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Rozza AM, Bakó I, Oláh J. Theoretical insights into water network of B-DNA duplex with Watson-Crick and Hoogsteen base pairing geometries. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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2
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Herman KM, Stone AJ, Xantheas SS. A Classical Model for 3-body Interactions in Aqueous Ionic Systems. J Chem Phys 2022; 157:024101. [DOI: 10.1063/5.0095739] [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
We present a classical electrostatic induction model to evaluate the 3-body Ion-Water-Water (I-W-W) and (W-W-W) interactions in aqueous ionic systems. The monatomic ions were described by a point charge and a dipole-dipole polarizability, while for the polyatomic ions distributed multipoles up to hexadecapole and distributed polarizabilities up to quadrupole-quadrupole were used. The accuracy of the classical model is benchmarked against an accurate dataset of 936 (I-W-W) and 2,184 (W-W-W) 3-body terms for 13 different monatomic and polyatomic cation and anion systems. The classical model shows excellent agreement with the reference MP2 and CCSD(T) 3-body energies. The Root-Mean-Square-Errors (RMSEs) for monatomic cations, monatomic anions, and polyatomic ions were 0.29 kcal/mol, 0.25 kcal/mol, and 0.12 kcal/mol, respectively. The corresponding RMSE for 1,744 CCSD(T)/aVTZ 3-body (W-W-W) energies, used to train MB-pol, was 0.12 kcal/mol. The accuracy of the classical model demonstrates that the 3-body term for aqueous ionic systems can be accurately modeled classically, without the need to fit to tens of thousands of high-level ab initio calculations. This approach provides a fast but accurate and efficient path towards modeling the 3-body effect in aqueous ionic systems that is fully transferable across systems with different ions.
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Affiliation(s)
- Kristina M. Herman
- University of Washington Department of Chemistry, United States of America
| | - Anthony J. Stone
- University Chemical Laboratory, University of Cambridge Department of Chemistry, United Kingdom
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Wang X, Gonçalves W, Lacroix D, Isaiev M, Gomès S, Termentzidis K. Thermal conductivity temperature dependence of water confined in nanoporous silicon. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:305701. [PMID: 35405665 DOI: 10.1088/1361-648x/ac664b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/11/2022] [Indexed: 05/27/2023]
Abstract
Recently, it has been shown that high density nanoconfined water was the reason of the important enhancement of the effective thermal conductivity up to a factor of 50% of a nanoporous silicon filled with water. In this work, using molecular dynamics simulations, we further investigate the role of the temperatureT(from 285 to 360 K) on the thermal conductivity enhancement of nanohybrid porous silicon and water system. Furthermore, by studying and analysing several structural and dynamical parameters of the nanoconfined water, we give physical insights of the observed phenomena. Upon increasing the temperature of the system, the thermal conductivity of the hybrid system increases reaching a maximum forT= 300 K. With this article, we prove the existence of new heat flux channels between a solid matrix and a nanoconfined liquid, with clear signatures both in the radial distribution function, mean square displacements, water molecules orientation, hydrogen bond networks and phonon density of states.
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Affiliation(s)
- Xiaorui Wang
- Univ. Lyon, INSA-Lyon, CETHIL CNRS-UMR5008, F-69621, Villeurbanne, France
| | - William Gonçalves
- Univ. Lyon, INSA-Lyon, CETHIL CNRS-UMR5008, F-69621, Villeurbanne, France
| | - David Lacroix
- Université de Lorraine, CNRS, LEMTA, Nancy F-54000, France
| | - Mykola Isaiev
- Université de Lorraine, CNRS, LEMTA, Nancy F-54000, France
| | - Séverine Gomès
- Univ. Lyon, INSA-Lyon, CETHIL CNRS-UMR5008, F-69621, Villeurbanne, France
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Choi S, Parameswaran S, Choi JH. Effects of molecular shape on alcohol aggregation and water hydrogen bond network behavior in butanol isomer solutions. Phys Chem Chem Phys 2021; 23:12976-12987. [PMID: 34075966 DOI: 10.1039/d1cp00634g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite butanol isomers such as n-butanol, sec-butanol, isobutanol and tert-butanol having the same chemical formula, their liquid-liquid phase diagrams are distinct. That is, tert-butanol is miscible in water at all concentrations, while the other three butanol isomers are partially miscible under ambient conditions. The molecular shape of tert-butanol is close to globular and differs from the other three butanol molecules with a relatively long carbon chain. By performing molecular dynamics simulations and graph theoretical analysis of the four water-butanol isomer mixtures at varying concentrations, we show how distinct butanol aggregates are formed which depend upon the molecular shape and affect the water H-bond network structure and phase diagram in the binary liquid. The three butanol isomers of n-butanol, sec-butanol and isobutanol at concentrated solutions form chain-like alcohol aggregates, but tert-butanol forms small aggregates due to the distinct packing behavior caused by its globular molecular shape. By employing the graph theoretical analysis such as the degree distribution and the eigenvalue spectrum from the adjacency matrix in the graphical representation of the alcohol H-bond network, we show that the tert-butanol aggregates have a different morphological structure from that of the other three butanol isomers in aqueous solution. The graph theoretically distinct butanol aggregates are categorized into two groups, water-compatible and water-incompatible, depending upon the interaction between the alcohol and water molecules. Based upon our observations, we propose that the water-incompatible networks of n-butanol, sec-butanol and isobutanol aggregates do not change the water structure significantly, forming two separate liquid phases that are alcohol-rich and water-rich. However, the water-compatible network of tert-butanol aggregates has a considerable interaction with the water molecules and causes significant disruption of the water H-bond network, forming a homogeneous solution. Understanding the alcohol aggregation behavior and water structure in butanol-water mixtures provides a critical clue in appreciating fundamental issues such as miscibility and phase separation in aqueous solution systems.
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Affiliation(s)
- Seungeui Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Saravanan Parameswaran
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
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Theoretical insight into the hybridization effect of donor and acceptor atoms on the cooperativity of C-H···N hydrogen bonds. J Mol Model 2021; 27:119. [PMID: 33818695 DOI: 10.1007/s00894-021-04724-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
In the present work, the influence of hybridization on cooperativity between C-H···N hydrogen bonds is theoretically investigated. Here, C2H6, C2H4, and C2H2 are considered as hydrogen bonding donor while NH3, N2H4, N2H2, and N2 act as the hydrogen bonding acceptor. The calculations are performed at MP2/aug-cc-pVTZ level. It is observed that the stability of systems is amplified as C(sp) > C(sp2) > C(sp3) and also N(sp3) > N(sp2) > N(sp). The role of interaction and deformation energies on the stability of the systems is examined. The results indicate the contribution of interaction energy is dominant in all complexes. The strength of C-H···N hydrogen bond is estimated using interaction energy. In agreement with cooperative energies, the C-H···N hydrogen bond is respectively weakened/strengthened in the triads containing C(sp) and C(sp2)/C(sp3) where two hydrogen bonds coexist. On the other hand, the C-H···N hydrogen bond is strengthened in the ternary systems including N(sp3) and N(sp2) while an opposite behavior is obtained in the triad having N(sp).
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Alkorta I, Elguero J, Del Bene JE, Mó O, Montero-Campillo MM, Yáñez M. Mutual Influence of Pnicogen Bonds and Beryllium Bonds: Energies and Structures in the Spotlight. J Phys Chem A 2020; 124:5871-5878. [PMID: 32538087 DOI: 10.1021/acs.jpca.0c03689] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pnicogen bonds, which are weak noncovalent interactions (NCIs), can be significantly modified by the presence of beryllium bonds, one of the strongest NCIs known. We demonstrate the importance of this influence by studying ternary complexes in which both NCIs are present, that is, the ternary complexes formed by a nitrogen base (NH3, NHCH2, and NCH), a phosphine (fluorophosphane, PH2F) and a beryllium derivative (BeH2, BeF2, BeCl2, BeCO3, and BeSO4). Energies, structures, and nature of the chemical bonding in these complexes are studied by means of ab initio computational methods. The pnicogen bond between the nitrogen base and the phosphine and the beryllium bond between the fluorine atom of fluorophosphane and the beryllium derivative show large cooperativity effects both on energies and geometries, with dissociation energies up to 296 kJ mol-1 and cooperativity up to 104 kJ mol-1 in the most strongly bound complex, CH2HN:PH2F:BeSO4. In the complexes between the strongest nitrogen bases and the strongest beryllium donors, phosphorus-shared and phosphorus-transfer bonds are found.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA
| | - Otilia Mó
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
| | - M Merced Montero-Campillo
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
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Milovanović B, Stanojević A, Etinski M, Petković M. Intriguing Intermolecular Interplay in Guanine Quartet Complexes with Alkali and Alkaline Earth Cations. J Phys Chem B 2020; 124:3002-3014. [DOI: 10.1021/acs.jpcb.0c01165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Ana Stanojević
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
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Pothoczki S, Pusztai L, Bakó I. Molecular Dynamics Simulation Studies of the Temperature-Dependent Structure and Dynamics of Isopropanol–Water Liquid Mixtures at Low Alcohol Content. J Phys Chem B 2019; 123:7599-7610. [DOI: 10.1021/acs.jpcb.9b05631] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Szilvia Pothoczki
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly-Thege M. út 29-33, H-1121 Budapest, Hungary
| | - László Pusztai
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly-Thege M. út 29-33, H-1121 Budapest, Hungary
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Imre Bakó
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
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Ren T, Lin X, Zhang Q, You D, Liu X, Tao X, Gou J, Zhang Y, Yin T, He H, Tang X. Encapsulation of Azithromycin Ion Pair in Liposome for Enhancing Ocular Delivery and Therapeutic Efficacy on Dry Eye. Mol Pharm 2018; 15:4862-4871. [DOI: 10.1021/acs.molpharmaceut.8b00516] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pothoczki S, Pusztai L, Bakó I. Variations of the Hydrogen Bonding and Hydrogen-Bonded Network in Ethanol–Water Mixtures on Cooling. J Phys Chem B 2018; 122:6790-6800. [DOI: 10.1021/acs.jpcb.8b02493] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Szilvia Pothoczki
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly Thege M. út 29-33., H-1121 Budapest, Hungary
| | - László Pusztai
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly Thege M. út 29-33., H-1121 Budapest, Hungary
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, 860-8555 Kumamoto, Japan
| | - Imre Bakó
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
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