1
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Chaboksavar M, Soltanabadi A. Experimental and computational study of binary mixture ethanolamine and 2-amino-2-methyl-1-propanol. J Mol Graph Model 2024; 131:108816. [PMID: 38909381 DOI: 10.1016/j.jmgm.2024.108816] [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: 03/26/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/25/2024]
Abstract
The present work involves experimental and computational investigations into the density of pure and mixed states of ethanolamine (ET) and 2-amino-2-methyl-1-propanol (AMP) under a pressure of 1 atm and temperatures ranging from 293.15 K to 333.15 K The density data were used to derive the excess molar volume, thermal expansion coefficient, and isothermal coefficient of pressure excess molar enthalpy. The Redlich-Kister equation was employed to calculate the excess molar and its accompanying coefficients. In the gas phase, density functional theory (DFT) was utilized to explore the most stable structures of ET … ET, AMP … AMP, and the ET … AMP mixture. Molecular dynamics simulation (MD) was used to calculate the structural properties of these mixtures in the liquid phase. Radial distribution function (RDFs) combined distribution function (CDF) and spatial distribution function (SDF) in different mole fractions calculated in the liquid phase. The intramolecular and intermolecular interactions of ethanolamine and AMP were obtained using the radial distribution function in different molar fractions. It was found that the ethanolamine molecule has a greater tendency to form intramolecular hydrogen bonds, while the AMP molecule has a greater tendency to form intermolecular hydrogen bonds.
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Affiliation(s)
- Mastaneh Chaboksavar
- Department of Physical Chemistry, Faculty of Chemistry, Razi University, Kermanshah, 6714414971, Iran.
| | - Azim Soltanabadi
- Department of Physical Chemistry, Faculty of Chemistry, Razi University, Kermanshah, 6714414971, Iran.
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2
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Cortés-Morales EC, Rathee VS, Ghobadi A, Whitmer JK. A molecular view of plasticization of polyvinyl alcohol. J Chem Phys 2021; 155:174903. [PMID: 34742193 DOI: 10.1063/5.0065964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although macromolecules such as polymers are in widespread industrial use, pure formulations rarely have precisely the properties new applications demand. Pure polymer is often too brittle and inflexible, necessitating plasticizers to soften or toughen films and bulk polymer materials. In practice, new formulations are developed by extensive trial-and-error methods, as no general molecular explanations exist for the mechanism of plasticization to aid in determining the optimal structure and concentration of plasticizers. Here, through atomistic molecular simulations augmented with advanced sampling techniques, we develop an atomic-level picture of the processes in plasticization by directly calculating free energies that govern the interaction between polymers and small-molecule plasticizers. This work focuses on the influence of two common plasticizer molecules-glycerol and sorbitol-interacting with polyvinyl alcohol (PVA), a frequently used component of polymer films. In particular, we focus on conformational and hydrogen bond structure changes induced in globules of PVA by the plasticizer molecules, with the hypothesis that hydrogen bonding plays a role in the incorporation of these plasticizers into PVA and, thus, in the observed mechanical properties. While we focus on nanoscopic systems, we observe distinct preferences in the conformational free energy that can be connected to the performance of polymer materials at laboratory and industrial scales. This work presents a new molecular perspective from which effective plasticizers can be developed and presents a firm basis from which important analyses of plasticization in complex chemical environments relevant to industry may be developed.
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Affiliation(s)
- Ernesto C Cortés-Morales
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Vikramjit S Rathee
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Ahmad Ghobadi
- Corporate R & D, Data and Modeling Sciences, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Jonathan K Whitmer
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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3
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Altun Z, Bleda EA, Trindle C. Focal Point Evaluation of Energies for Tautomers and Isomers for 3-Hydroxy-2-Butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N). Molecules 2021; 26:molecules26092623. [PMID: 33946257 PMCID: PMC8124485 DOI: 10.3390/molecules26092623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH.
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Affiliation(s)
- Zikri Altun
- Physics Department, Marmara University, Göztepe Kampus, Istanbul 34772, Turkey; (Z.A.); (E.A.B.)
| | - Erdi Ata Bleda
- Physics Department, Marmara University, Göztepe Kampus, Istanbul 34772, Turkey; (Z.A.); (E.A.B.)
| | - Carl Trindle
- Chemistry Department, University of Virginia, Charlottesville, VA 22902, USA
- Correspondence: ; Tel.: +1-4347709197
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4
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Lin S, Tong Q, Jiang P, Li B, Li Y, Yang Y. Effect of C 12H 25O– substituent position on the self-assembly behaviour of C 6H 5COO–Ala–Ala dipeptide. NEW J CHEM 2021. [DOI: 10.1039/d1nj01148k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intramolecular hydrogen bonding and steric hindrance of side chain lead the different molecular packing of dipeptides and the morphological transformation of self-assemblies’ nanostructures.
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Affiliation(s)
- Shuwei Lin
- Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province & Key Lab of Modern Optical Technologies of Education Ministry of China
- School of Optoelectronics Science and Engineering
- Soochow University
- Suzhou 215123
- China
| | - Qiyun Tong
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Pan Jiang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
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5
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Kitzmiller NL, Wolf ME, Turney JM, Schaefer HF. The HOX⋯SO 2 (X=F, Cl, Br, I) Binary Complexes: Implications for Atmospheric Chemistry. Chemphyschem 2020; 22:112-126. [PMID: 33090675 DOI: 10.1002/cphc.202000746] [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: 08/31/2020] [Revised: 10/16/2020] [Indexed: 11/07/2022]
Abstract
Sulfur dioxide and hypohalous acids (HOX, X=F, Cl, Br, I) are ubiquitous molecules in the atmosphere that are central to important processes like seasonal ozone depletion, acid rain, and cloud nucleation. We present the first theoretical examination of the HOX⋯SO2 binary complexes and the associated trends due to halogen substitution. Reliable geometries were optimized at the CCSD(T)/aug-cc-pV(T+d)Z level of theory for HOF and HOCl complexes. The HOBr and HOI complexes were optimized at the CCSD(T)/aug-cc-pV(D+d)Z level of theory with the exception of the Br and I atoms which were modeled with an aug-cc-pwCVDZ-PP pseudopotential. 27 HOX⋯SO2 complexes were characterized and the focal point method was employed to produce CCSDT(Q)/CBS interaction energies. Natural Bond Orbital analysis and Symmetry Adapted Perturbation Theory were used to classify the nature of each principle interaction. The interaction energies of all HOX⋯SO2 complexes in this study ranged from 1.35 to 3.81 kcal mol-1 . The single-interaction hydrogen bonded complexes spanned a range of 2.62 to 3.07 kcal mol-1 , while the single-interaction halogen bonded complexes were far more sensitive to halogen substitution ranging from 1.35 to 3.06 kcal mol-1 , indicating that the two types of interactions are extremely competitive for heavier halogens. Our results provide insight into the interactions between HOX and SO2 which may guide further research of related systems.
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Affiliation(s)
- Nathaniel L Kitzmiller
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
| | - Mark E Wolf
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
| | - Justin M Turney
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
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de Oliveira BG, Zabardasti A, do Rego DG, Pour MM. The formation of H···X hydrogen bond, C···X carbon-halide or Si···X tetrel bonds on the silylene-halogen dimers (X = F or Cl): intermolecular strength, molecular orbital interactions and prediction of covalency. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02644-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Zierkiewicz W, Michalczyk M, Scheiner S. Competition between Intra and Intermolecular Triel Bonds. Complexes between Naphthalene Derivatives and Neutral or Anionic Lewis Bases. Molecules 2020; 25:E635. [PMID: 32024163 PMCID: PMC7037318 DOI: 10.3390/molecules25030635] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
: A TrF2 group (Tr = B, Al, Ga, In, Tl) is placed on one of the α positions of naphthalene, and its ability to engage in a triel bond (TrB) with a weak (NCH) and strong (NC-) nucleophile is assessed by ab initio calculations. As a competitor, an NH2 group is placed on the neighboring Cα, from which point it forms an intramolecular TrB with the TrF2 group. The latter internal TrB reduces the intensity of the π-hole on the Tr atom, decreasing its ability to engage in a second external TrB. The intermolecular TrB is weakened by a factor of about two for the smaller Tr atoms but is less severe for the larger Tl. The external TrB can be quite strong nonetheless; it varies from a minimum of 8 kcal/mol for the weak NCH base, up to as much as 70 kcal/mol for CN-. Likewise, the appearance of an external TrB to a strong base like CN- lessens the ability of the Tr to engage in an internal TrB, to the point where such an intramolecular TrB becomes questionable.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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8
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Awatani A, Suzuki M. Circular linkage of intramolecular multi-hydrogen bonding frameworks through nucleophilic substitutions of β-dicarbonyls onto cyanuric chloride and subsequent tautomerisation. RSC Adv 2020; 10:39033-39036. [PMID: 35518411 PMCID: PMC9057380 DOI: 10.1039/d0ra07677e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/13/2020] [Indexed: 11/21/2022] Open
Abstract
Nucleophilic substitution reactions of cyanuric chloride with a series of β-dicarbonyls give triply β-dicarbonyl-embedded 1,3,5-triazines. Their subsequent but spontaneous tautomeric transformation leads to circularly linked, intramolecular, multi-hydrogen bonding networks. Their structural elucidation by X-ray crystallography showed elongated double bonds and shortened single bonds. This is likely due to a resonance hybrid formed via tautomerisation and simultaneous proton transfer. Triply β-dicarbonyl-embedded 1,3,5-triazine derivatives result in formation of circular linkage of resonance-assisted hydrogen bonding interactions, which can be regarded as well-delocalized resonance hybrids.![]()
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Affiliation(s)
- Ayano Awatani
- Graduate School of Natural Science and Technology
- Shimane University
- Matsue
- Japan
| | - Masaaki Suzuki
- Graduate School of Natural Science and Technology
- Shimane University
- Matsue
- Japan
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Sauceda HE, Chmiela S, Poltavsky I, Müller KR, Tkatchenko A. Construction of Machine Learned Force Fields with Quantum Chemical Accuracy: Applications and Chemical Insights. MACHINE LEARNING MEETS QUANTUM PHYSICS 2020. [DOI: 10.1007/978-3-030-40245-7_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Intramolecular Hydrogen Bonds in Normal and Sterically Compressed o-Hydroxy Aromatic Aldehydes. Isotope Effects on Chemical Shifts and Hydrogen Bond Strength. Molecules 2019; 24:molecules24244533. [PMID: 31835750 PMCID: PMC6943505 DOI: 10.3390/molecules24244533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/24/2019] [Accepted: 12/03/2019] [Indexed: 11/17/2022] Open
Abstract
A number of o-hydroxy aromatic aldehydes have been synthesized to illustrate the effect of steric compression and O···O distances on the intramolecular hydrogen bond and the hydrogen bond energies. Hydrogen bond energies have been calculated using the 'hb and out' method using either the MP2 method or the B3LYP functional with the basis set 6-311++G(d,p). However, several compounds cannot be treated this way. Hydrogen bond energies are also determined using electron densities at bond critical points and these results are in good agreement with the results of the 'hb and out' model. Two-bond deuterium isotope effects on 13C chemical shifts are suggested as an experimental way to obtain information on hydrogen bond energies as they easily can be measured. Isotope effects on aldehyde proton chemical shifts have also been measured. The former show very good correlation with the hydrogen bond energies and the latter are related to short O···O distances. Short O···O distances can be obtained as the result of short C=C bond lengths, conjugative effects, and steric compression of the aldehyde group. Short O···O distances are in general related to high hydrogen bond energies in these intramolecularly hydrogen-bonded systems of resonance assisted hydrogen bond (RAHB) type.
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11
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Sauceda HE, Chmiela S, Poltavsky I, Müller KR, Tkatchenko A. Molecular force fields with gradient-domain machine learning: Construction and application to dynamics of small molecules with coupled cluster forces. J Chem Phys 2019; 150:114102. [DOI: 10.1063/1.5078687] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Huziel E. Sauceda
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Stefan Chmiela
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany
| | - Igor Poltavsky
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany
- Department of Brain and Cognitive Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul 02841, South Korea
- Max Planck Institute for Informatics, Stuhlsatzenhausweg, 66123 Saarbrücken, Germany
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
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12
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Colizzi F, Hospital A, Zivanovic S, Orozco M. Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics. Angew Chem Int Ed Engl 2019; 58:3759-3763. [DOI: 10.1002/anie.201810922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/17/2019] [Indexed: 01/23/2023]
Affiliation(s)
- Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Sanja Zivanovic
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
- Departament de Bioquímica i Biomedicina, Facultat de BiologiaUniversitat de Barcelona Avgda Diagonal 647 Barcelona 08028 Spain
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13
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Colizzi F, Hospital A, Zivanovic S, Orozco M. Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Sanja Zivanovic
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
- Departament de Bioquímica i Biomedicina, Facultat de BiologiaUniversitat de Barcelona Avgda Diagonal 647 Barcelona 08028 Spain
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