Article
Chemistry, Physical
Anisha Bandyopadhyay, Jahur Alam Mondal
Summary: The interaction between a molecular hydrophobe and water is crucial for their mutual structure and reactivity. This study investigates the hydrogen-bonding structure and intermolecular vibrational coupling of water in the hydration shell of charged and uncharged molecular hydrophobes. The results show that the positive charge and branching of the alkyl chain reinforce the intermolecular vibrational coupling of water in the hydration shell. Additionally, weakly interacting dangling OH groups are found in the hydrophobic hydration shells. The net charge and alkyl chain configuration of the hydrophobe strongly affect the collective nature of water and the prevalence of dangling OH groups.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Nuno Galamba
Summary: Using molecular dynamics, it was demonstrated that the hydration free energy of model hydrocarbons in supercooled water exhibits a convergence temperature. The hydration entropy and enthalpy minima are associated with structural differences between shell-bulk water, similar to those observed between low-density liquid and high-density liquid water.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Yuqing Zheng, Zhoujie Bao, Yaxun Fan, Xiaoyong Wang
Summary: The hydrophobic hydration plays an important role in the formation of Tween-60 micelles upon entrapping bioactive curcumin. The stronger hydrophobic hydration of Tween-60/curcumin complexes compared to curcumin alone is supported by increased values of pyrene polarity index. The formation of hydrogen bond network and the weakened contact of curcumin with water suggest the involvement of hydrophobic hydration in the entrapment of curcumin to surfactant micelles.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Engineering, Chemical
Usman L. Abbas, Qi Qiao, Manh Tien Nguyen, Jian Shi, Qing Shao
Summary: Hydrophobic deep eutectic solvents rely on heterogeneous hydrogen bond environments, with each solvent possessing multiple types of hydrogen bonds that impact diffusivity and molecular association. The dominating hydrogen bonds determine intra- or inter-component associations, with diffusivity showing an inverse relationship with hydrogen bond strength.
Article
Engineering, Chemical
Usman L. Abbas, Qi Qiao, Manh Tien Nguyen, Jian Shi, Qing Shao
Summary: By investigating the structural features of hydrophobic DES-aqueous interfaces, it was found that variations in dipole moment and hydrogen bonds can influence the extraction ability of DESs by adjusting the partition and kinetics of organic substrates in the DES-aqueous biphasic systems. The relationship between these interfacial features' variations and the size and hydrophobicity of DES components was also analyzed.
Article
Chemistry, Multidisciplinary
Jiahui Zhang, Ruoqi Pei, Junjun Tan, Zijian Ni, Shuji Ye, Yi Luo
Summary: Using femtosecond sum frequency generation vibrational spectroscopy, the presence of monomeric H2O and chiral OH-(H2O) complexes in hydrophobic Teflon was observed for the first time. These species are unevenly distributed inside the Teflon and at the surface. The findings provide insights into water permeation and charging mechanism of fluorinated compounds.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Construction & Building Technology
Regina Kalpokaite-Dickuvien, Stase Irena Lukosiute, Arunas Baltusnikas, Jurate Cesniene
Summary: The study investigated the impact of different hydrophobic organically modified clays on hydration, microstructure, mechanical, and water absorption properties of cement formulations. Results showed that OC with aromatic substitute groups and larger d(001) demonstrated higher mechanical strength and lower sorptivity in cement compositions.
CONSTRUCTION AND BUILDING MATERIALS
(2021)
Review
Biochemistry & Molecular Biology
Qiang Sun
Summary: Hydrophobic interactions are fundamental driving forces in many chemical and biological phenomena. The hydration free energy depends on the size of the solute, and the origin of hydrophobic effects can be attributed to the structural competition between interfacial and bulk water hydrogen bonding.
Article
Chemistry, Physical
Evgeny V. Tararushkin, Vasily V. Pisarev, Andrey G. Kalinichev
Summary: Nitrite admixtures in cement and concrete have both corrosion inhibition and anti-freezing effects. Using molecular dynamics simulation, we studied the adsorption mechanism of nitrites on portlandite surface. The results showed that nitrites are adsorbed through hydrogen bonding with hydroxyls on the portlandite surface. Furthermore, we demonstrated that nitrites can be adsorbed together with hydrated sodium ions or separately.
Article
Polymer Science
Qionghai Chen, Wanhui Huang, Liqun Zhang, Li Xi, Jun Liu
Summary: The incorporation of sacrificial hydrogen bonds is critical for the development of rubber materials with exceptional properties. In this study, molecular dynamics simulations were used to investigate the impact of hydrogen bonds on the structure, mechanical properties, and viscoelasticity of rubber materials. The results showed that increasing the hydrogen bond content can increase the glass transition temperature and adjusting the hydrogen bond crosslinking network can achieve optimal mechanical properties and low mechanical losses. Furthermore, adjusting the hydrogen bond cluster can improve the self-healing efficiency of the materials.
Article
Chemistry, Physical
Rafael M. Madero-Castro, Sofia Calero, A. Ozgur Yazaydin
Summary: Dehydration of bioalcohols is a major cost factor in biofuel production, and this study investigates the liquid phase separation of water from methanol and ethanol in a siliceous MFI pervaporation membrane. Molecular dynamic simulations show that hydrogen bonding between water and alcohol molecules may hinder complete alcohol selectivity, but suggest the potential for functionalizing membrane surfaces to overcome this issue and improve separation efficiency.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Mrityunjay K. Jha, Akshay Malik, Hemant K. Kashyap
Summary: Hydrophobic deep eutectic solvents (HDESs) have gained attention as green alternative media for extracting compounds from water, and this study uses molecular dynamics simulations to understand the microscopic structure, dynamics, and interactions in N,N-diisooctylacetamide (DOA) plus decanol (DEO) based HDESs. The analysis reveals nanoscale heterogeneous structure in all compositions, with polarity ordering observed in DOA:DEO (1:2) HDES at longer length-scales compared to other compositions. Liquid morphologies show polar and apolar self-segregation. Strong hydrogen bonding interactions dominate the microstructure of these HDESs, with DEO-DEO and DEO-DOA interactions playing a significant role. The translational mobility of the components decreases as DOA concentration increases, with DEO molecules diffusing faster in bulk HDES. Water content leads to enhanced segregation and weaker hydrogen bond interactions between DOA and DEO.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biology
Laura Lupi, Brenda Bracco, Paola Sassi, Silvia Corezzi, Assunta Morresi, Daniele Fioretto, Lucia Comez, Marco Paolantoni
Summary: The dynamics of aqueous solutions of hydrophilic peptide NAGMA and amphiphilic peptide NALMA have been investigated, revealing that both peptides slow down the mobility of water molecules and cause far-reaching spatial perturbations. The concentration dependence of hydration number is explained by the random superposition of different hydration shells. Additionally, rotational dynamics play a key role in influencing solute and solvent motions.
Article
Spectroscopy
Kunal R. Patil, Seema S. Barge, Babasaheb D. Bhosale, Dilip H. Dagade
Summary: This study focused on the H-bonding analysis of model peptides and ionic liquids in aqueous solutions, revealing stronger and shorter H-bonds around peptides and PILs, as well as ice-like structures in the hydration shell. The influence of PILs on the hydration behavior of peptides involves H-bonding, cooperativity, hydrophobicity, and ionic interactions.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Yuan Gao, Mengtian Yin, Haozhe Zhang, Baoxing Xu
Summary: This study presents a method of suppressing the outflow of liquid confined in hydrophobic nanopores by using an electric field. Molecular dynamics simulations demonstrate that the presence of an electric field can strengthen hydrogen bonds and delay degradations of the associated networks during the outflow process. The extracted outflow deformation and strength quantitatively characterize the electrical suppression effect and agree well with the simulations. This research proposes a practical means of impeding fast liquid outflow in hydrophobic nanopores, potentially useful for devising nanofluidics-based functional structures and devices with controllable performance.
Review
Biochemistry & Molecular Biology
Dmitry Tolmachev, Natalia Lukasheva, Ruslan Ramazanov, Victor Nazarychev, Natalia Borzdun, Igor Volgin, Maria Andreeva, Artyom Glova, Sofia Melnikova, Alexey Dobrovskiy, Steven A. Silber, Sergey Larin, Rafael Maglia de Souza, Mauro Carlos Costa Ribeiro, Sergey Lyulin, Mikko Karttunen
Summary: This review focuses on the computational research of deep eutectic solvents (DESs), describing the technical features of DES simulations and discussing various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Cecilia Chavez-Garcia, Mikko Karttunen
Summary: This study compared the biophysical parameters of triosephosphate isomerases (TIMs) from Trypanosoma cruzi and Trypanosoma brucei using molecular dynamics simulations. The results showed significant differences in the amino acid interactions and hydrogen bond networks between the two proteins. This research provides important insights into the mechanisms underlying the different behaviors of these proteins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Cecilia Chavez-Garcia, Jerome Henin, Mikko Karttunen
Summary: This research characterizes the structure and dynamics of MeCP2 protein and provides a computational model that is compatible with experimental data. The study reveals two main conformations of MeCP2 and compares the model with experimental observations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Materials Science, Multidisciplinary
Hossein Ravanbakhsh, Razyeh Behbahani, Hamidreza Yazdani Sarvestani, Elham Kiyani, Meysam Rahmat, Mikko Karttunen, Behnam Ashrafi
Summary: This study evaluates and assists the design of interlocked ceramics under thermal shock loading using finite-element and machine learning methods. The approach successfully finds the optimal designs among over 2 million cases.
ADVANCED ENGINEERING MATERIALS
(2023)
Article
Biophysics
Matthew Davies, A. D. Reyes-Figueroa, Andrey A. Gurtovenko, Daniel Frankel, Mikko Karttunen
Summary: A new method combining mixed radial-angular, three-particle correlation function and unsupervised machine learning was used to investigate the emergence of the ripple phase in DPPC lipid bilayers. Data from atomistic molecular dynamics simulations of varying system sizes were analyzed, revealing four distinct conformational populations of lipids. The presence of ordered, disordered, and splayed tail lipids was observed, with spatial clustering of disordered lipids in the groove side of the ripple phase. Principal component analysis confirmed the existence of the four lipid groups.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Dmitry Tolmachev, Victor Nazarychev, Veronika Fedotova, Vitaly Vorobiov, Natalia Lukasheva, Michael Smirnov, Mikko Karttunen
Summary: This study investigates the structure and properties of polymerizable deep eutectic solvents (DESs) based on choline chloride and acrylic acid for 3D printing inks, using multiscale simulations and experiments. The results reveal the physical mechanisms of DES formation and the network-like structure of the mixture with Cl- ions as connecting nodes.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Sepideh Soltani, Shahin Sowlati-Hashjin, Conrard Giresse Tetsassi Feugmo, Mikko Karttunen
Summary: The study focused on the self-assembly of DHICA-eumelanin in aqueous solutions, revealing that charged protomolecules favor solubility while uncharged protomolecules tend to aggregate.
Article
Physics, Multidisciplinary
Razyeh Behbahani, Hamidreza Yazdani Sarvestani, Erfan Fatehi, Elham Kiyani, Behnam Ashrafi, Mikko Karttunen, Meysam Rahmat
Summary: Laser machining is a flexible manufacturing technique that relies on simulation methods and machine learning to optimize processing parameters and reduce experimental costs. These techniques can be applied to a variety of ceramic laser machining processes.
Article
Engineering, Multidisciplinary
Elham Kiyani, Khemraj Shukla, George Em Karniadakis, Mikko Karttunen
Summary: This article proposes a framework and algorithm for directly uncovering the unknown parts of nonlinear equations from data. By augmenting the original X-PINN method with flux continuity across domain interfaces, the approach demonstrates excellent accuracy in predicting the unknown part of the equation. The results are further validated through symbolic regression to determine the closed form of the equation's unknown part.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Rohoullah Firouzi, Shahin Sowlati-Hashjin, Cecilia Chavez-Garcia, Mitra Ashouri, Mohammad Hossein Karimi-Jafari, Mikko Karttunen
Summary: The assembly of amyloid-beta peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Targeting the monomeric form of Aβ with small molecules or antibodies to disrupt amyloid assembly is a promising therapeutic strategy. This study proposes a computational pipeline, using ensemble docking strategy, to identify catechins' binding sites in monomeric Aβ(42) and explores the crucial interactions for binding. The results suggest that catechins, especially EGCG, can act as potent inhibitors against amyloid aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys
Summary: The stability, solubility, and function of a protein are determined by its net charge and the protonation states of its individual residues. The study demonstrates the applicability of a nonequilibrium alchemical free energy method for accurately predicting pK(a) values, which is comparable to current state-of-the-art predictors. The research also highlights the performance disparity associated with lysine partial charges in certain models and mentions an underused fix for this issue.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Editorial Material
Multidisciplinary Sciences
Vojtech Sadek, Shahin Sowlati-Hashjin, SeyedAbdolreza Sadjadi, Mikko Karttunen, Angel Martin-Pendas, Cina Foroutan-Nejad
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Behnaz Bagheri, Phansiri Boonnoy, Jirasak Wong-ekkabut, Mikko Karttunen
Summary: Oxidized phospholipids have significant effects on the structure and permeability of cell membranes, depending on the degree and concentration of oxidation. Adding PoxnoPC to phospholipid bilayers leads to a reduction in thickness and increased order in the structure, while adding PazePC results in a more significant reduction in thickness and increased disorder. These structural changes enhance the permeability of the bilayers, but the specific effect depends on the type and concentration of the oxidized products.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Mahmood Mazarei, Jan Astrom, Jan Westerholm, Mikko Karttunen
Summary: The universality of interfacial roughness in growing epithelial tissue has been a controversial issue. However, using a simulation model, it is found that the geometric shape of the tissue and the strength of cell-cell adhesion determine the scaling behavior, resolving the controversy.
Article
Physics, Fluids & Plasmas
Elham Kiyani, Steven Silber, Mahdi Kooshkbaghi, Mikko Karttunen
Summary: This paper presents data-driven architectures based on machine learning algorithms for discovering nonlinear equations of motion for phase-field models. The experimental results show that we can effectively learn the time derivatives of the field and use the data-driven partial differential equations (PDEs) to propagate the field in time, achieving results in good agreement with the original PDEs.