandler Greenwell, Jan Rezac, Gregory J. O. Beran
Summary: A spin-component-scaled, dispersion-corrected MP2 model (SCS-MP2D) is proposed to address the limitations of MP2 in describing dispersion interactions and reaction thermochemistry. Experimental results show that SCS-MP2D considerably improves the accuracy of MP2 and is comparable in accuracy and computational cost to state-of-the-art density functionals.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
J. Rezac, J. J. P. Stewart
Summary: Semiempirical quantum-mechanical computational methods are widely used in the study of biomolecular systems, but their ability to accurately describe protein structures is not well understood. In this study, the structures of 19 proteins were optimized using several semiempirical QM methods, and compared to high-resolution crystal structures. Some methods showed good agreement with the experimental structures, while others introduced artificial close contacts that could be improved through reparameterization.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Kristian Kriz, Jan Rezac
Summary: The SH250x10 dataset extends the Non-Covalent Interactions Atlas database to complexes bound by sigma-hole interactions and is used for testing various DFT functionals and semiempirical quantum-mechanical methods.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Jan Rezac
Summary: The Non-Covalent Interactions Atlas has expanded with two data sets to study benchmark interaction energies in complexes dominated by London dispersion. These high-quality data sets enable comprehensive testing of various non-covalent interactions in a wide range of chemical space.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Ondrej Gutten, Petr Jurecka, Zahra Aliakbar Tehrani, Milos Budesinsky, Jan Rezac, Lubomir Rulisek
Summary: The performance of computational methods in modeling cyclic dinucleotides has been evaluated through two benchmarks, showing that most density functional approximations are accurate enough, but struggle in reproducing the conformation of purine bases. The overrepresentation of syn-conformation of guanine in PC1 indicates the need for improvement in implicit solvation models and force-field parameters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Jindrich Fanfrlik, Adam Pecina, Jan Rezac, Martin Lepsik, Menyhart B. Sarosi, Drahomir Hnyk, Pavel Hobza