Article
Biochemistry & Molecular Biology
Krzysztof Szalewicz, Bogumil Jeziorski
Summary: SAPT is a method for computational studies of noncovalent interactions, providing clear physical interpretations and specific dependence on intermolecular separation. It connects interaction energies with monomers' properties through the asymptotic multipole expansion.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Chemistry, Multidisciplinary
Jorge Echeverria
Summary: This study combines structural and computational analysis to investigate short contacts between thiocyanato ligands in transition-metal complexes. The unique electron density distribution of thiocyanato allows it to engage in various interaction topologies involving sulfur, carbon, and nitrogen atoms. Through computational studies and analysis of interaction energies, the strength of different interaction geometries was calibrated, shedding light on the nature of the interactions through various quantum theory methods.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Chemistry, Physical
Ehsan Masumian, A. Daniel Boese
Summary: This study investigates the role of pi-resonance in the enhancement of intramolecular hydrogen bonds (IMHBs) by comparing pi-conjugated systems to their saturated planar counterparts. The results show that pi-resonance primarily affects the induction and electrostatics contributions to the IMHB energies. The stabilization of IMHBs is achieved by reducing the repulsion caused by the exchange term. These findings are consistent with expected trends in resonance assisted hydrogen bonds (RAHBs) and validate the fragmentation procedures used in this study.
Article
Chemistry, Physical
Sharon A. Ochieng, Konrad Patkowski
Summary: This study constructed a benchmark dataset containing 20 heteromolecular trimers and analyzed their interaction energies. The results showed that the three-body interaction energies were mainly dominated by induction, but had a small influence on the overall bonding type of the complex.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Chemistry, Multidisciplinary
Kevin Carter-Fenk, Ka Un Lao, John M. Herbert
Summary: Non-covalent forces are essential in molecular interactions. Symmetry-adapted perturbation theory (SAPT) provides an accurate method to calculate these interactions, decomposing the energy into meaningful components and aiding in the construction of transferable force fields.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Jishnunil Chakraborty
Summary: This study investigates the nature of weak noncovalent interactions in the self-assembled dimers of two metal complexes using density functional theory. The results provide insights into the structural patterns and physical components of interaction energies, and further analysis is conducted using absorption spectra and reactivity parameters.
Article
Computer Science, Interdisciplinary Applications
A. Mercenne, K. D. Launey, T. Dytrych, J. E. Escher, S. Quaglioni, G. H. Sargsyan, D. Langr, J. P. Draayer
Summary: We study the effectiveness of a new ab initio framework that combines the symmetry-adapted nocore shell-model approach with the resonating group method for unified descriptions of nuclear structure and reactions. Ab initio neutron-nucleus interactions are obtained for 4He, 16O, and 20Ne targets. The study demonstrates the efficacy of the proposed framework and its scalability with particle numbers and model space dimensions, with the aim of ab initio descriptions of nucleon scattering and capture reactions in the medium-mass region.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Thufail M. Ismail, Neetha Mohan, P. K. Sajith
Summary: The intermolecular hydrogen bonding of nitroxide radicals with various electron acceptors is studied comprehensively and quantitatively in this work. The electronic effects of nitroxide radicals are assessed through the analysis of molecular electrostatic potential, establishing a linear relationship between V-min and interaction energy values. The nature of hydrogen bonding in these systems is found to be dependent on the substituents present in the nitroxide radicals' structural motif, with electrostatic components playing a large role in the interaction energy.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Physical
Emran Masoumifeshani, Tatiana Korona
Summary: A novel molecular fragmentation method based on the SMF model has been proposed, allowing for cheaper calculations with accurate results. Numerical tests show that the Symmetrized SMF method can accurately reproduce molecular energies and dipole moments, making it suitable for complex molecular structures.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Bartosz Dzieciol, Irina Osadchuk, Janusz Cukras, Jan Lundell
Summary: A comprehensive analysis was conducted on the intermolecular interaction energy and anharmonic vibrations of 41 structures of the HXeYMIDLINE HORIZONTAL ELLIPSISHX (X, Y = F, Cl, Br, I) family of noble-gas-compound complexes. New structures were identified, and their interaction energies were studied using symmetry-adapted perturbation theory, up to second-order corrections. The results showed that the induction and dispersion corrections were the main driving forces of the interaction, and the entire group of complexes, except for those with HI, could be considered naturally blueshifting.
Article
Chemistry, Physical
Weiwei He, Xiangyun Qiu, Serdal Kirmizialtin
Summary: Condensation of DNA is essential for its biological functions and controlled nucleic acid assemblies. This study elucidates the mechanism of DNA condensation in different salt conditions and with different DNA sequences, by constructing free energy surfaces and analyzing cation distributions. The findings highlight the importance of localized cation dynamics in DNA condensation, which are strongly influenced by salt conditions and DNA sequences.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Maciej Bujak, Hans-Georg Stammler, Yury V. Vishnevskiy, Norbert W. Mitzel
Summary: The cocrystals (CH3)3As•C6F5I and (CH3)3Sb•C6F5I exhibit very unique I•••As and I•••Sb interactions, which are the shortest C-I•••As and C-I•••Sb halogen bonds found to date in experimentally characterized molecular (co)crystals. Comparisons with other compounds further validate the occurrence and hierarchy of these specific interactions.
Article
Biochemistry & Molecular Biology
Jia-An Chen, Sheng D. Chao
Summary: This paper proposes a machine learning approach to construct a force field model for intermolecular non-bonded interactions in organic polymer systems. The proposed model shows promising feasibility in accurately predicting interaction energies.
Article
Chemistry, Physical
Yi Xie, Daniel G. A. Smith, C. David Sherrill
Summary: This study presents an implementation of a symmetry-adapted perturbation theory algorithm based on density functional theory, utilizing density-fitting treatment of hybrid exchange-correlation kernels for describing monomers with hybrid functionals. The algorithm shows improved numerical stability and computational efficiency, performing well for systems with up to 3000 basis functions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Kousik Ghosh, Antonio Frontera, Shouvik Chattopadhyay
Summary: A heteronuclear cobalt/potassium complex has been synthesized and characterized, forming discrete I-3(-) dimers in the solid state with anti-electrostatic halogen-halogen interaction, which is energetically favorable in solution.
Article
Chemistry, Physical
Lukasz Orzel, Dorota Rutkowska-Zbik, Rudi van Eldik, Leszek Fiedor, Grazyna Stochel
Summary: Copper(II) chloride in organic solvents exhibit extensive speciation that allows switching between different chlorophyll transmetalation pathways, with one pathway particularly suitable for forming and stabilizing chlorophyll pi-cation radicals due to its unique redox cycling. In the presence of a proton donor, the system shows behavior similar to superoxide dismutase (SOD), and chlorophyll acts as an electron transfer mediator regardless of light conditions.
Article
Chemistry, Physical
Emran Masoumifeshani, Tatiana Korona
Summary: A novel molecular fragmentation method based on the SMF model has been proposed, allowing for cheaper calculations with accurate results. Numerical tests show that the Symmetrized SMF method can accurately reproduce molecular energies and dipole moments, making it suitable for complex molecular structures.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2021)
Article
Chemistry, Inorganic & Nuclear
Olga Mazuryk, Ewelina Janczy-Cempa, Justyna Lagosz, Dorota Rutkowska-Zbik, Agata Machnicka, Aneta Krasowska, Piotr Pietrzyk, Grazyna Stochel, Malgorzata Brindell
Summary: This study investigated the correlation between the spectroscopic and photophysical properties of Ru(ii) polypyridyl complexes and their photodynamic activity in vitro. The Ru(ii) complexes were found to exhibit phototoxic activity mainly through the generation of H2O2 and O-1(2), highlighting the importance of electron-transfer processes in their observed photodynamic activity. The compounds also retained their cytotoxic activity under hypoxic conditions, suggesting a potential for overcoming limitations in photodynamic therapy.
DALTON TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Malgorzata Smolilo-Utrata, Karolina A. Tarach, Katarzyna Samson, Mariusz Gackowski, Ewa Madej, Jozef Korecki, Grzegorz Mordarski, Michal Sliwa, Sebastian Jarczewski, Jerzy Podobinski, Piotr Kustrowski, Jerzy Datka, Dorota Rutkowska-Zbik, Kinga Gora-Marek
Summary: This study used various spectroscopic techniques to study the properties of vanadium species introduced into different zeolites, finding that basicity plays a critical role in the catalytic activity of the oxidative dehydrogenation of propane. Modifying zeolite through caustic treatment can adjust its basicity, aiding in the adsorption of vanadium species and increasing selectivity to propene.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
M. Sliwa, J. Podobinski, D. Rutkowska-Zbik, J. Datka
Summary: Catalytic conversion of ethanol into hydrogen is a promising method. This study focused on the transformations of ethanol on CuO/ZrO2 (Cu/Zr) mixed oxides with the addition of ZnO and NiO. It was found that CuO oxidized ethanol into acetaldehyde and water, while Cu/Zr performed both oxidation and dehydrogenation of ethanol, producing acetaldehyde, water, and hydrogen. ZnO facilitated the formation of acetone, and NiO caused the decomposition of acetaldehyde into methane and CO.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Thermodynamics
Justyna Kuczek, Magdalena Szumera, Dorota Rutkowska-Zbik, Mariusz Gackowski, Justyna Sulowska
Summary: This study focused on the preparation and characterization of multicomponent cobalt phosphate-silicate glasses and the investigation of the influence of cobalt ions on the glass structure. The induced crystallization experiment revealed that the crystallization temperature was correlated with the formed crystalline phases. Data related to different parameters were obtained through techniques such as infrared spectroscopy. This research is of significance for further exploration of cobalt phosphate-silicate glasses and the understanding of the phosphate glass family.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2023)
Article
Chemistry, Physical
Tatiana Korona, Emran Masoumifeshani, Michas Chojecki
Summary: The applicability of the systematic molecular fragmentation (SMF) model, denoted as symmetrized SMF (SSMF), has been studied for reproducing the correlation part of intermolecular interaction energies. The results show that the SSMF3 approach can accurately reproduce this contribution with a small error. In contrast, the Hartree-Fock part is only qualitatively correct for large intermolecular distances.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Ilona Gurgul, Olga Mazuryk, Dorota Rutkowska-Zbik, Michal Lomzik, Aneta Krasowska, Piotr Pietrzyk, Grazyna Stochel, Malgorzata Brindell
Summary: Ru(II) polypyridyl complexes are being studied as potential photodynamic therapy agents. In this study, three complexes were synthesized to shift their absorption towards longer wavelengths. The compounds showed photodynamic activity through the generation of 1O2 and H2O2, and demonstrated high activity in inhibiting cancer cell detachment.
Article
Biochemistry & Molecular Biology
Emran Masoumifeshani, Michal Chojecki, Dorota Rutkowska-Zbik, Tatiana Korona
Summary: This contribution explores the intermolecular complexes formed between calix[6]arenes and amino acids. By using techniques such as SAPT, F-SAPT, and SMF, the study aims to explain the varying number and strength of noncovalent bonds between different calixarene conformers and guest molecules. The partitioning of interaction energy allows for the identification of hydrogen bonds, as well as other noncovalent bonds, and helps explain phenomena such as the red shift of IR stretching frequency.
Article
Chemistry, Inorganic & Nuclear
Dominika Porebska, Lukasz Orzel, Dorota Rutkowska-Zbik, Grazyna Stochel, Rudi van Eldik
Summary: The increased affinity of cyanocobalamin (CblCN) for cancer cells allows it to be used as a carrier of inorganic cytostatics to reduce chemotherapy side effects. In this study, the effect of different ligands on the stability of platinum(II) conjugates with CblCN was investigated. Spectrophotometric monitoring, MS-ESI, 195Pt NMR, and IR spectroscopy confirmed the formation of desired binuclear complexes. Molecular modelling indicated that expanding the coordination sphere of the therapeutic metal negatively affects the stability of conjugates with CblCN, which aligns with their anticipated intercalation ability.
Article
Chemistry, Multidisciplinary
Tatiana Korona, Joanna Jankowska, Emran Masoumifeshani
Summary: A comprehensive theoretical study of the lowest electronic vertical excitations of the CBCN defect in the monolayer of hexagonal boron nitride has been performed using both periodic boundary conditions approach and finite-cluster simulation. High-level ab initio calculations with methods like EOM-CCSD, ADC(2), and TD-CC2 were performed for the smallest clusters. The results indicate similar lowest excitation energies between TD-DFT with the CAM-B3LYP functional and other high-level methods.
CANADIAN JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Inorganic & Nuclear
Maria Oszajca, Angelika Jodlowska, Dorota Rutkowska-Zbik, Konrad Kieca, Grazyna Stoche
Summary: Conversion of NO to stable S-nitrosothiols is a significant biological strategy of NO storage and signal transduction, and metal ions and metalloproteins can promote the formation of S-nitrosothiols from NO. This study investigates the incorporation of NO to biologically relevant thiols using a model protein heme center. The formation of S-nitrosothiols is confirmed under anaerobic conditions, and the molecular mechanism involving N-coordinated S-nitrosothiols is elucidated. This work highlights the importance of reversible NO binding as a biological strategy for NO storage.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
K. P. Korona, J. Binder, A. K. Dabrowska, J. Iwanski, A. Reszka, T. Korona, M. Tokarczyk, R. Stepniewski, A. Wysmolek
Summary: Defects in semiconductors play a critical role in their functional properties, and understanding and controlling these defects is essential for their application. This study investigates the UV luminescence of intentionally introduced defects in hexagonal boron nitride grown by MOVPE. Photoluminescence and cathodoluminescence experiments revealed several characteristic lines, including X230, C300, and C380, corresponding to well-known and rarely observed defect bands. The study also found that the color center bands C were replaced by broad bands D in samples grown at high temperatures, indicating a different defect formation mechanism. Time-resolved photoluminescence analysis provided insight into the lifetimes and phonon interaction of the different defect lines.
Article
Chemistry, Physical
A. Aathif Basha, Attar Kubaib, Mohammad Azam
Summary: The properties of a set of compounds were comprehensively assessed using various analytical techniques, revealing their stability and favorable drug-like characteristics. Potential antiviral and antioxidant properties were predicted, indicating promise for biological efficacy.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Meiqi Liu, Baoming Hou, Yuheng Li, Yuyu Pan, Bing Yang
Summary: This paper investigates the application potential of thermally activated delayed fluorescent (TADF) molecules with donor-acceptor-donor-acceptor pi-conjugated macrocycle structures in organic light-emitting diodes. The study finds that the macrocyclic structure has a smaller energy gap between the first singlet excited state and the first triplet excited state compared to the linear structure. The TADF efficiency is also analyzed and explained based on spin-orbit coupling and intersystem crossing rates.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Run Liu, Jiahui Liu, Jiarui Fang, Xiruo Bai, Dan Wang, Yixuan Qie, Shuqi Zu, Guancheng Wang, Xinyi Sui, Runyao Chang, Yizhu Wang, Ziheng Li
Summary: This paper investigates the remodeling effect of H2O molecules and their adsorption behavior on Co2+-doped SnO2 (221) crystal plane materials. The results show that H2O molecules remodel the crystal plane by creating oxygen defects, leading to hydroxylation. The hydroxylated crystal surface adsorbs O2 and then H2O molecules, affecting the electrical conductivity of the crystal plane.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Marisol Ibarra-Rodriguez, Paul Horley, Mario Sanchez
Summary: In this study, the functionalized borophene was investigated as a potential sensor or transporter of glucose for biomedical applications. The adsorption of glucose molecules on different boron-based complexes was studied, and the results showed that these complexes have high binding energies and can efficiently adsorb glucose molecules. The findings suggest that borophene-based systems with different oxidation states hold promise for intelligent drug delivery and biosensor design.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Syed Hassan Sarwar, Saad Jawaid Khan, Syed Faraz Jawed
Summary: The medical community is currently focusing on targeted and controlled drug delivery, and many researchers are utilizing computational resources to understand drugnanocarrier combinations and develop targeted drug delivery systems. This study used molecular dynamics to investigate the encapsulation capacity of Carbazochrome, a hemostatic drug, in Single-Walled Carbon Nanotubes of different morphological variations. The results showed that the nanotube radius and length had the most significant impact on the encapsulation capacity, followed by nanotube chirality. Temperature also affected the drug encapsulation when the nanotube radius was not very large and the chiral angle was near 30 degrees.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
Article
Chemistry, Physical
Yinquan Sui, Mengying Sun, Yongxin Wang, Zhitong Xu, Jinglu Yan, Huanpeng Liu
Summary: In this study, the structural and hydrogen storage properties of loaded Pt atoms were investigated using density functional theory (DFT) with and without substitution of B atoms on the edges of conical graphene layers (CGL). It was found that the position of the substituted B atom at the edge of the CGL has an important effect on the position of the loaded Pt atom and its hydrogen adsorption and storage properties.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2024)
