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Efremenko Y, Mirsky VM. Chemosensitive Properties of Electrochemically Synthesized Poly-3-Thienylboronic Acid: Conductometric Detection of Glucose and Other Diol-Containing Compounds under Electrical Affinity Control. Polymers (Basel) 2024; 16:1938. [PMID: 39000794 PMCID: PMC11244235 DOI: 10.3390/polym16131938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/15/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
Due to the presence of the boronic acid moieties, poly-3-thienylboronic acid has an affinity for saccharides and other diol-containing compounds. Thin films of this novel chemosensitive polymer were synthesized electrochemically on the gold surface. The adhesion of the polymer was enhanced by the deposition of a monomolecular layer of thiophenol. The technology was used to fabricate conductometric sensors for glucose and other diol-containing compounds. Simultaneous two- and four-electrode conductivity measurements were performed. The chemical sensitivity to sorbitol, fructose, glucose, and ethylene glycol was studied at different pH and electrode potentials, and the corresponding binding constants were obtained. Depending on the electrode potential, the reciprocal values of the binding constants of glucose to poly-3-thienylboronic acid at neutral pH are in the range of 0.2 mM-1.0 mM. The affinity for glucose has been studied in buffer solutions and in solutions containing the major components of human blood. It was shown that the presence of human serum albumin increases the affinity of poly-3-thienylboronic acid for diol-containing compounds.
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Affiliation(s)
| | - Vladimir M. Mirsky
- Nanobiotechnology Department, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
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2
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Bakó I, Jicsinszky L, Pothoczki S. Systematic Study of Different Types of Interactions in α-, β- and γ-Cyclodextrin: Quantum Chemical Investigation. Molecules 2024; 29:2205. [PMID: 38792067 PMCID: PMC11124371 DOI: 10.3390/molecules29102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, β-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using "Atom in molecules" (AIM), "Natural Bond Orbital" (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.
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Affiliation(s)
- Imre Bakó
- HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - László Jicsinszky
- Dipartimento di Scienza e Tecnologia del Farmaco, University of Turin, Via P. Giuria, 9, 10125 Turin, Italy;
| | - Szilvia Pothoczki
- HUN-REN Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest, Hungary
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3
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Fleck M, Darouich S, Hansen N, Gross J. Transferable Anisotropic Mie Potential Force Field for Alkanediols. J Phys Chem B 2024. [PMID: 38709669 DOI: 10.1021/acs.jpcb.4c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The development of force fields for polyfunctional molecules, such as alkanediols, requires a careful account of different average intramolecular conformations for gas states compared to dense liquid states, where intra- and intermolecular hydrogen bonds compete. In the present work, the transferable anisotropic Mie (TAMie) potential is extended to 1,n-alkanediols. Using the convention that intramolecular nonbonded interactions up to and including the third neighbor are excluded, all force field parameters developed previously for 1-alcohols were transferred to 1,5-pentanediol and beyond, with good agreement with experimental phase equilibrium data. To obtain trans-gauche ratios of 1,2-ethanediol and 1,3-propanediol that are consistent with experimental results, the propensities for intra- and intermolecular hydrogen bonds had to be balanced. This was achieved by parameterizing the intramolecular dihedral energy functions governing the O-C-C-O and O-C-C-C angles while intramolecular charge-charge interactions were active. All partial charges belonging to a functional group are collected in a charge group and all interactions among two charge groups are evaluated even if they are separated by less than three bonds. With this approach, it is possible to apply the nonbonded parameters from 1-alcohols to alkanediols without further refinement. The agreement with experimental phase equilibrium and shear viscosity data is of similar quality as for the 1-alcohols and the trans-gauche ratio agrees with literature results from spectroscopic measurements and ab initio calculations.
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Affiliation(s)
- Maximilian Fleck
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Samir Darouich
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
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4
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Gaur A, Balasubramanian S. Liquid-Vapor Interface of Aqueous Ethylene Glycol Solutions: A Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:230-240. [PMID: 38150706 DOI: 10.1021/acs.langmuir.3c02431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
While the organic constituent in an aqueous binary solution enriches its liquid-vapor (l-v) interface, the extent of enrichment can depend nonlinearly on its mole fraction. A microscopic quantification and rationalization of this behavior are crucial to understand the dependence of properties such as surface tension and evaporation rate of the solution on its composition. Extensive all-atom molecular dynamics simulations of aqueous ethylene glycol (EG) solutions show that the composition of the solution at the l-v interface deviates the most from that in the bulk solution at an EG mole fraction of 0.3. The population of EG molecules with their central C-C dihedral in the gauche conformation was found to be higher at the l-v interface than that in the bulk solution to facilitate the orientation of its hydrophobic methyl groups toward the vapor phase. Free energy calculations reveal that in dilute EG solutions, an EG molecule is most stable at the l-v interface. The behavior of vapor pressure in aqueous EG solutions is ideal and follows Raoult's law, while in contrast, the aqueous solution of dimethyl sulfoxide does not. A rationale for the same is provided through the orientational distribution of interfacial water molecules in the respective solutions.
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Affiliation(s)
- Anjali Gaur
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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5
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Yang B, Ren P, Xing L, Sun C, Men Z. Hydrogen-Bond Dynamics and Water Structure in Aqueous Ethylene Glycol Solution via Two-Dimensional Raman Correlation Spectroscopy. J Phys Chem Lett 2023; 14:1641-1649. [PMID: 36752643 DOI: 10.1021/acs.jpclett.2c03695] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The hydrogen-bond (H-bond) dynamics and water structural transitions in aqueous ethylene glycol (EG) solution were investigated on the basis of concentration- and temperature-dependent two-dimensional Raman correlation spectroscopy (2D Raman-COS). At room temperature, EG-induced enhancement of the water structure when the EG/water molar ratio is less than 1:28 resulted from the hydrophobic effect around the methylene groups of EG. The decrease in the temperature caused an enhancement of the Raman peak at about 3200 cm-1, representing an increase in the orderliness of water molecules. Further analysis of the water-specific structures by 2D Raman-COS reveals that the strong H-bond structure preferentially responds to external perturbations and induces a weak H-bond structural transition in water. Finally, EG-induced water structural transitions were calculated by the density functional theory (DFT). Hopefully, 2D Raman-COS combined with DFT calculations would advance the study of solute-induced water structural transitions in water-organic chemistry.
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Affiliation(s)
- Bo Yang
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Panpan Ren
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Lu Xing
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Chenglin Sun
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
- College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Zhiwei Men
- Key Laboratory of Physics and Technology for Advanced Batteries, College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
- College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China
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6
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Ortiz Restrepo SA, Adams A. Fast quantification of water content in glycols by compact 1H NMR spectroscopy. Talanta 2023; 253:123973. [PMID: 36206628 DOI: 10.1016/j.talanta.2022.123973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 12/13/2022]
Abstract
Glycols are key chemicals for many applications in different fields of activities. Being highly hydroscopic, glycols contain usually water. The presence of water, even in tiny amounts, can affect their chemical and physical properties. Therefore, the accurate determination of water content is essential for any intended applications. In this context, a novel method using low-field Nuclear Magnetic Resonance (NMR) spectroscopy is introduced. The proposed approach offers a straightforward, fast, low-cost, and versatile solution for water quantification in glycols without the need for reagents or calibration data. It is demonstrated by quantifying the water concentration up to 11 wt% in aqueous ethylene glycol (EG) and triethylene glycol (TEG) mixtures with the help of lineshape analysis of the corresponding proton spectra. The limit of detection, achieved within 1 min of measuring time, was 0.05 wt% for water in EG and 0.15 wt% in TEG. The excellent agreement between the NMR results and those from the Karl-Fischer titration indicates that the proposed NMR-based approach has a great potential to be used as an alternative to the Karl-Fischer method. In addition, it is expected that the same methodology can be applied for water quantification in more complex glycolic solutions and other mixtures.
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Affiliation(s)
| | - Alina Adams
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University, Templergraben 55, Aachen, 52056, Germany.
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7
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Liubimovskii SO, Novikov VS, Ustynyuk LY, Ivchenko PV, Prokhorov KA, Kuzmin VV, Sagitova EA, Godyaeva MM, Gudkov SV, Darvin ME, Nikolaeva GY. Raman structural study of ethylene glycol and 1,3-propylene glycol aqueous solutions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121927. [PMID: 36209716 DOI: 10.1016/j.saa.2022.121927] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/10/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Raman spectra of ethylene glycol (EG) and 1,3-propylene glycol (1,3-PG) aqueous solutions with the diol content from 10 to 90 mol% were measured. The diol content weakly influences the EG and 1,3-PG Raman bands in the spectra of the solutions in the region 250-1800 cm-1. This fact means that the conformational compositions of both the diols do not change significantly with dissolving in water. The intensity of the OH stretching band with respect to the diol bands intensities is the linear function of the ratio of the mole contents of water and the diol in the solutions. The spectral region 2800-3800 cm-1 can be used to evaluate the chemical composition of these binary solutions. DFT modeling of the Raman spectra of EG molecule in water shell confirms the prevalence of the gauche-conformation of EG in the aqueous solutions.
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Affiliation(s)
- S O Liubimovskii
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation.
| | - V S Novikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation
| | - L Yu Ustynyuk
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russian Federation
| | - P V Ivchenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russian Federation; A. V. Topchiev Institute of Petrochemical Synthesis of the Russian Academy of Sciences, Leninsky Avenue 29, 119991 Moscow, Russian Federation
| | - K A Prokhorov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation
| | - V V Kuzmin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation
| | - E A Sagitova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation
| | - M M Godyaeva
- Soil Science Faculty, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, 119991 Moscow, Russian Federation; Federal Scientific Agronomic and Engineering Center VIM, 1st Institutsky proezd, 5, 109428 Moscow, Russian Federation
| | - S V Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation; Federal Scientific Agronomic and Engineering Center VIM, 1st Institutsky proezd, 5, 109428 Moscow, Russian Federation
| | - M E Darvin
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venerology and Allergology, Center of Experimental and Applied Cutaneous Physiology, Charitéplatz 1, 10117 Berlin, Germany
| | - G Yu Nikolaeva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov Str. 38, 119991 Moscow, Russian Federation
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8
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Rodriguez SA, Tran JV, Sabatino SJ, Paluch AS. Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models. J Comput Aided Mol Des 2022; 36:687-705. [PMID: 36117236 DOI: 10.1007/s10822-022-00474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Blind predictions of octanol/water partition coefficients and pKa at 298.15 K for 22 drug-like compounds were made for the SAMPL7 challenge. Octanol/water partition coefficients were predicted from solvation free energies computed using electronic structure calculations with the SM12, SM8 and SMD solvation models. Within these calculations we compared the use of gas- and solution-phase optimized geometries of the solute. Based on these calculations we found that in general the use of solution phase-optimized geometries increases the affinity of the solutes for water as compared to octanol, with the use of gas-phase optimized geometries resulting in the better agreement with experiment. The pKa is computed using the direct approach, scaled solvent-accessible surface model, and the inclusion of an explicit water molecule, where the latter two methods have previously been shown to offer improved predictions as compared to the direct approach. We find that the use of an explicit water molecule provides superior predictions, and that the predicted macroscopic pKa is sensitive to the employed microstates.
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Affiliation(s)
- Sergio A Rodriguez
- Instituto de Ciencias Químicas, Facultad de Agronomía y Agroindustrias, Universidad Nacional de Santiago del Estero, CONICET, Santiago del Estero, Argentina
| | - Jasmine Vy Tran
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Spencer J Sabatino
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA.
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9
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Gaur A, Balasubramanian S. Conformer Selection Upon Dilution with Water: The Fascinating Case of Liquid Ethylene Glycol Studied via Molecular Dynamics Simulations. Chemistry 2022:e202200132. [PMID: 35950559 DOI: 10.1002/open.202200132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/14/2022] [Indexed: 12/24/2022]
Abstract
The aqueous solution of ethylene glycol (EG) is a binary liquid mixture that displays rich conformational and structural behaviour, which has not yet been adequately explored through atomistic molecular dynamics simulations. Herein, employing an accurate force field for EG, several physical properties of this solution are calculated to be in quantitative agreement with experimental data. While 79 % of molecules in neat liquid EG exist with their central OCCO dihedral in the gauche state, this fraction increases to 89 % in the dilute aqueous solution, largely in response to the increase in the static dielectric constant of the solution from that of neat liquid EG. The increase in gauche conformers increases the mean dipole moment of EG molecules in the solution which is additionally contributed by specific conformational states of the two terminal HOCC dihedral angles.
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Affiliation(s)
- Anjali Gaur
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560 064, India
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10
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Reis GSA, de Souza RM, Ribeiro MCC. Molecular Dynamics Simulation Study of the Far-Infrared Spectrum of a Deep Eutectic Solvent. J Phys Chem B 2022; 126:5695-5705. [PMID: 35858287 DOI: 10.1021/acs.jpcb.2c03277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Deep eutectic solvents (DESs) are similar to ionic liquids (IL) in terms of physicochemical properties and technical uses. In ILs, far-infrared (FIR) spectroscopy has been utilized to reveal ionic interactions and even to produce a signature of the strengthening of the cation-anion hydrogen bond. However, for the situation of the DES, where the mixing of a salt and a molecular species makes the interplay between multiple intermolecular interactions even more complex, a full investigation of FIR spectra is still absent. In this work, the FIR spectrum of the DES, often referred to as ethaline, which is a 1:2 mixture of choline chloride and ethylene glycol, is calculated using classical molecular dynamics (MD) simulations and compared to experimental data. To explore the induced dipole effect on the computed FIR spectrum, MD simulations were run with both nonpolarizable and polarizable models. The calculation satisfactorily reproduces the position of the peak at ∼110 cm-1 and the bandwidth seen in the experimental FIR spectrum of ethaline. The MD simulations show that the charge current is the most important contributor to the FIR spectrum, but the cross-correlation between the charge current and dipole reorientation also plays a role in the polarizable model. The dynamics of the chloride-ethylene glycol correlation span a wide frequency range, with a maximum at ∼150 cm-1, but it participates as a direct mechanism only in the charge current-dipole reorientation cross-term. Anion correlations, whose dynamics are regulated via correlation with both ethylene glycol and choline, make the most significant contribution to the charge current mechanism. The MD simulations were also utilized to investigate the effect on the FIR spectrum of adding water to the DES and switching to a 1:1 composition.
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Affiliation(s)
- Gabriela S A Reis
- Laboratório de Espectroscopia Molecular, Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05513-970 São Paulo, São Paulo, Brazil
| | - Rafael M de Souza
- Laboratório de Espectroscopia Molecular, Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05513-970 São Paulo, São Paulo, Brazil
| | - Mauro C C Ribeiro
- Laboratório de Espectroscopia Molecular, Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05513-970 São Paulo, São Paulo, Brazil
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11
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Gaur A, Balasubramanian S. Liquid Ethylene Glycol: Prediction of Physical Properties, Conformer Population and Interfacial Enrichment with a Refined Non-Polarizable Force Field. Phys Chem Chem Phys 2022; 24:10985-10992. [DOI: 10.1039/d2cp00633b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Periodic density functional theory based molecular dynamics simulations confirm the fraction of molecules in neat liquid ethylene glycol with their central OCCO dihedral in the trans conformation to be 21%,...
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12
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Kuzmin V, Novikov V, Sagitova E, Ustynyuk L, Prokhorov K, Ivchenko P, Nikolaeva G. Correlations among the Raman spectra and the conformational compositions of ethylene glycol, 1,2- and 1,3-propylene glycols. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Jindal A, Arunachalam V, Vasudevan S. Search for H-Bonded Motifs in Liquid Ethylene Glycol Using a Machine Learning Strategy. J Phys Chem B 2021; 125:5909-5919. [PMID: 34060849 DOI: 10.1021/acs.jpcb.1c01308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trajectories of atomic positions derived from ab initio molecular dynamics (AIMD) simulations of H-bonded liquids contain a wealth of information on dominant structural motifs and recurrent patterns of association. Extracting this information from a detailed search of the trajectories over multiple time frames is, however, a daunting exercise. Here, we use a machine learning strategy based on the neural inspired approach of the self-organizing maps (SOM), a type of artificial neural network that uses unsupervised competitive learning, to analyze the AIMD trajectories of liquid ethylene glycol (EG). The objective was to find whether there are H-bonded fragments, of two or more H-bonded EG molecules, that are recurrent in the liquid and to identify them. The SOM represents a set of high-dimensional data mapped onto a two-dimensional, grid of neurons or nodes, while preserving the topological properties of the input space. We show here that clustering of the fragments by SOM in terms of the molecular conformation of the individual EG molecules of the fragment and their H-bond connectivity pattern facilitates the search for H-bonded motifs. Using this approach, we are able to identify a H-bonded cyclic dimer and a bifurcated H-bonded structure as recurring motifs that appear in the longer H-bonded fragments present in liquid EG.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Vaishali Arunachalam
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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14
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Jindal A, Vasudevan S. Ethylene Glycol Dihedral Angle Dynamics: Relating Molecular Conformation to the Raman Spectrum of the Liquid. J Phys Chem B 2021; 125:1888-1895. [DOI: 10.1021/acs.jpcb.0c10921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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15
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Jindal A, Vasudevan S. Molecular Conformation and Hydrogen Bond Formation in Liquid Ethylene Glycol. J Phys Chem B 2020; 124:9136-9143. [PMID: 32945675 DOI: 10.1021/acs.jpcb.0c06324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ethylene glycol (EG) molecule, HOCH2CH2OH, adopts a conformation where the central OCCO dihedral is exclusively gauche in the gaseous and crystalline states, but in the liquid state, for close to 20% of the molecules, the central OCCO adopts the energetically unfavorable trans conformation. Here we report calculations, based on ab initio molecular dynamics simulations, on the thermodynamics associated with hydrogen bond formation in the liquid state of EG between donor-acceptor pairs with different molecular conformations. We establish an operational, geometric definition of hydrogen bonds in liquid EG from an analysis of the proton NMR data and show that the key feature, irrespective of the conformation, is marked directionality with almost linear ∠HO···O angles. The free energy for hydrogen bond formation estimated as the potential of mean force for the reversible work associated with the passage from a hypothetical state where hydrogen bonding is absent and donor-acceptor pairs are randomly oriented to the hydrogen-bonded state where the pairs are oriented showed comparable magnitudes irrespective of the molecular conformation of either the donor or acceptor. The results suggest that the presence of the trans conformer in liquid EG would require an understanding of its role in the extended hydrogen-bonded network of the liquid.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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16
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Are There Magic Compositions in Deep Eutectic Solvents? Effects of Composition and Water Content in Choline Chloride/Ethylene Glycol from Ab Initio Molecular Dynamics. J Phys Chem B 2020; 124:7433-7443. [DOI: 10.1021/acs.jpcb.0c04844] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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17
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Jindal A, Vasudevan S. Hydrogen Bonding in the Liquid State of Linear Alcohols: Molecular Dynamics and Thermodynamics. J Phys Chem B 2020; 124:3548-3555. [PMID: 32242419 DOI: 10.1021/acs.jpcb.0c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linear monohydroxy alcohols are strongly hydrogen-bonded liquids that are considered to be homologues of water. Here, we report ab initio molecular dynamics simulations of the liquid alcohols, methanol to pentanol, and from the combined radial-angular probability distribution of the intermolecular O···O distances and HO···O angles determine the geometrical parameters that define the hydrogen bonds in these systems. The key feature of hydrogen bonds in the liquid alcohols, irrespective of the size of the alkyl group, is the strong orientation dependence with the donor-acceptor HO···O angle being close to zero, similar to that observed in liquid water. Hydrogen bond formation is consequently considered to be the passage from a state where donor-acceptor pairs show no preferred orientation to one where they are almost linear. The potential of mean force, the reversible work associated with this process, is computed from the pair probability density distributions obtained from the simulations and that for a hypothetical state where donor-acceptor pairs are randomly oriented. We find that the magnitude of the free energy for hydrogen bond formation is maximum for ethanol and show that this arises from a larger electrostatic contribution to hydrogen bond formation in ethanol as compared to the other alcohols.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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Kaur S, Malik A, Kashyap HK. Anatomy of Microscopic Structure of Ethaline Deep Eutectic Solvent Decoded through Molecular Dynamics Simulations. J Phys Chem B 2019; 123:8291-8299. [DOI: 10.1021/acs.jpcb.9b06624] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Supreet Kaur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Akshay Malik
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Kaur S, Shobhna, Kashyap HK. Insights Gained from Refined Force-Field for Pure and Aqueous Ethylene Glycol through Molecular Dynamics Simulations. J Phys Chem B 2019; 123:6543-6553. [DOI: 10.1021/acs.jpcb.9b03950] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Supreet Kaur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shobhna
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Zhang N, Li MR, Zhang FS. Structure and dynamics properties of liquid ethylene glycol from molecular dynamics simulations. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Loskutov VV, Kosova GN. Molecular Structure of an Ethylene Glycol–Water Solution at 298 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s003602441902016x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ghanghas R, Jindal A, Vasudevan S. Distinguishing Intra- and Intermolecular Interactions in Liquid 1,2-Ethanediol by 1H NMR and Ab Initio Molecular Dynamics. J Phys Chem B 2018; 122:9757-9762. [DOI: 10.1021/acs.jpcb.8b07750] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ritu Ghanghas
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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Jadżyn J, Swiergiel J. The viscous consequence of different trends in clustering of 1,2-diol and 1,n-diol molecules. Phys Chem Chem Phys 2018; 20:21640-21646. [PMID: 30101265 DOI: 10.1039/c8cp03687j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents the molecular basis for the quite different behavior of the viscosity of 1,2- and 1,n-diols in dependence of the length of the alkyl part of the molecules of these compounds. The experimental data on the dipolar orientational effects revealed a decidedly different role of that part of the molecules in creating a microstructure of both the hydrogen-bonded liquids. In the case of 1,n-diols, an increase in the alkyl radical length, i.e. an increasing of the distance between the OH groups within the molecule, highly stimulates molecular self-assembly in form of gradually longer and wider ribbon-like clusters. This effect yields a quite important increase in the viscosity of 1,n-diols as n increases. In the case of 1,2-diols, due to gradual separation of the hydrophilic and hydrophobic parts of the molecules, the situation is quite different. Two OH groups situated on one of the ends of the hydrocarbon radical form the clusters of a micelle-like shape, however, the dipole moment is not compensated. Along with an increase in the hydrocarbon part in 1,2-diol molecules, one only observes an increase in the intermolecular consolidation within the micelle-like entities. This manifests as a gradual decrease in the polarity of these clusters. So, actually, there are no relevant reasons for essential differences of viscosities in the series of 1,2-diols.
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Affiliation(s)
- Jan Jadżyn
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, PL-60-179 Poznań, Poland.
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