1
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Schneck E, Reed J, Seki T, Nagata Y, Kanduč M. Experimental and simulation-based characterization of surfactant adsorption layers at fluid interfaces. Adv Colloid Interface Sci 2024; 331:103237. [PMID: 38959812 DOI: 10.1016/j.cis.2024.103237] [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: 11/07/2023] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 07/05/2024]
Abstract
Adsorption of surfactants to fluid interfaces occurs in numerous technological and daily-life contexts. The coverage at the interface and other properties of the formed adsorption layers determine the performance of a surfactant with regard to the desired application. Given the importance of these applications, there is a great demand for the comprehensive characterization and understanding of surfactant adsorption layers. In this review, we provide an overview of suitable experimental and simulation-based techniques and review the literature in which they were used for the investigation of surfactant adsorption layers. We come to the conclusion that, while these techniques have been successfully applied to investigate Langmuir monolayers of water-insoluble surfactants, their application to the study of Gibbs adsorption layers of water-soluble surfactants has not been fully exploited. Finally, we emphasize the great potential of these methods in providing a deeper understanding of the behavior of soluble surfactants at interfaces, which is crucial for optimizing their performance in various applications.
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Affiliation(s)
- Emanuel Schneck
- Department of Physics, Technische Universität Darmstadt, Hochschulstrasse 8, 64289 Darmstadt, Germany.
| | - Joshua Reed
- Department of Physics, Technische Universität Darmstadt, Hochschulstrasse 8, 64289 Darmstadt, Germany
| | - Takakazu Seki
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, 036-8561 Aomori, Japan
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Matej Kanduč
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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2
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Torre MF, Amadeo A, Cassone G, Tommasini M, Mráziková K, Saija F. Water Dimer under Electric Fields: An Ab Initio Investigation up to Quantum Accuracy. J Phys Chem A 2024; 128:5490-5499. [PMID: 38976361 DOI: 10.1021/acs.jpca.4c01553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
It is well-established that strong electric fields (EFs) can align water dipoles, partially order the H-bond network of liquid water, and induce water splitting and proton transfers. To illuminate the fundamental behavior of water under external EFs, we present the first benchmark, to the best of our knowledge, of DFT calculations of the water dimer exposed to intense EFs against coupled cluster calculations. The analyses of the vibrational Stark effect and electron density provide a consistent picture of the intermolecular charge transfer effects driven along the H-bond by the increasing applied field at all theory levels. However, our findings prove that at extreme field regimes (∼1-2 V/Å) DFT calculations significantly exaggerate by ∼10-30% the field-induced strengthening of the H-bond, both within the GGA, hybrid GGA, and hybrid meta-GGA approximations. Notably, a linear correlation emerges between the vibrational Stark effect on OH stretching and H-bond strengthening: a 1 kcal mol-1 increase corresponds to an 80 cm-1 red-shift in OH stretching frequency.
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Affiliation(s)
- Marco Francesco Torre
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98166 Messina, Italy
| | - Alessandro Amadeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98166 Messina, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Matteo Tommasini
- Dipartimento di Chimica, Materiali e Ing. Chimica "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Klaudia Mráziková
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
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3
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Kawai K, Shirakashi R. Water rotational relaxation time measurement by shortwave infrared micro spectroscopy(SWIR) at sub-zero temperatures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124707. [PMID: 38964024 DOI: 10.1016/j.saa.2024.124707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/17/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
The shortwave infrared spectroscopy (SWIR) is the noble method which allows to evaluate the rotational relaxation time of water (RRTW) in a sample. Because SWIR requires the reference sample of pure water, the measurement temperature is limited only at above 0 °C. In this study, we expanded this temperature limitation of SWIR by using alternative reference solutions with freezing points below 0 °C, including sugar and glycerol solutions. The results showed that some reference sample solutions are useable for evaluating RRTW in samples below 0 °C. It was found that RRTW in solution measured by newly proposed SWIR agrees with RRTW measured by dielectric spectroscopy in 10% accuracy when it is shorter than 100psec.
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Affiliation(s)
- Kosei Kawai
- Department of Mechanical Engineering, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Japan.
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Japan.
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4
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Zhang J, Shirakashi R. Measurement of the rotational relaxation time of intracellular water in dried yeast and Jurkat cells by near infrared spectroscopy. Biochem Biophys Res Commun 2024; 710:149857. [PMID: 38583232 DOI: 10.1016/j.bbrc.2024.149857] [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: 02/25/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Molecular mobility of intracellular water is a crucial parameter in the study of the mechanism of desiccation tolerance. As one of the parameters that reflecting molecular mobility, the viscosity of intracellular water has been found intimately related with the protection of the phospholipid membrane because it quantifies the diffusion ability of water and mass in the intracellular environment. In this work we measured the intracellular water relaxation time, which can be translated into water viscosity, by using a previously established NIR-dielectric method to monitor the drying process of baker's yeast and Jurkat cells with different desiccation tolerance. We found that intracellular saccharide can significantly decrease the intracellular water viscosity. Also, the intracellular water diffusion coefficient obtained from this method were found in good agreement with other reports.
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Affiliation(s)
- Junkai Zhang
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo, 153-8505, Japan.
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo, 153-8505, Japan
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5
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Ojha D, Henao A, Zysk F, Kühne TD. Nuclear quantum effects on the vibrational dynamics of the water-air interface. J Chem Phys 2024; 160:204114. [PMID: 38804494 DOI: 10.1063/5.0204071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
We have applied path-integral molecular dynamics simulations to investigate the impact of nuclear quantum effects on the vibrational dynamics of water molecules at the water-air interface. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time series analysis, while the time scales of vibrational spectral diffusion are determined from frequency-time correlation functions and joint probability distributions. We find that the inclusion of nuclear quantum effects leads not only to a redshift in the vibrational frequency distribution by about 120 cm-1 for both the bulk and interfacial water molecules but also to an acceleration of the vibrational dynamics at the water-air interface by as much as 35%. In addition, a blueshift of about 45 cm-1 is seen in the vibrational frequency distribution of interfacial water molecules compared to that of the bulk. Furthermore, the dynamics of water molecules beyond the topmost molecular layer was found to be rather similar to that of bulk water.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Andrés Henao
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Frederik Zysk
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Thomas D Kühne
- Center for Advanced Systems Understanding (CASUS), Untermarkt 20, D-02826 Görlitz, Germany, Helmholtz Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, D-01328 Dresden, Germany, and TU Dresden, Institute of Artificial Intelligence, Chair of Computational System Sciences, Nöthnitzer Straße 46, D-01187 Dresden, Germany
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6
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Ojha D, Penschke C, Saalfrank P. Vibrational dynamics and spectroscopy of water at porous g-C 3N 4 and C 2N surfaces. Phys Chem Chem Phys 2024; 26:11084-11093. [PMID: 38530253 DOI: 10.1039/d3cp05964b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Porous graphitic materials containing nitrogen are promising catalysts for photo(electro)chemical reactions, notably water splitting, but can also serve as "molecular sieves". Nitrogen increases the hydrophilicity of the graphite parent material, among other effects. A deeper understanding of how water interacts with C- and N-containing layered materials, if and which differences exist between materials with different N content and pore size, and what the role of water dynamics is - a prerequsite for catalysis and sieving - is largely absent, however. Vibrational spectroscopy can answer some of these questions. In this work, the vibrational dynamics and spectroscopy of deuterated water molecules (D2O) mimicking dense water layers at room temperature on the surfaces of two different C/N-based materials with different N content and pore size, namely graphitic C3N4 (g-C3N4) and C2N, are studied using ab initio molecular dynamics (AIMD). In particular, time-dependent vibrational sum frequency generation (TD-vSFG) spectra of the OD modes and also time-averaged vSFG spectra and OD frequency distributions are computed. This allows us to distinguish "free" (dangling) OD bonds from OD bonds that are bound in a H-bonded water network or at the surface - with subtle differences between the two surfaces and also to a pure water/air interface. It is found that the temporal decay of OD modes is very similar on both surfaces with a correlation time near 4 ps. In contrast, TD-vSFG spectra reveal that the interconversion time from "bonded" to "free" OD bonds is about 8 ps for water on C2N and thus twice as long as for g-C3N4, demonstrating a propensity of the former material to stabilize bonded OD bonds.
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Affiliation(s)
- Deepak Ojha
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam-Golm, Germany.
| | - Christopher Penschke
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam-Golm, Germany.
| | - Peter Saalfrank
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam-Golm, Germany.
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7
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Iglesias-Reguant A, Reis H, Medved' M, Ośmiałowski B, Zaleśny R, Luis JM. Decoding the infrared spectra changes upon formation of molecular complexes: the case of halogen bonding in pyridine⋯perfluorohaloarene complexes. Phys Chem Chem Phys 2023. [PMID: 37466634 DOI: 10.1039/d3cp02412a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
A recently developed computational scheme is employed to interpret changes in the infrared spectra of halogen-bonded systems in terms of intermolecular interaction energy components (electrostatic, exchange, induction, dispersion) taking pyridine⋯perfluorohaloarene complexes as examples. For all complexes, we find a strong linear correlation between the different terms of the interaction-induced changes of the IR band associated with an intermolecular halogen bond stretching mode and the corresponding terms of the interaction energy, which implies that the interaction components play similar roles in both properties. This is not true for other vibrational modes localized in one of the monomers studied here, for which the corresponding interaction-induced changes in IR bands may present a completely different decomposition than the interaction energy.
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Affiliation(s)
- Alex Iglesias-Reguant
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, PL-87100 Toruń, Poland
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
| | - Heribert Reis
- Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), Vassileos Constantinou Ave 48th, 116 35 Athens, Greece
| | - Miroslav Medved'
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovak Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University in Olomouc, Šlechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, PL-87100 Toruń, Poland
| | - Robert Zaleśny
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Josep M Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
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8
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Tang CG, Syafiqah MN, Koh QM, Ang MCY, Choo KK, Sun MM, Callsen M, Feng YP, Chua LL, Png RQ, Ho PKH. Water binding and hygroscopicity in π-conjugated polyelectrolytes. Nat Commun 2023; 14:3978. [PMID: 37407561 DOI: 10.1038/s41467-023-39215-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 05/26/2023] [Indexed: 07/07/2023] Open
Abstract
The presence of water strongly influences structure, dynamics and properties of ion-containing soft matter. Yet, the hydration of such matter is not well understood. Here, we show through a large study of monovalent π-conjugated polyelectrolytes that their reversible hydration, up to several water molecules per ion pair, occurs chiefly at the interface between the ion clusters and the hydrophobic matrix without disrupting ion packing. This establishes the appropriate model to be surface hydration, not the often-assumed internal hydration of the ion clusters. Through detailed analysis of desorption energies and O-H vibrational frequencies, together with OPLS4 and DFT calculations, we have elucidated key binding motifs of the sorbed water. Type-I water, which desorbs below 50 °C, corresponds to hydrogen-bonded water clusters constituting secondary hydration. Type-II water, which typically desorbs over 50-150 °C, corresponds to water bound to the anion under the influence of a proximal cation, or to a cation‒anion pair, at the cluster surface. This constitutes primary hydration. Type-III water, which irreversibly desorbs beyond 150 °C, corresponds to water kinetically trapped between ions. Its amount varies strongly with processing and heat treatment. As a consequence, hygroscopicity-which is the water sorption capacity per ion pair-depends not only on the ions, but also their cluster morphology.
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Affiliation(s)
- Cindy Guanyu Tang
- Department of Physics, National University of Singapore, Lower Kent Ridge Road, S117550, Singapore, Singapore
| | - Mazlan Nur Syafiqah
- Department of Chemistry, National University of Singapore, Lower Kent Ridge Road, S117552, Singapore, Singapore
| | - Qi-Mian Koh
- Department of Chemistry, National University of Singapore, Lower Kent Ridge Road, S117552, Singapore, Singapore
| | - Mervin Chun-Yi Ang
- Department of Chemistry, National University of Singapore, Lower Kent Ridge Road, S117552, Singapore, Singapore
| | - Kim-Kian Choo
- Department of Chemistry, National University of Singapore, Lower Kent Ridge Road, S117552, Singapore, Singapore
| | - Ming-Ming Sun
- Department of Chemistry, National University of Singapore, Lower Kent Ridge Road, S117552, Singapore, Singapore
| | - Martin Callsen
- Department of Physics, National University of Singapore, Lower Kent Ridge Road, S117550, Singapore, Singapore
| | - Yuan-Ping Feng
- Department of Physics, National University of Singapore, Lower Kent Ridge Road, S117550, Singapore, Singapore
| | - Lay-Lay Chua
- Department of Chemistry, National University of Singapore, Lower Kent Ridge Road, S117552, Singapore, Singapore.
| | - Rui-Qi Png
- Department of Physics, National University of Singapore, Lower Kent Ridge Road, S117550, Singapore, Singapore.
| | - Peter K H Ho
- Department of Physics, National University of Singapore, Lower Kent Ridge Road, S117550, Singapore, Singapore.
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9
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Begušić T, Blake GA. Two-dimensional infrared-Raman spectroscopy as a probe of water's tetrahedrality. Nat Commun 2023; 14:1950. [PMID: 37029146 PMCID: PMC10082090 DOI: 10.1038/s41467-023-37667-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
Two-dimensional spectroscopic techniques combining terahertz (THz), infrared (IR), and visible pulses offer a wealth of information about coupling among vibrational modes in molecular liquids, thus providing a promising probe of their local structure. However, the capabilities of these spectroscopies are still largely unexplored due to experimental limitations and inherently weak nonlinear signals. Here, through a combination of equilibrium-nonequilibrium molecular dynamics (MD) and a tailored spectrum decomposition scheme, we identify a relationship between the tetrahedral order of liquid water and its two-dimensional IR-IR-Raman (IIR) spectrum. The structure-spectrum relationship can explain the temperature dependence of the spectral features corresponding to the anharmonic coupling between low-frequency intermolecular and high-frequency intramolecular vibrational modes of water. In light of these results, we propose new experiments and discuss the implications for the study of tetrahedrality of liquid water.
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Affiliation(s)
- Tomislav Begušić
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Geoffrey A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
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10
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Zhang J, Matsuura H, Shirakashi R. A method for measuring dielectric relaxation of water by
NIR
spectroscopy: Applicability and application to measurement of water diffusion coefficient. J FOOD PROCESS ENG 2023. [DOI: 10.1111/jfpe.14335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Junkai Zhang
- Institute of Industrial Science The University of Tokyo 4‐6‐1 Komaba, Meguro City Tokyo 153‐8505 Japan
| | - Hiroaki Matsuura
- Institute of Industrial Science The University of Tokyo 4‐6‐1 Komaba, Meguro City Tokyo 153‐8505 Japan
| | - Ryo Shirakashi
- Institute of Industrial Science The University of Tokyo 4‐6‐1 Komaba, Meguro City Tokyo 153‐8505 Japan
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11
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Zarayeneh N, Kumar N, Kalyanaraman A, Clark AE. Dynamic Community Detection Decouples Multiple Time Scale Behavior of Complex Chemical Systems. J Chem Theory Comput 2022; 18:7043-7051. [PMID: 36374620 DOI: 10.1021/acs.jctc.2c00454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Although community or cluster identification is becoming a standard tool within the simulation community, traditional algorithms are challenging to adapt to time-dependent data. Here, we introduce temporal community identification using the Δ-screening algorithm, which has the flexibility to account for varying community compositions, merging and splitting behaviors within dynamically evolving chemical networks. When applied to a complex chemical system whose varying chemical environments cause multiple time scale behavior, Δ-screening is able to resolve the multiple time scales of temporal communities. This computationally efficient algorithm is easily adapted to a wide range of dynamic chemical systems; flexibility in implementation allows the user to increase or decrease the resolution of temporal features by controlling parameters associated with community composition and fluctuations therein.
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Affiliation(s)
- Neda Zarayeneh
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington99164, United States
| | - Nitesh Kumar
- Department of Chemistry, Washington State University, Pullman, Washington99164, United States
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington99164, United States
| | - Aurora E Clark
- Department of Chemistry, Washington State University, Pullman, Washington99164, United States.,Pacific Northwest National Laboratory, Richland, Washington99354, United States
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12
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Schienbein P, Blumberger J. Nanosecond solvation dynamics of the hematite/liquid water interface at hybrid DFT accuracy using committee neural network potentials. Phys Chem Chem Phys 2022; 24:15365-15375. [PMID: 35703465 DOI: 10.1039/d2cp01708c] [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
Metal oxide/water interfaces play an important role in biology, catalysis, energy storage and photocatalytic water splitting. The atomistic structure at these interfaces is often difficult to characterize by experimental techniques, whilst results from ab initio molecular dynamics simulations tend to be uncertain due to the limited length and time scales accessible. In this work, we train a committee neural network potential to simulate the hematite/water interface at the hybrid DFT level of theory to reach the nanosecond timescale and systems containing more than 3000 atoms. The NNP enables us to converge dynamical properties, not possible with brute-force ab initio molecular dynamics. Our simulations uncover a rich solvation dynamics at the hematite/water interface spanning three different time scales: picosecond H-bond dynamics between surface hydroxyls and the first water layer, in-plane/out-of-plane tilt motion of surface hydroxyls on the 10 ps time scale, and diffusion of water molecules from the oxide surface characterized by a mean residence lifetime of about 60 ps. Calculation of vibrational spectra confirm that H-bonds between surface hydroxyls and first layer water molecules are stronger than H-bonds in bulk water. Our study showcases how state of the art machine learning approaches can routinely be utilized to explore the structural dynamics at transition metal oxide interfaces with complex electronic structure. It foreshadows that c-NNPs are a promising tool to tackle the sampling problem in ab initio electrochemistry with explicit solvent molecules.
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Affiliation(s)
- Philipp Schienbein
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London, WC1E 6BT, UK.
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London, WC1E 6BT, UK.
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13
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Zhang J, Matsuura H, Shirakashi R. Prediction of water relaxation time using near infrared spectroscopy. J FOOD PROCESS ENG 2022. [DOI: 10.1111/jfpe.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junkai Zhang
- Institute of Industrial Science, The University of Tokyo Tokyo Japan
| | - Hiroaki Matsuura
- Institute of Industrial Science, The University of Tokyo Tokyo Japan
- Research Fellow of the Japan Society for the Promotion of Science Tokyo Japan
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo Tokyo Japan
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14
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Intramolecular resonance-assisted hydrogen bonds: Insights from symmetry adapted perturbation theory. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Brünig FN, Geburtig O, Canal AV, Kappler J, Netz RR. Time-Dependent Friction Effects on Vibrational Infrared Frequencies and Line Shapes of Liquid Water. J Phys Chem B 2022; 126:1579-1589. [PMID: 35167754 PMCID: PMC8883462 DOI: 10.1021/acs.jpcb.1c09481] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
From ab initio simulations
of liquid water, the time-dependent
friction functions and time-averaged nonlinear effective bond potentials
for the OH stretch and HOH bend vibrations are extracted. The obtained
friction exhibits not only adiabatic contributions at and below the
vibrational time scales but also much slower nonadiabatic contributions,
reflecting homogeneous and inhomogeneous line broadening mechanisms,
respectively. Intermolecular interactions in liquid water soften both
stretch and bend potentials compared to the gas phase, which by itself
would lead to a red-shift of the corresponding vibrational bands.
In contrast, nonadiabatic friction contributions cause a spectral
blue shift. For the stretch mode, the potential effect dominates,
and thus, a significant red shift when going from gas to the liquid
phase results. For the bend mode, potential and nonadiabatic friction
effects are of comparable magnitude, so that a slight blue shift results,
in agreement with well-known but puzzling experimental findings. The
observed line broadening is shown to be roughly equally caused by
adiabatic and nonadiabatic friction contributions for both the stretch
and bend modes in liquid water. Thus, the quantitative analysis of
the time-dependent friction that acts on vibrational modes in liquids
advances the understanding of infrared vibrational frequencies and
line shapes.
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16
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Kovács F, Yan H, Li H, Kunsági-Máté S. Temperature-Induced Change of Water Structure in Aqueous Solutions of Some Kosmotropic and Chaotropic Salts. Int J Mol Sci 2021; 22:ijms222312896. [PMID: 34884702 PMCID: PMC8657926 DOI: 10.3390/ijms222312896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
The hydrogen bond structure of water was examined by comparing the temperature dependent OH-stretching bands of water and aqueous NaClO4, KClO4, Na2SO4, and K2SO4 solutions. Results called attention to the role of cations on top of the importance of anions determining the emerging structure of a multi-layered system consisting single water rings or multi-ring water-clusters.
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Affiliation(s)
- Ferenc Kovács
- Institute of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, Honvéd útja 1, H-7624 Pécs, Hungary;
- Department of Physical Chemistry and Materials Science, Faculty of Sciences, University of Pécs, Ifjúság útja 6, H-7624 Pécs, Hungary
| | - Hui Yan
- Tianjin Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China;
- Key Laboratory of Display Materials and Photoelectric Devices, Tianjin University of Technology, Ministry of Education, Tianjin 300384, China
| | - Heng Li
- Fujian Provincial Key Laboratory of Semiconductors and Applications, Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Department of Physics, Xiamen University, Xiamen 361005, China;
- Jiujiang Research Institute, Xiamen University, Jiujiang 332000, China
| | - Sándor Kunsági-Máté
- Institute of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, Honvéd útja 1, H-7624 Pécs, Hungary;
- János Szentágothai Research Center, Ifjúság útja 20, H-7624 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-503600 (ext. 35449)
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17
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Corsaro C, Fazio E. From Critical Point to Critical Point: The Two-States Model Describes Liquid Water Self-Diffusion from 623 to 126 K. Molecules 2021; 26:molecules26195899. [PMID: 34641442 PMCID: PMC8512083 DOI: 10.3390/molecules26195899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/02/2022] Open
Abstract
Liquid’s behaviour, when close to critical points, is of extreme importance both for fundamental research and industrial applications. A detailed knowledge of the structural–dynamical correlations in their proximity is still today a target to reach. Liquid water anomalies are ascribed to the presence of a second liquid–liquid critical point, which seems to be located in the very deep supercooled regime, even below 200 K and at pressure around 2 kbar. In this work, the thermal behaviour of the self-diffusion coefficient for liquid water is analyzed, in terms of a two-states model, for the first time in a very wide thermal region (126 K < T < 623 K), including those of the two critical points. Further, the corresponding configurational entropy and isobaric-specific heat have been evaluated within the same interval. The two liquid states correspond to high and low-density water local structures that play a primary role on water dynamical behavior over 500 K.
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18
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Gittus OR, Bresme F. Thermophysical properties of water using reactive force fields. J Chem Phys 2021; 155:114501. [PMID: 34551553 DOI: 10.1063/5.0057868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The widescale importance and rich phenomenology of water continue to motivate the development of computational models. ReaxFF force fields incorporate many characteristics desirable for modeling aqueous systems: molecular flexibility, polarization, and chemical reactivity (bond formation and breaking). However, their ability to model the general properties of water has not been evaluated in detail. We present comprehensive benchmarks of the thermophysical properties of water for two ReaxFF models, the water-2017 and CHON-2017_weak force fields. These include structural, electrostatic, vibrational, thermodynamic, coexistence, and transport properties at ambient conditions (300 K and 0.997 g cm-3) and along the standard pressure (1 bar) isobar. Overall, CHON-2017_weak predicts more accurate thermophysical properties than the water-2017 force field. Based on our results, we recommend potential avenues for improvement: the dipole moment to quadrupole moment ratio, the self-diffusion coefficient, especially for water-2017, and the gas phase vibrational frequencies with the aim to improve the vibrational properties of liquid water.
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Affiliation(s)
- Oliver R Gittus
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
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19
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20
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Taylor C, Schönberger N, Laníková A, Patzschke M, Drobot B, Žídek L, Lederer F. Investigation of the structure and dynamics of gallium binding to high-affinity peptides elucidated by multi-scale simulation, quantum chemistry, NMR and ITC. Phys Chem Chem Phys 2021; 23:8618-8632. [PMID: 33876023 DOI: 10.1039/d1cp00356a] [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
Gallium (as Ga3+) is a Group IIIa metal and its recovery from wastewaters has become increasingly important for its reuse. The use of peptides for recycling offers a low-cost and environmentally-friendly option but the structural characteristics of peptides likely to bind Ga3+ are largely unknown. Multiple computational methods, coupled with experimental verification via NMR and Isothermal Calorimetry (ITC), were used to establish that Ga3+ binds with high affinity to peptide sequences and to elucidate the structural characteristics that contributed. It was demonstrated that peptide pre-organisation is key to Ga3+ binding and that a favourable binding position is necessarily governed by the size and shape of the electrostatic environment as much as individual electrostatic interactions with peptide residues themselves. Given favourable conditions, Ga3+ retrieved plausible binding positions involving both charged and uncharged residues that greatly increases the range of bonding possibilities with other peptide sequences and offers insights for binding other metals. The addition of pH buffer substantially improved the affinity of Ga3+ and a structural role for a buffer component was demonstrated.
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Affiliation(s)
- Corey Taylor
- Department of Chemistry of the f-elements, Institute of Resource Ecology (IRE), Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
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21
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Hassan I, Ferraro F, Imhof P. Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide. Molecules 2021; 26:2148. [PMID: 33917998 PMCID: PMC8068333 DOI: 10.3390/molecules26082148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent's effect on the vibrational frequency.
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Affiliation(s)
- Irtaza Hassan
- Institute for Theoretical Physics, Freie Universtiät Berlin, Arnimallee 14, 14195 Berlin, Germany;
| | - Federica Ferraro
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany;
| | - Petra Imhof
- Institute for Theoretical Physics, Freie Universtiät Berlin, Arnimallee 14, 14195 Berlin, Germany;
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany;
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22
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Ojha D, Kühne TD. Hydrogen bond dynamics of interfacial water molecules revealed from two-dimensional vibrational sum-frequency generation spectroscopy. Sci Rep 2021; 11:2456. [PMID: 33510246 PMCID: PMC7844302 DOI: 10.1038/s41598-021-81635-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 11/17/2022] Open
Abstract
Vibrational sum-frequency generation (vSFG) spectroscopy allows the study of the structure and dynamics of interfacial systems. In the present work, we provide a simple recipe, based on a narrowband IR pump and broadband vSFG probe technique, to computationally obtain the two-dimensional vSFG spectrum of water molecules at the air-water interface. Using this technique, to study the time-dependent spectral evolution of hydrogen-bonded and free water molecules, we demonstrate that at the interface, the vibrational spectral dynamics of the free OH bond is faster than that of the bonded OH mode.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany.
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany.
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23
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Di Muzio S, Ramondo F, Gontrani L, Ferella F, Nardone M, Benassi P. Choline Hydrogen Dicarboxylate Ionic Liquids by X-ray Scattering, Vibrational Spectroscopy and Molecular Dynamics: H-Fumarate and H-Maleate and Their Conformations. Molecules 2020; 25:E4990. [PMID: 33126573 PMCID: PMC7663696 DOI: 10.3390/molecules25214990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/18/2020] [Accepted: 10/24/2020] [Indexed: 11/30/2022] Open
Abstract
We explore the structure of two ionic liquids based on the choline cation and the monoanion of the maleic acid. We consider two isomers of the anion (H-maleate, the cis-isomer and H-fumarate, the trans-isomer) having different physical chemical properties. H-maleate assumes a closed structure and forms a strong intramolecular hydrogen bond whereas H-fumarate has an open structure. X-ray diffraction, infrared and Raman spectroscopy and molecular dynamics have been used to provide a reliable picture of the interactions which characterize the structure of the fluids. All calculations indicate that the choline cation prefers to connect mainly to the carboxylate group through OH⋯O interactions in both the compounds and orient the charged head N(CH3)3+ toward the negative portion of the anion. However, the different structure of the two anions affects the distribution of the ionic components in the fluid. The trans conformation of H-fumarate allows further interactions between anions through COOH and CO2- groups whereas intramolecular hydrogen bonding in H-maleate prevents this association. Our theoretical findings have been validated by comparing them with experimental X-ray data and infrared and Raman spectra.
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Affiliation(s)
- Simone Di Muzio
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
| | - Fabio Ramondo
- Department of Chemistry, University of Rome La Sapienza, P.le A. Moro 5, 00185 Rome, Italy;
| | - Lorenzo Gontrani
- Department of Chemistry, University of Rome La Sapienza, P.le A. Moro 5, 00185 Rome, Italy;
| | - Francesco Ferella
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
- INFN, Gran Sasso National Laboratories, I-67100 Assergi (AQ), Italy
| | - Michele Nardone
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
| | - Paola Benassi
- Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, I-67100 L’Aquila, Italy; (S.D.M.); (F.F.); (M.N.); (P.B.)
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24
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Seki T, Chiang KY, Yu CC, Yu X, Okuno M, Hunger J, Nagata Y, Bonn M. The Bending Mode of Water: A Powerful Probe for Hydrogen Bond Structure of Aqueous Systems. J Phys Chem Lett 2020; 11:8459-8469. [PMID: 32931284 PMCID: PMC7584361 DOI: 10.1021/acs.jpclett.0c01259] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/15/2020] [Indexed: 05/16/2023]
Abstract
Insights into the microscopic structure and dynamics of the water's hydrogen-bonded network are crucial to understand the role of water in biology, atmospheric and geochemical processes, and chemical reactions in aqueous systems. Vibrational spectroscopy of water has provided many such insights, in particular using the O-H stretch mode. In this Perspective, we summarize our recent studies that have revealed that the H-O-H bending mode can be an equally powerful reporter for the microscopic structure of water and provides more direct access to the hydrogen-bonded network than the conventionally studied O-H stretch mode. We discuss the fundamental vibrational properties of the water bending mode, such as the intermolecular vibrational coupling, and its effects on the spectral lineshapes and vibrational dynamics. Several examples of static and ultrafast bending mode spectroscopy illustrate how the water bending mode provides an excellent window on the microscopic structure of both bulk and interfacial water.
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Affiliation(s)
- Takakazu Seki
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kuo-Yang Chiang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Chun-Chieh Yu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Xiaoqing Yu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Masanari Okuno
- Department
of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Johannes Hunger
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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25
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Change of liquid water structure under the presence of phosphate anion during changing its kosmotropic character to chaotropic along its deprotonation route. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Ojha D, Kühne TD. "On-The-Fly" Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface. Molecules 2020; 25:E3939. [PMID: 32872259 PMCID: PMC7504776 DOI: 10.3390/molecules25173939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/24/2022] Open
Abstract
In the present work, we provide an electronic structure based method for the "on-the-fly" determination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polarizability are approximated to be proportional to the second moment of Wannier functions. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Department of Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany;
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Department of Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany;
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
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27
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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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28
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Two-dimensional infrared spectroscopy of aqueous solutions from first principles simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, Golze D, Wilhelm J, Chulkov S, Bani-Hashemian MH, Weber V, Borštnik U, Taillefumier M, Jakobovits AS, Lazzaro A, Pabst H, Müller T, Schade R, Guidon M, Andermatt S, Holmberg N, Schenter GK, Hehn A, Bussy A, Belleflamme F, Tabacchi G, Glöß A, Lass M, Bethune I, Mundy CJ, Plessl C, Watkins M, VandeVondele J, Krack M, Hutter J. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J Chem Phys 2020; 152:194103. [PMID: 33687235 DOI: 10.1063/5.0007045] [Citation(s) in RCA: 907] [Impact Index Per Article: 226.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
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Affiliation(s)
- Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mauro Del Ben
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Teodoro Laino
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, CH-801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Ole Schütt
- Department of Materials, ETH Zürich, CH-8092 Zürich, Switzerland
| | | | - Dorothea Golze
- Department of Applied Physics, Aalto University, Otakaari 1, FI-02150 Espoo, Finland
| | - Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sergey Chulkov
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | | | - Valéry Weber
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | | | | | | | | | - Hans Pabst
- Intel Extreme Computing, Software and Systems, Zürich, Switzerland
| | - Tiziano Müller
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Robert Schade
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Manuel Guidon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Samuel Andermatt
- Integrated Systems Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Gregory K Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Anna Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Augustin Bussy
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100 Como, Italy
| | - Andreas Glöß
- BASF SE, Carl-Bosch-Straße 38, D-67056 Ludwigshafen am Rhein, Germany
| | - Michael Lass
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Iain Bethune
- Hartree Centre, Science and Technology Facilities Council, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Christian Plessl
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Matt Watkins
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Joost VandeVondele
- Swiss National Supercomputing Centre (CSCS), ETH Zürich, Zürich, Switzerland
| | - Matthias Krack
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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30
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Charge transfer as a ubiquitous mechanism in determining the negative charge at hydrophobic interfaces. Nat Commun 2020; 11:901. [PMID: 32060273 PMCID: PMC7021814 DOI: 10.1038/s41467-020-14659-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/22/2020] [Indexed: 01/17/2023] Open
Abstract
The origin of the apparent negative charge at hydrophobic–water interfaces has fueled debates in the physical chemistry community for decades. The most common interpretation given to explain this observation is that negatively charged hydroxide ions (OH–) bind strongly to the interfaces. Using first principles calculations of extended air–water and oil–water interfaces, we unravel a mechanism that does not require the presence of OH–. Small amounts of charge transfer along hydrogen bonds and asymmetries in the hydrogen bond network due to topological defects can lead to the accumulation of negative surface charge at both interfaces. For water near oil, some spillage of electron density into the oil phase is also observed. The computed surface charge densities at both interfaces is approximately \documentclass[12pt]{minimal}
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\setlength{\oddsidemargin}{-69pt}
\begin{document}$$-0.015\ {\rm{e}}/{{\rm{nm}}}^{2}$$\end{document}−0.015e∕nm2 in agreement with electrophoretic experiments. We also show, using an energy decomposition analysis, that the electronic origin of this phenomena is rooted in a collective polarization/charge transfer effect. The accumulation of negative charge at hydrophobic–water interfaces has been a source of debate for a long time. Here the authors use ab initio calculations to show that the charge accumulation at air–water and oil–water interfaces is caused by subtle charge transfer processes.
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31
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Elgabarty H, Kühne TD. Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences. Phys Chem Chem Phys 2020; 22:10397-10411. [DOI: 10.1039/c9cp06960g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.
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Affiliation(s)
- Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design
- Chair of Theoretical Chemistry
- University of Paderborn
- Paderborn
- Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design
- Chair of Theoretical Chemistry
- University of Paderborn
- Paderborn
- Germany
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32
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Schienbein P, Marx D. Assessing the properties of supercritical water in terms of structural dynamics and electronic polarization effects. Phys Chem Chem Phys 2020; 22:10462-10479. [DOI: 10.1039/c9cp05610f] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evolution of water's structural dynamics from ambient liquid to supercritical dense liquid-like and dilute gas-like conditions.
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Affiliation(s)
- Philipp Schienbein
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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33
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Ehrhard AA, Jäger S, Malm C, Basaran S, Hunger J. CF3-groups critically enhance the binding of thiourea catalysts to ketones – a NMR and FT-IR study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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Ojha D, Kaliannan NK, Kühne TD. Time-dependent vibrational sum-frequency generation spectroscopy of the air-water interface. Commun Chem 2019. [DOI: 10.1038/s42004-019-0220-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Abstract
Vibrational sum-frequency generation spectroscopy is a powerful method to study the microscopic structure and dynamics of interfacial systems. Here we demonstrate a simple computational approach to calculate the time-dependent, frequency-resolved vibrational sum-frequency generation spectrum (TD-vSFG) of the air-water interface. Using this approach, we show that at the air-water interface, the transition of water molecules with bonded OH modes to free OH modes occurs at a time scale of $$\sim$$
~
3 ps, whereas water molecules with free OH modes rapidly make a transition to a hydrogen-bonded state within $$\sim$$
~
2 ps. Furthermore, we also elucidate the origin of the observed differential dynamics based on the time-dependent evolution of water molecules in the different local solvent environments.
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Cassone G, Sponer J, Trusso S, Saija F. Ab initio spectroscopy of water under electric fields. Phys Chem Chem Phys 2019; 21:21205-21212. [PMID: 31368466 DOI: 10.1039/c9cp03101d] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whereas a broad range of literature exists on the spectroscopy of water in disparate conditions, infrared (IR) and Raman spectra of water subjected to electric fields have never extensively been investigated so far. Based on ab initio molecular dynamics simulations, here we present IR and Raman spectra of bulk liquid water under the effect of static electric fields. A contraction of the entire frequency range is recorded upon increasing the field intensity both in the IR and in the Raman spectra. Whilst the OH stretching band is progressively shifted toward lower frequencies - indicating a field-induced strengthening of the H-bond network - all the other bands are up-shifted by the field. Furthermore, an evident modification of the librational mode band appears in all the spectra. Finally, the order-maker action of the field emerges also from the increase of the water orientational tetrahedral order. Upon field exposure, the water structure becomes more "ice like".
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic.
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Ojha D, Chandra A. Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations. J Comput Chem 2019; 40:2086-2095. [PMID: 31099905 DOI: 10.1002/jcc.25860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/27/2019] [Accepted: 04/29/2019] [Indexed: 11/06/2022]
Abstract
A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, Uttar Pradesh, India
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Cha S, Marekha B, Wagner M, Hunger J. Hydrogen-Bond Structure and Dynamics of TADDOL Asymmetric Organocatalysts Correlate with Catalytic Activity. Chemistry 2019; 25:9984-9990. [PMID: 31090245 DOI: 10.1002/chem.201901594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 11/07/2022]
Abstract
The catalytic efficiency of diol-based organocatalysts has been shown to strongly depend on the diols molecular structure including hydrogen-bonding, yet, the underlying molecular-level origins have remained elusive. Herein a study on the inter- and intramolecular hydrogen-bonding of two isomeric diol-based catalysts (TADDOLs) in solution is presented: 1-Naphthyl substituted TADDOL (1nTADDOL), which exhibits high catalytic efficiency, and 2-naphthyl substituted TADDOL (2nTADDOL), which is a poor catalyst. Using nuclear magnetic resonance and infrared spectroscopy, comparable hydrogen-bond strengths for both TADDOLs in solution were found, however, significantly slower bonding dynamics for 1nTADDOL. In aromatic solvents, 1nTADDOL forms less, but longer-lived, intermolecular OH⋅⋅⋅π bonds to solvent molecules, as compared to 2nTADDOL. Thus, rather than previously suggested differences in intermolecular hydrogen-bonding strengths, the results suggest that the hydrogen-bonding kinetics and entropies differ for both TADDOLs, which also explains their vastly different catalytic activities.
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Affiliation(s)
- Seoncheol Cha
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Bogdan Marekha
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
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Ojha D, Chandra A. Urea in Water: Structure, Dynamics, and Vibrational Echo Spectroscopy from First-Principles Simulations. J Phys Chem B 2019; 123:3325-3336. [DOI: 10.1021/acs.jpcb.9b01904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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Ojha D, Chandra A. Temperature dependence of the ultrafast vibrational echo spectroscopy of OD modes in liquid water from first principles simulations. Phys Chem Chem Phys 2019; 21:6485-6498. [DOI: 10.1039/c8cp07121g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The temperature dependence of the vibrational spectral diffusion of OD modes in liquid water is investigated through calculations of vibrational echo spectral observables from first principles molecular dynamics.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India
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