Article
Chemistry, Physical
Ahmed M. Rozza, Danny E. P. Vanpoucke, Eva-Maria Krammer, Julie Bouckaert, Ralf Blossey, Marc F. Lensink, Mary Jo Ondrechen, Imre Bako, Julianna Olah, Goedele Roos
Summary: In this study, the hydration structure of PEG and POM oligomers is characterized by investigating how they disrupt the water structure compared to the bulk solvent and how the solute chains interact with the solvent. The folding degree of the chain affects its solvation, which can be measured by various parameters. Atomic charges calculated on the oligomers in gas phase do not determine solvation, but hydration induces charge transfer from the solute molecule to the solvent, depending on the degree of hydration.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Holehundi J. Shankara Prasad, Haleyur G. Anil Kumar, Thaluru M. Mohan Kumar, Channappa N. Kavitha, Devaraju, Hemmige S. Yathirajan, Sean R. Parkin, Lilianna Checinska
Summary: Six new salts containing 4-(2-methoxyphenyl)piperazin-1-ium cation (2-MeOPP) or 4-phenylpiperazin-1-ium cation (PP) with various organic-acid anions have been structurally characterized. The crystal-packing architectures and hydrogen bonding interactions have been discussed. The binding energies of the ionic pairs have been calculated and compared, and trends and correlations have been analyzed.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Physical
Caroline M. Loe, Chelsea Liekhus-Schmaltz, Niranjan Govind, Munira Khalil
Summary: This study investigates the excited-state intramolecular proton transfer (ESIPT) process in 10-hydroxybenzo[h]quinoline (HBQ) using computational methods such as linear-response time-dependent density functional theory (LR-TDDFT) and time-resolved X-ray absorption spectroscopy (XAS). The results reveal clear X-ray spectral signatures of coupled electronic and atomic motions during and following ESIPT at the oxygen and nitrogen K-edge, providing insight for future experiments at X-ray free electron lasers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Jose L. F. Santos, Gabriel L. C. de Souza
Summary: In this study, the stability and photoinduced degradation mechanism of terbuthylazine (TBA) were investigated. The results revealed the significant influence of water molecules and H2O2 on the photoinduced degradation of TBA, as observed through experimental and computational approaches.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Debashree Manna, Rabindranath Lo, Dana Nachtigallova, Zdenek Travnicek, Pavel Hobza
Summary: The study investigates the impact of solvent dielectric constant on the dative bond in Lewis electron pair bonding systems. By comparing two systems, H3B <- NH3 and {Zn <-(NH3)}(2+), in solvents with different dielectric constants, and utilizing state-of-the-art computational methods, it is found that the stability of the neutral H3B <- NH3 system increases with solvent polarity, while the positively charged {Zn <-(NH3)}(2+) system shows the opposite trend. These changes are attributed to different charge redistributions in neutral and charged complexes, reflecting the response to the solvent and quantified by changes in solvation energies.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
G. Nottoli, B. Ballotta, S. Rampino
Summary: Charge-displacement (CD) analysis is a quantitative method for analyzing charge redistribution during intermolecular interactions. However, when complex interactions involving multiple concurrent charge flows occur, ordinary CD analysis only provides an averaged picture. In this study, LCD analysis, which combines CD analysis with Hirshfeld partitioning, allows for a detailed characterization of individual charge flows.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Lei Li, Wei Sun, Zhibo Tong, Maolin Bo, Kostya Ken Ostrikov, Yongli Huang, Chang Q. Sun
Summary: This study investigates the performance of individual ions in salt solutions and the impact of ionic hydration on hydrogen bonding network distortion, surface stress, and solution viscosity. The findings reveal that ions occupy the interstitial space of water eccentrically to form hydration cells, and the polarization of ions affects the length and stiffness of H-O bonds. Furthermore, the screening effect of hydrating water dipoles limits the size of cation hydration cells, while inter-anion repulsion reduces the hydration volume. The polarization of cations and anions contributes to the linear and nonlinear components of viscosity and surface stress.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Amberley D. Stephens, Johanna Koelbel, Rani Moons, Chyi Wei Chung, Michael T. Ruggiero, Najet Mahmoudi, Talia A. Shmool, Thomas M. McCoy, Daniel Nietlispach, Alexander F. Routh, Frank Sobott, J. Axel Zeitler, Gabriele S. Kaminski Schierle
Summary: The solvation shell plays a crucial role in protein folding and function, but its involvement in protein misfolding and aggregation is still not fully understood. We found that the mobility of water molecules within the solvation shell affects the aggregation rate of alpha-synuclein, a protein associated with Parkinson's disease. Decreasing the mobility of water molecules by the presence of NaCl increases alpha-synuclein aggregation, while increasing solvation shell mobility with CsI decreases aggregation. Changing the solvent from H2O to D2O also promotes aggregation, indicating a solvent-driven effect.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Engineering, Environmental
Yidong Hu, Yunteng Qu, Yansong Zhou, Zhiyuan Wang, Huijuan Wang, Bo Yang, Zhenqiang Yu, Yuen Wu
Summary: The introduction of atomically dispersed Pt in graphitic carbon nitride as Pt SAs/C3N4 photocatalyst, with Pt-N bonds serving as a bridge for electron transfer, significantly improves the photocatalytic efficiency for hydrogen evolution.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Diego Sorbelli, Leonardo Belpassi, Paola Belanzoni
Summary: A gold-aluminyl complex has been reported to have an unconventional gold nucleophilic center, with the reaction mechanism found to be cooperative. The Au-Al bond is primarily of an electron-sharing nature, with the metal fragments displaying a diradical-like reactivity with CO2.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Zhe Tang, Qingtong Liu, Siping Liu, Jinfeng Zhao, Daoyuan Zheng
Summary: This study used density functional theory to investigate the excited state dynamics and photophysical properties of a series of compounds, and found that the hydrogen bond geometry has a significant influence on these properties. The state-specific solvation model was also found to better explain the relationship between hydrogen bond strength and energy barrier.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Dipankar Roy, Andriy Kovalenko
Summary: The 3D-reference interaction site model (3D-RISM) molecular solvation theory in combination with the Kovalenko-Hirata (KH) closure was used to investigate the liquid states of seven heterocyclic liquids and to test the performance of the theory in solvation free energy (SFE) calculations. The computed results were compared with molecular dynamics simulations and experimental data, showing good agreement in most cases.
Article
Biochemistry & Molecular Biology
Jinfeng Zhao, Chang Liu
Summary: Inspired by the regulated properties of 2-(20-hydroxyphenyl)benzazole derivatives, this study explores the photo-induced behaviors of the novel BBTHQ fluorophore associated with different atomic electronegativities. It is found that low electronegativity enhances hydrogen bonding effects in the S1 state, particularly in the BBTHQ-SO and BBTHQ-SSe compounds. The study also presents an atomic electronegativity-regulated ESDPT mechanism based on potential energy surfaces and ESDPT paths.
Article
Chemistry, Multidisciplinary
Jolanta Nieszporek, Tomasz Panczyk, Krzysztof Nieszporek
Summary: Different mechanisms of H-bond formation between sulfate anion and water are presented using molecular dynamics simulations. Multi-centered hydrogen bonds were observed, with hydrogen bridge making/breaking going according to the large angular jump mechanism. Classical, bifurcated and trifurcated hydrogen bonds between water and sulfate have transitional character, supported by free energies of binding of water to sulfate ion for particular types of hydrogen bridges. This phenomenon is similar to that observed in the hydration shell of perchlorate anion, although the amplitudes of angular jump and hydrogen bond lifetimes differ in both cases.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2021)
Article
Chemistry, Organic
Christian Laurence, Sergui Mansour, Daniela Vuluga, Khadija Sraidi, Julien Legros
Summary: This study highlights the shortcomings of the current methods used to determine the hydrogen bonding donation ability parameter and proposes three replacement methods. These new methods have significant implications for the measurement of solvent parameters.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Kamalika Banerjee, Ruchika Bhat, V. U. Bhaskara Rao, Anshu Nain, Kartik Lakshmi Rallapalli, Sohona Gangopadhyay, R. P. Singh, Manidipa Banerjee, Bhyravabhotla Jayaram
Article
Biochemistry & Molecular Biology
Bhaskar K. Chatterjee, Abhilash Jayaraj, Vinay Kumar, Brian Blagg, Rachel E. Davis, B. Jayaram, Shashank Deep, Tapan K. Chaudhuri
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Pradeep Pant, Amita Pathak, B. Jayaram
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2020)
Article
Biochemistry & Molecular Biology
Pradeep Pant, B. Jayaram
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2019)
Article
Biology
Ali Khosravi, Morteza Kouhsar, Bahram Goliaei, B. Jayaram, Ali Masoudi-Nejad
COMPUTERS IN BIOLOGY AND MEDICINE
(2019)
Article
Biochemistry & Molecular Biology
Ali Khosravi, B. Jayaram, Bahram Goliaei, Ali Masoudi-Nejad
MOLECULAR MEDICINE
(2019)
Article
Biochemical Research Methods
Akhilesh Mishra, Sahil Dhanda, Priyanka Siwach, Shruti Aggarwal, B. Jayaram
Article
Biochemistry & Molecular Biology
Anjali Soni, Ruchika Bhat, B. Jayaram
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2020)
Article
Chemistry, Multidisciplinary
Pritam Mahawar, Mishi Kaushal Wasson, Mahendra Kumar Sharma, Chandan Kumar Jha, Goutam Mukherjee, Perumal Vivekanandan, Selvarajan Nagendran
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Engineering, Chemical
Ruchika Bhat, Rahul Kaushik, Ankita Singh, Debarati DasGupta, Abhilash Jayaraj, Anjali Soni, Ashutosh Shandilya, Vandana Shekhar, Shashank Shekhar, B. Jayaram
CHEMICAL ENGINEERING SCIENCE
(2020)
Article
Virology
Praveen Kumar Tripathi, Anjali Soni, Shiv Pratap Singh Yadav, Ankit Kumar, Nitika Gaurav, Siva Raghavendhar, Pradeep Sharma, Sujatha Sunil, Ashish, Bhyravabhotla Jayaram, Ashok Kumar Patel
Article
Chemistry, Multidisciplinary
Pritam Mahawar, Pratima Shukla, Prakash Chandra Joshi, Dharmendra Singh, Hemant Kumar, Goutam Mukherjee, Selvarajan Nagendran
Summary: Germacarbonyl compounds, which are the germanium analogs of carbonyl compounds, are typically unstable under ambient conditions due to the lability of the Ge=E bonds. However, this study presents the first examples of germacarbonyl compounds synthesized under ambient conditions by utilizing dipyrromethene ligand stabilization. These compounds exhibit stability and can form stable copper(i) complexes when reacted with copper(i) halides under atmospheric conditions.
Article
Multidisciplinary Sciences
Fereshteh Mataeimoghadam, M. A. Hakim Newton, Abdollah Dehzangi, Abdul Karim, B. Jayaram, Shoba Ranganathan, Abdul Sattar
SCIENTIFIC REPORTS
(2020)
Article
Mathematical & Computational Biology
Ankita Singh, Rahul Kaushik, Dheeraj Kumar Chaurasia, Manpreet Singh, B. Jayaram
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2020)
Article
Chemistry, Organic
Venkatesan Santhanam, Pradeep Pant, B. Jayaram, Namakkal G. Ramesh
ORGANIC & BIOMOLECULAR CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)