Article
Chemistry, Physical
Cameron Mackie, Alexander Zech, Martin Head-Gordon
Summary: This study examines the effects of cooperative or nonadditive interactions on the pairwise noncovalent interaction between two molecules in a cluster or condensed phase. General expressions for an effective two-body interaction are provided, which are correct to increasing orders in the many-body expansion. The research demonstrates that electrical polarization has the largest impact on cooperative effects on the central hydrogen bond.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Xiaoting Wang, Bin Li, Hui Wang, Qi Song, Yuxiang Ni, Hongyan Wang
Summary: This study investigates the construction of cr-hole triel-bonded and cation-pi interactions in binary and ternary complexes, and demonstrates that the cooperative effects between these interactions are positive and will be weakened in a water environment.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Sunil L. Dhonnar, Vishnu A. Adole, Rajendra H. Patil, Bhushan B. Khairnar, Thansing B. Pawar, Nutan Sadgir, Bapu S. Jagdale
Summary: A series of thiazole Schiff bases (4a-4q) were synthesized and tested for their antibiofilm potential against C. albicans. Compounds 4a, 4b, 4c, 4p, and 4q exhibited significant antibiofilm activity, with compounds 4a, 4b, and 4c showing activity at 100 µg/mL concentrations and compounds 4p and 4q showing activity at around 50 µg/mL concentrations. Microscope study supported the antibiofilm activity of these compounds. The molecular mechanism of action was investigated by analyzing gene expression levels related to biofilm formation, and molecular docking simulations revealed the interactions of these compounds with CYP51.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Physical
Sergi Burguera, Antonio Bauza, Antonio Frontera
Summary: This study provides evidence that Hg(II)& sdot;& sdot;& sdot;d(8)[M] interactions should be more accurately described as spodium bonds.
Article
Chemistry, Physical
Sergey V. Baykov, Marina V. Tarasenko, Artem V. Semenov, Evgeniy A. Katlenok, Anton A. Shetnev, Vadim P. Boyarskiy
Summary: A series of cyclohexane and cyclohexene carboxylic acids bearing 1,2,4-oxadiazole substituent were prepared via condensation reactions. The compounds were characterized by HRMS, 1 H and 13 C NMR, and the crystal structures of five acids were determined using X-ray diffraction analysis. Computational investigations revealed previously undescribed noncovalent interactions between the oxadiazole ring and carboxylic group, which were found to be caused by packing effects and have electrostatic and dispersive nature.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Physical
Svetlana A. Katkova, Alexander S. Mikherdov, Elina Sokolova, Alexander S. Novikov, Galina L. Starova, Mikhail A. Kinzhalov
Summary: A series of platinum(II) isocyanide complexes were synthesized and characterized in this study. Noncovalent interactions between the isocyanide group and platinum atom were identified using X-ray diffraction analysis and confirmed by DFT calculations and analysis of the electron density distribution. The contacts between the isocyanide moiety and various metal centers were also verified.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
Jiri Czernek, Jiri Brus, Vladimira Czernekova, Libor Kobera
Summary: This study investigates the strength of C-H···O and O-H···O hydrogen bonding in C-2h-symmetric dimers of acrylic acid. The intrinsic strength of the C-H···O interaction is found to be about a quarter of its O-H···O counterpart, contrary to expectation.
Article
Chemistry, Organic
Nabil Al-Zaqri, T. Pooventhiran, Ali Alsalme, D. Jagadeeswara Rao, Siriki Srinivasa Rao, A. Sankar, Renjith Thomas
Summary: This study investigates the structure, reactivity, and physicochemical properties of istradefylline using molecular modeling techniques. The compound shows potential as a nonlinear optical material and exhibits high light-harvesting efficiency in the near UV region.
POLYCYCLIC AROMATIC COMPOUNDS
(2022)
Article
Chemistry, Multidisciplinary
Sergey Baykov, Daniil M. Ivanov, Svetlana O. Kasatkina, Bartomeu Galmes, Antonio Frontera, Giuseppe Resnati, Vadim Y. Kukushkin
Summary: The co-crystallization of tetracyanobenzene with haloarenes was studied, and it was found that the stacking interactions and lone pair-pi-hole bonds between the molecules promote the strength of halogen bonding. The stacking interactions increase the ability of haloarenes to act as halogen bonding donors.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
G. Vijayakumari, N. Iyandurai, A. Thamarai, Jamal M. Khaled, Ghulam Abbas, S. Muthu
Summary: This study used spectral data analysis and density functional theory simulation to explore the impact of the compound on biology and medicine, and found that clemastine is the most effective anti-allergic drug for use in contemporary therapeutic targets.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Review
Multidisciplinary Sciences
Ilya G. Shenderovich
Summary: This review focuses on molecular adducts with symmetric structures and evaluates the influence of surroundings, steric hindrances, competition between noncovalent interactions, and experimental methods for studying symmetry at different time scales. Key binding units such as hydrogen, halogen, metal, and water are considered.
Article
Chemistry, Physical
S. Manivel, Bhavya S. Gangadharappa, N. Elangovan, Renjith Thomas, Ola A. Abu Ali, Dalia Saleh
Summary: A new Schiff base compound was synthesized and characterized using various spectroscopic techniques. The electronic structure of the compound and its interaction with solvent water were studied computationally. The compound was found to exhibit antibacterial and antifungal activity, which was confirmed by predictions and experimental studies.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
B. S. Chethan, N. K. Lokanath
Summary: A novel cocrystal based on hydrogen bonding interactions was designed and characterized using experimental and theoretical methods. The results showed that intramolecular charge transfer stabilizes the crystal structure, and weak noncovalent interactions play an important role in the crystal structure.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Organic
Michel Chiarucci, Andrea Mazzanti, Paolo Righi, Giorgio Bencivenni, Michele Mancinelli
Summary: A series of 1,8-bis(1-naphthyl)-naphthalenes with different substituents have been synthesized to investigate noncovalent interactions between stacked arenes. DFT calculations, NMR, and ECD experiments were used to determine the best geometries and understand the role of dispersive and electrostatic contributions. The study revealed that electrostatic contributions greatly influence the interaction energy of the two naphthyl rings, while dispersive forces play a minor role in determining the parallel displaced geometry.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Huifang Xing, Qiyu Meng, Liangrong Yang, Congmei Chen, Huizhou Liu
Summary: The study employed the PWPB95-D3 double-hybrid functional with precise dispersion description to calculate the thermodynamic properties of complexes formed by 1,3-Diisopropoxycalix[4]arenecrown-6 (BPC6) and alkali metal cations (Li', Na', K', Rb', and Cs') in gas phase and various solutions. Symmetry-adapted perturbation theory (SAPT) and IGM based on Hirshfeld partition of molecular density (IGMH) were used for the first time to analyze the interactions of these complexes. The results showed that the electrostatic energy dominated the interaction energy in the gas phase, while the dielectric screen of solvents and the presence of protic solvents influenced the binding Gibbs free energy. The dispersion interaction also played a significant role in the complexation with large cations in solvents.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Lamya H. Al-Wahaibi, Nandakumar Santhosh Kumar, Ali A. El-Emam, Natarajan S. Venkataramanan, Hazem A. Ghabbour, Abdul-Malek S. Al-Tamimi, Judith Percino, Subbiah Thamotharan
JOURNAL OF MOLECULAR STRUCTURE
(2019)
Article
Chemistry, Physical
Biswajit Mohanty, Natarajan Sathiyamoorthy Venkataramanan
JOURNAL OF PHYSICAL CHEMISTRY C
(2019)
Article
Chemistry, Physical
Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha, Ryoji Sahara
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2019)
Review
Materials Science, Multidisciplinary
Mohammad Khazaei, Avanish Mishra, Natarajan S. Venkataramanan, Abhishek K. Singh, Seiji Yunoki
CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE
(2019)
Article
Biochemistry & Molecular Biology
A. Suvitha, N. S. Venkataramanan, R. Sahara, Y. Kawazoe
JOURNAL OF MOLECULAR MODELING
(2019)
Article
Chemistry, Multidisciplinary
Natarajan Sathiyamoorthy Venkataramanan
Summary: Density functional theory calculations and wave functional analysis were used to study the (SO2)n and (SO2)n-H2O clusters, revealing that S-O chalcogen bonds are easier to form than hydrogen bonds, and the reactivity of sulfur dioxide with water increases with cluster size. Strong electrostatic interactions between S and O atoms in the clusters contribute to stability, while weak hydrogen bonds play a cooperative role.
STRUCTURAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Venkataramanan Natarajan Sathiyamoorthy, Ambigapathy Suvitha, Ryoji Sahara, Yoshiyuki Kawazoe
Summary: The study investigated the nature of interactions between ribonucleosides and deoxyribonucleosides with water molecules using dispersion corrected density functional theory and wave functional analysis. It found specific binding sites for water in nucleosides and deoxynucleosides, with consistent behavior in terms of interaction energy and hydration properties compared to experimental findings. Additionally, electrostatic potential analysis revealed unique patterns near hydrogens in ribose units, indicating different binding characteristics between nucleosides and deoxynucleosides.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
A. Suvitha, N. S. Venkataramanan, R. Sahara
Summary: In this study, the structure, stability, and interactions of SO3 and hydrated SO3 clusters were examined using density functional theory calculations. The results show that the most stable isomers of SO3 clusters are formed by S•••O and O•••O chalcogen bonding, and a maximum of three hydrogen bonds occur in hydrated SO3 clusters. Thermodynamic parameters indicate that the formation of hydrated sulfur trioxide clusters is driven by enthalpy and shows a large entropy contribution. The electrostatic attraction is dominant in the interactions, and orbital interaction increases with the cluster size in hydrated SO3 clusters.
MONATSHEFTE FUR CHEMIE
(2022)
Article
Chemistry, Multidisciplinary
Venkataramanan Natarajan Sathiyamoorthy, Ambigapathy Suvitha, Ryoji Sahara
Summary: The complexation behavior of diprotonated phenylenediamine isomers with decamethylene cucurbit[6]uril (Me(12)Q[6]) in different stoichiometries was investigated using density functional theory (DFT). The results showed that o-phenylenediamine (oPDA) forms an exclusion complex in a 1:1 stoichiometry, while other isomers form inclusion complexes. The reorganization of the complexes depends on the mode of interaction of the guest molecule.
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Ambigapathy Suvitha, Natarajan Sathiyamoorthy Venkataramanan, Ryoji Sahara
Summary: The structure, stability, and intermolecular interactions in SO3-(H2O)n (n = 1-7) clusters were investigated using density functional and wave functional methods. The addition of water molecules can increase the existing water cluster network, and the number of water molecules determines the sequential hydration process. Molecular electrostatic potentials and quantum theory of atoms in molecules further reveal the interactions between SO3 and water molecules.
STRUCTURAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha, Ryoji Sahara, Yoshiyuki Kawazoe
Summary: In this study, the formation of complexes between gemcitabine drug and host cucurbit[n]urils (Q[n]) was investigated using density functional theory (DFT). The most stable configuration was found to be a fully encapsulated complex. Thermodynamic parameters showed that the encapsulation process is spontaneous and driven by enthalpy. Molecular orbital analysis indicated that the encapsulation occurs through physical adsorption. Non-covalent interactions, including hydrogen bonding and C···F interactions, were responsible for stabilizing the complexes. The presence of steric repulsion and weak van der Waals interactions was observed.
STRUCTURAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
N. S. Venkataramanan, A. Suvitha, R. Sahara, Y. Kawazoe
Summary: Density functional theory studies have shown that the binding properties of 1,ω-bisbenzimidazolyl derivatives with cucurbit[6]uril and cyclohexanocucurbit[6]uril hosts are influenced by factors such as the structure of the host and hydrogen bonding interactions. The energetic analysis indicates a stronger complexation ability of guests with Q[6] compared to Cy6Q[6] host. Charge transfer calculations and electron density difference maps support the occurrence of charge transfer from the guest to the host molecule. Additionally, weak interactions such as hydrogen bonding and electrostatic interactions contribute to the stability of the complexes.
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Yvonne E. Moussa, Natarajan S. Venkataramanan, Nial J. Wheate
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha, Yoshuyuki Kawazoe
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
A. Suvitha, M. Souissi, R. Sahara, N. S. Venkataramanan
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY
(2019)