1
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Dodia M, Rouxel JR, Cho D, Zhang Y, Keefer D, Bonn M, Nagata Y, Mukamel S. Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer. J Chem Theory Comput 2024; 20:4254-4264. [PMID: 38727197 DOI: 10.1021/acs.jctc.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
We propose an X-ray Raman pump-X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information about the entire molecular ensemble. A combination of molecular dynamics and ab initio quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, we extracted solvation shell dynamics.
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Affiliation(s)
- Mayank Dodia
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Jérémy R Rouxel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Daeheum Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yu Zhang
- Ames National Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Daniel Keefer
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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2
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Tan J, Wang M, Zhang J, Ye S. Determination of the Thickness of Interfacial Water by Time-Resolved Sum-Frequency Generation Vibrational Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18573-18580. [PMID: 38051545 DOI: 10.1021/acs.langmuir.3c02906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The physics and chemistry of a charged interface are governed by the structure of the electrical double layer (EDL). Determination of the interfacial water thickness (diw) of the charged interface is crucial to quantitatively describe the EDL structure, but it can be utilized with very scarce experimental methods. Here, we propose and verify that the vibrational relaxation time (T1) of the OH stretching mode at 3200 cm-1, obtained by time-resolved sum frequency generation vibrational spectroscopy with ssp polarizations, provides an effective tool to determine diw. By investigating the T1 values at the SiO2/NaCl solution interface, we established a time-space (T1-diw) relationship. We find that water has a T1 lifetime of ≥0.5 ps for diw ≤ 3 Å, while it displays bulk-like dynamics with T1 ≤ 0.2 ps for diw ≥ 9 Å. T1 decreases as diw increases from ∼3 Å to 9 Å. The hydration water at the DPPG lipid bilayer and LK15β protein interfaces has a thickness of ≥9 Å and shows a bulk-like feature. The time-space relationship will provide a novel tool to pattern the interfacial topography and heterogeneity in Ångstrom-depth resolution by imaging the T1 values.
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Affiliation(s)
- Junjun Tan
- Hefei National Research Center for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Mengmeng Wang
- Hefei National Research Center for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jiahui Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Shuji Ye
- Hefei National Research Center for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
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3
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Cassone G, Saija F, Sponer J, Shaik S. The Reactivity-Enhancing Role of Water Clusters in Ammonia Aqueous Solutions. J Phys Chem Lett 2023; 14:7808-7813. [PMID: 37623433 PMCID: PMC10494223 DOI: 10.1021/acs.jpclett.3c01810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023]
Abstract
Among the many prototypical acid-base systems, ammonia aqueous solutions hold a privileged place, owing to their omnipresence in various planets and their universal solvent character. Although the theoretical optimal water-ammonia molar ratio to form NH4+ and OH- ion pairs is 50:50, our ab initio molecular dynamics simulations show that the tendency of forming these ionic species is inversely (directly) proportional to the amount of ammonia (water) in ammonia aqueous solutions, up to a water-ammonia molar ratio of ∼75:25. Here we prove that the reactivity of these liquid mixtures is rooted in peculiar microscopic patterns emerging at the H-bonding scale, where the highly orchestrated motion of 5 solvating molecules modulates proton transfer events through local electric fields. This study demonstrates that the reaction of water with NH3 is catalyzed by a small cluster of water molecules, in which an H atom possesses a high local electric field, much like the effect observed in catalysis by water droplets [ PNAS 2023, 120, e2301206120].
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Affiliation(s)
- Giuseppe Cassone
- Institute
for Physical-Chemical Processes, Italian
National Research Council (CNR-IPCF), Viale Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Franz Saija
- Institute
for Physical-Chemical Processes, Italian
National Research Council (CNR-IPCF), Viale Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Jiri Sponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
| | - Sason Shaik
- Institute
of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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4
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Conti Nibali V, Maiti S, Saija F, Heyden M, Cassone G. Electric-field induced entropic effects in liquid water. J Chem Phys 2023; 158:2889002. [PMID: 37154276 DOI: 10.1063/5.0139460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/13/2023] [Indexed: 05/10/2023] Open
Abstract
Externally applied electric fields in liquid water can induce a plethora of effects with wide implications in electrochemistry and hydrogen-based technologies. Although some effort has been made to elucidate the thermodynamics associated with the application of electric fields in aqueous systems, to the best of our knowledge, field-induced effects on the total and local entropy of bulk water have never been presented so far. Here, we report on classical TIP4P/2005 and ab initio molecular dynamics simulations measuring entropic contributions carried by diverse field intensities in liquid water at room temperature. We find that strong fields are capable of aligning large fractions of molecular dipoles. Nevertheless, the order-maker action of the field leads to quite modest entropy reductions in classical simulations. Albeit more significant variations are recorded during first-principles simulations, the associated entropy modifications are small compared to the entropy change involved in the freezing phenomenon, even at intense fields slightly beneath the molecular dissociation threshold. This finding further corroborates the idea that electrofreezing (i.e., the electric-field-induced crystallization) cannot take place in bulk water at room temperature. In addition, here, we propose a molecular-dynamics-based analysis (3D-2PT) that spatially resolves the local entropy and the number density of bulk water under an electric field, which enables us to map their field-induced changes in the environment of reference H2O molecules. By returning detailed spatial maps of the local order, the proposed approach is capable of establishing a link between entropic and structural modifications with atomistic resolution.
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Affiliation(s)
- Valeria Conti Nibali
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, 98166 Messina, Italy
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Sthitadhi Maiti
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
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5
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Cassone G, Sponer J, Sponer JE, Saija F. Electrofreezing of Liquid Ammonia. J Phys Chem Lett 2022; 13:9889-9894. [PMID: 36255376 PMCID: PMC9619927 DOI: 10.1021/acs.jpclett.2c02576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 05/25/2023]
Abstract
Here we prove that, in addition to temperature and pressure, another important thermodynamic variable permits the exploration of the phase diagram of ammonia: the electric field. By means of (path integral) ab initio molecular dynamics simulations, we predict that, upon applying intense electric fields on ammonia, the electrofreezing phenomenon occurs, leading the liquid toward a novel ferroelectric solid phase. This study proves that electric fields can generally be exploited as the access key to otherwise-unreachable regions in phase diagrams, unveiling the existence of new condensed-phase structures. Furthermore, the reported findings have manifold practical implications, from the safe storage and transportation of ammonia to the understanding of the solid structures this compound forms in planetary contexts.
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Affiliation(s)
- Giuseppe Cassone
- Institute
for Chemical-Physical Processes, National
Research Council of Italy, Viale F. Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Jiri Sponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
- Regional
Center of Advanced Technologies and Materials, The Czech Advanced
Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 77900 Olomouc, Czechia
| | - Judit E. Sponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czechia
| | - Franz Saija
- Institute
for Chemical-Physical Processes, National
Research Council of Italy, Viale F. Stagno d’Alcontres 37, 98158 Messina, Italy
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6
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You X, Baiz CR. Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective. J Phys Chem A 2022; 126:5881-5889. [PMID: 35968816 DOI: 10.1021/acs.jpca.2c03803] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.
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Affiliation(s)
- Xiao You
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
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7
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Amante G, Sponer JE, Sponer J, Saija F, Cassone G. A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1012. [PMID: 35892991 PMCID: PMC9394336 DOI: 10.3390/e24081012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022]
Abstract
The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter-including its quantum nature-under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)-such as ab initio molecular dynamics-and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.
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Affiliation(s)
- Gabriele Amante
- Department of Mathematical and Computer Science, Physical Sciences and Earth Sciences, Università degli Studi di Messina, V. le F. Stagno d’Alcontres 31, 98166 Messina, Italy;
| | - Judit E. Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Franz Saija
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
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8
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Ngoepe MP, Clayton HS. Metal Complexes as DNA Synthesis and/or Repair Inhibitors: Anticancer and Antimicrobial Agents. PHARMACEUTICAL FRONTS 2021. [DOI: 10.1055/s-0041-1741035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AbstractMedicinal inorganic chemistry involving the utilization of metal-based compounds as therapeutics has become a field showing distinct promise. DNA and RNA are ideal drug targets for therapeutic intervention in the case of various diseases, such as cancer and microbial infection. Metals play a vital role in medicine, with at least 10 metals known to be essential for human life and a further 46 nonessential metals having been involved in drug therapies and diagnosis. These metal-based complexes interact with DNA in various ways, and are often delivered as prodrugs which undergo activation in vivo. Metal complexes cause DNA crosslinking, leading to the inhibition of DNA synthesis and repair. In this review, the various interactions of metal complexes with DNA nucleic acids, as well as the underlying mechanism of action, were highlighted. Furthermore, we also discussed various tools used to investigate the interaction between metal complexes and the DNA. The tools included in vitro techniques such as spectroscopy and electrophoresis, and in silico studies such as protein docking and density-functional theory that are highlighted for preclinical development.
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Affiliation(s)
| | - Hadley S. Clayton
- Department of Chemistry, University of South Africa, Pretoria, South Africa
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9
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Mollazadeh S, Yazdimamaghani M, Yazdian-Robati R, Pirhadi S. New insight into the structural changes of apoferritin pores in the process of doxorubicin loading at an acidic pH: Molecular dynamics simulations. Comput Biol Med 2021; 141:105158. [PMID: 34952337 DOI: 10.1016/j.compbiomed.2021.105158] [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: 10/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022]
Abstract
Apoferritin (APO-Fr) is one of the most investigated proteins proposed as an advanced structure for drug delivery systems. Herein, molecular dynamics simulation was employed to compare the opening of 3-fold and 4-fold pores in APO-Fr during the partial disassembly process at an acidic pH. We showed that more hydrophilic residues in the surface of 3-fold pores compared to 4-fold pores facilitate increased flexibility and a higher tendency to open. In particular, dissociation is induced by the presence of Doxorubicin (DOX) close to 3-fold pores. Our simulations showed loaded DOXs on the APO-Fr surface were mainly involved in the hydrogen bond interactions with the hydrophilic residues, suggesting the difficulty of hydrophobic drugs loading in APO-Fr with the partial disassembly process. However, π-π interactions as well as hydrogen bonds between protein and DOXs were mediated by the basic and acidic amino acids such as HIP128, GLU17, and LYS143 at the open pores, providing penetration of DOXs into the H-Apo-Fr. We conclude that increased drug encapsulations and loading capacity of hydrophobic drugs into the cavity of APO-Fr are feasible by further disassembly of openings to access the internal hydrophobic portions of the protein.
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Affiliation(s)
- Shirin Mollazadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical, Iran
| | - Mostafa Yazdimamaghani
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Rezvan Yazdian-Robati
- Pharmaceutical Sciences Research Centre, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Somayeh Pirhadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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10
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Cassone G, Sponer J, Saija F. Molecular dissociation and proton transfer in aqueous methane solution under an electric field. Phys Chem Chem Phys 2021; 23:25649-25657. [PMID: 34782902 DOI: 10.1039/d1cp04202e] [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
Methane-water mixtures are ubiquitous in our solar system and they have been the subject of a wide variety of experimental, theoretical, and computational studies aimed at understanding their behaviour under disparate thermodynamic scenarios, up to extreme planetary ice conditions of pressures and temperatures [Lee and Scandolo, Nat. Commun., 2011, 2, 185]. Although it is well known that electric fields, by interacting with condensed matter, can produce a range of catalytic effects which can be similar to those observed when material systems are pressurised, to the best of our knowledge, no quantum-based computational investigations of methane-water mixtures under an electric field have been reported so far. Here we present a study relying upon state-of-the-art ab initio molecular dynamics simulations where a liquid aqueous methane solution is exposed to strong oriented static and homogeneous electric fields. It turns out that a series of field-induced effects on the dipoles, polarisation, and the electronic structure of both methane and water molecules are recorded. Moreover, upon increasing the field strength, increasing fractions of water molecules are not only re-oriented towards the field direction, but are also dissociated by the field, leading to the release of oxonium and hydroxyde ions in the mixture. However, in contrast to what is observed upon pressurisation (∼50 GPa), where the presence of the water counterions triggers methane ionisation and other reactions, methane molecules preserve their integrity up to the strongest field explored (i.e., 0.50 V Å-1). Interestingly, neither the field-induced molecular dissociation of neat water (i.e., 0.30 V Å-1) nor the proton conductivity typical of pure aqueous samples at these field regimes (i.e., 1.3 S cm-1) are affected by the presence of hydrophobic interactions, at least in a methane-water mixture containing a molar fraction of 40% methane.
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Affiliation(s)
- Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy.
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolska 135, 61265 Brno, Czech Republic
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy.
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11
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Marzec E, Olszewski J. Dielectric response to thermal denaturation of lenses in healthy and diabetic rabbits. Bioelectrochemistry 2021; 142:107923. [PMID: 34385118 DOI: 10.1016/j.bioelechem.2021.107923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/14/2021] [Accepted: 08/01/2021] [Indexed: 11/28/2022]
Abstract
The relative permittivity and conductivity of healthy and alloxane-induced diabetic rabbits lenses were measured over a frequency range of 500 Hz to 100 kHz in an electric field and at temperatures from 25 to 150 °C. The dielectric spectra for both tissues showed two separate relaxations with a characteristic frequency of around 4 and 25 kHz assigned to the cortical and nuclear zones, respectively. These two dispersions are due to the interfacial polarization at the surface of the α-crystallin molecules. The denaturation temperature for the non-diabetic lens and the diabetic lens is approximately 70 and 80 °C, respectively. Moreover, the relative permittivity and conductivity values are higher in the diabetic lens than in the non-diabetic tissue at the same temperature and frequency. Our dielectric studies provide a better understanding of the thermal stability of crystallin-water complexes in normal and diseased human lenses.
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Affiliation(s)
- E Marzec
- Department of Bionics and Bioimpedance, Poznan University of Medical Sciences, Parkowa 2, 60-775 Poznań, Poland.
| | - J Olszewski
- Department of Bionics and Bioimpedance, Poznan University of Medical Sciences, Parkowa 2, 60-775 Poznań, Poland
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12
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Cassone G, Sponer J, Saija F. Ab Initio Molecular Dynamics Studies of the Electric-Field-Induced Catalytic Effects on Liquids. Top Catal 2021. [DOI: 10.1007/s11244-021-01487-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Electric Field and Temperature Effects on the Ab Initio Spectroscopy of Liquid Methanol. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11125457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although many H-bonded systems have been extensively investigated by means of infrared (IR) spectroscopy, the vibrational response to externally applied electric fields of polar liquids remains poorly investigated. However, local electric fields along with quantum-mechanical interactions rule the behavior of H-bonded samples at the molecular level. Among the many H-bonded systems, liquid methanol holds a key place in that it exhibits a very simple H-bond network where, on average, each molecule acts as a single H-bond donor and, at the same time, as a single H-bond acceptor. Here we report on the IR spectra emerging from a series of state-of-the-art ab initio molecular dynamics simulations of bulk liquid methanol under the action of static and homogeneous electric fields. In addition, the same analysis is here conducted in the absence of the external field and for different temperatures. Although some electric-field-induced effects resemble the response of other polar liquids (such as the global contraction of the IR spectrum upon field exposure), it turns out that, distinctly from water, the “electrofreezing” phenomenon is unlikely to happen in liquid methanol. Finally, we provide atomistic analyses magnifying the completely different nature of electric-field- and temperature-induced effects on bulk liquid methanol and on its vibrational response.
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14
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Stabilization of Near Identical Hydrogen Bonded Octameric Water Clusters in Crystal Structures of Three Distinct Non-Charged Polyamide Macrocyclic Host Molecules. Molecules 2021; 26:molecules26092787. [PMID: 34065060 PMCID: PMC8125911 DOI: 10.3390/molecules26092787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
In this paper, we present a comparative analysis of the solid state structures of three well-resolved hydrates of macrocyclic host molecules 1a, 1b, and 2 containing an intrannular amide-aryl substituent (lariat arm) connected to a fixed 26-membered ring in a normal (-NHCOAr, hosts 1a and 1b) or reverse manner (-CONHAr, host 2). Despite different chemical structures, these hosts crystallize as isostructural tetrahydrates in the same P-1 space group. Moreover, their crystals exhibit identical hydrogen bond motifs resulting in a stabilization of an almost identical unusual octameric water cluster built from the cyclic tetramer core and four water molecules, attached sequentially in an "up-and-down" manner. Further analysis reveals that, among the series, the structure of host 2 provides the most suitable environment for the accommodation of this type of water cluster.
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15
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Cassone G. Nuclear Quantum Effects Largely Influence Molecular Dissociation and Proton Transfer in Liquid Water under an Electric Field. J Phys Chem Lett 2020; 11:8983-8988. [PMID: 33035059 DOI: 10.1021/acs.jpclett.0c02581] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proton transfer in liquid water controls acid-base chemistry, crucial enzyme reactions, and the functioning of fuel cells. Externally applied static electric fields in water are capable of dissociating molecules and transferring protons across the H-bond network. However, the impact of nuclear quantum effects (NQEs) on these fundamental field-induced phenomena has not yet been reported. By comparing state-of-the-art ab initio molecular dynamics (AIMD) and path integral AIMD simulations of water under electric fields, I show that quantum delocalization of the proton lowers the molecular ionization threshold to approximately one-third. Moreover, also the water behavior as a protonic semiconductor is considerably modified by the inclusion of NQEs. In fact, when the quantum nature of the nuclei is taken into account, the proton conductivity is ∼50% larger. This work proves that NQEs sizably affect the protolysis phenomenon and proton transfer in room-temperature liquid water.
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Affiliation(s)
- Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council, Viale F. Stagno d'Alcontres 37, 98158 Messina, Italy
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16
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Baruah I, Borgohain G. Structural and functional changes of the protein β-lactoglobulin under thermal and electrical processing conditions. Biophys Chem 2020; 267:106479. [PMID: 33027745 DOI: 10.1016/j.bpc.2020.106479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein β-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and β-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.
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Affiliation(s)
- Indrani Baruah
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India
| | - Gargi Borgohain
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India.
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Trofimov YA, Krylov NA, Efremov RG. Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel. Int J Mol Sci 2019; 20:ijms20174285. [PMID: 31480555 PMCID: PMC6747475 DOI: 10.3390/ijms20174285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different from those in the bulk. Furthermore, the behavior of water in confined volumes of a nanometer scale, including transmembrane pores of ion channels, is especially nontrivial. Knowledge at the molecular level of structural and dynamic parameters of water in such systems is necessary to understand the mechanisms of ion channels functioning. In this work, the results of molecular dynamics (MD) simulations of water in the pore and selectivity filter domains of TRPV1 (Transient Receptor Potential Vanilloid type 1) membrane channel are considered. These domains represent nanoscale volumes with strongly amphiphilic walls, where physical behavior of water radically differs from that of free hydration (e.g., at protein interfaces) or in the bulk. Inside the pore and filter domains, water reveals a very heterogeneous spatial distribution and unusual dynamics: It forms compact areas localized near polar groups of particular residues. Residence time of water molecules in such areas is at least 1.5 to 3 times larger than that observed for similar groups at the protein surface. Presumably, these water “blobs” play an important role in the functional activity of TRPV1. In particular, they take part in hydration of the hydrophobic TRPV1 pore by localizing up to six waters near the so-called “lower gate” of the channel and reducing by this way the free energy barrier for ion and water transport. Although the channel is formed by four identical protein subunits, which are symmetrically packed in the initial experimental 3D structure, in the course of MD simulations, hydration of the same amino acid residues of individual subunits may differ significantly. This greatly affects the microscopic picture of the distribution of water in the channel and, potentially, the mechanism of its functioning. Therefore, reconstruction of the full picture of TRPV1 channel solvation requires thorough atomistic simulations and analysis. It is important that the naturally occurring porous volumes, like ion-conducting protein domains, reveal much more sophisticated and fine-tuned regulation of solvation than, e.g., artificially designed carbon nanotubes.
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Affiliation(s)
- Yury A Trofimov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
- National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
- National Research Nuclear University Moscow Engineering Physics Institute, Kashirskoe Shosse, 31, 115409 Moscow, Russia
| | - Nikolay A Krylov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
- National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - Roman G Efremov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
- National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia.
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701 Moscow, Russia.
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Kirchberg H, Nalbach P, Bressler C, Thorwart M. Spectroscopic Signatures of the Dynamical Hydrophobic Solvation Shell Formation. J Phys Chem B 2019; 123:2106-2113. [PMID: 30731041 DOI: 10.1021/acs.jpcb.8b11885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
When a hydrophilic solute in water is suddenly turned into a hydrophobic species, for instance, by photoionization, a layer of hydrated water molecules forms around the solute on a time scale of a few picoseconds. We study the dynamic buildup of the hydration shell around a hydrophobic solute on the basis of a time-dependent dielectric continuum model. Information about the solvent is spectroscopically extracted from the relaxation dynamics of a test dipole inside a static Onsager sphere in the nonequilibrium solvent. The growth process is described phenomenologically within two approaches. First, we consider a time-dependent thickness of the hydration layer that grows from zero to a finite value over a finite time. Second, we assume a time-dependent complex permittivity within a finite layer region around the Onsager sphere. The layer is modeled as a continuous dielectric with a much slower fluctuation dynamics. We find a time-dependent frequency shift down to the blue of the resonant absorption of the dipole, together with a dynamically decreasing line width, as compared to bulk water. The blue shift reflects the work performed against the hydrogen-bonded network of the bulk solvent and is a directly measurable quantity. Our results are in agreement with an experiment on the hydrophobic solvation of iodine in water.
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Affiliation(s)
- Henning Kirchberg
- I.Institut für Theoretische Physik , Universität Hamburg , Jungiusstr. 9 , 20355 Hamburg , Germany
| | - Peter Nalbach
- Westfälische Hochschule , Münsterstr. 265 , 46397 Bocholt , Germany
| | - Christian Bressler
- The Hamburg Centre for Ultrafast Imaging , Universität Hamburg , 22607 Hamburg , Germany.,European XFEL , Holzkoppel 4 , 22869 Schenefeld , Germany
| | - Michael Thorwart
- I.Institut für Theoretische Physik , Universität Hamburg , Jungiusstr. 9 , 20355 Hamburg , Germany
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Duereh A, Sato Y, Smith RL, Inomata H. Correspondence between Spectral-Derived and Viscosity-Derived Local Composition in Binary Liquid Mixtures Having Specific Interactions with Preferential Solvation Theory. J Phys Chem B 2018; 122:10894-10906. [PMID: 30403857 DOI: 10.1021/acs.jpcb.8b09511] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Local interactions between unlike molecules (1-2) in solution are commonly measured with spectroscopy and used to estimate local composition. Herein, a viscosity model based on preferential solvation (PS) theory is developed for aqueous and nonaqueous binary liquid mixtures containing a dipolar aprotic solvent that provides local composition considering the hydration or solvation shell around complex (1-2) molecules. Spectral-derived and viscosity-derived local composition distributions showed similar trends with bulk composition, and their correspondence is attributed to characteristics of the hydration or solvation shell. Viscosity-derived local compositions were consistent with literature molecular simulations, whereas spectral-derived local composition distributions contained artifacts. The PS viscosity model is also applicable to nonpolar-polar mixtures for which self-association occurs, and it can be used to estimate solvent mixture dipolarity/polarizability. Since the PS viscosity model only requires bulk viscosity, it may provide a means to estimate microviscosity or the solvent environment around biomolecules.
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Zhang Q, Pan Z, Zhang L, Zhang R, Chen Z, Jin T, Wu T, Chen X, Zhuang W. Ion effect on the dynamics of water hydrogen bonding network: A theoretical and computational spectroscopy point of view. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
- Department of ChemistryBohai UniversityJinzhouChina
| | - Zhijun Pan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Ruiting Zhang
- School of Physics and Optoelectronic EngineeringXidian UniversityXi'anChina
| | - Zhening Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Tianmin Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Xian Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
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Dahanayake JN, Mitchell-Koch KR. Entropy connects water structure and dynamics in protein hydration layer. Phys Chem Chem Phys 2018; 20:14765-14777. [PMID: 29780979 PMCID: PMC6005386 DOI: 10.1039/c8cp01674g] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics. In particular, it was seen that regions of higher density exhibit faster water dynamics. This is analogous to the behavior of bulk water, where dynamics (diffusion coefficients) are connected to water structure (density and tetrahedrality) by excess (or pair) entropy, detailed in the Rosenfeld scaling relationship. Additionally, effects of protein surface topology and hydrophobicity on water structure and dynamics were evaluated using multiregression analysis, showing that topology has a somewhat larger effect on hydration layer structure-dynamics. Concave and hydrophobic protein surfaces favor a less dense and more tetrahedral solvation layer, akin to a more ice-like structure, with slower dynamics. Results show that pairwise entropies of local hydration layers, calculated from regional radial distribution functions, scale logarithmically with local hydration dynamics. Thus, the Rosenfeld relationship describes the heterogeneous structure-dynamics of the hydration layer around the enzyme CALB. These findings raise the question of whether this may be a general principle for understanding the structure-dynamics of biomolecular solvation.
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Martin DR, Forsmo JE, Matyushov DV. Complex Dynamics of Water in Protein Confinement. J Phys Chem B 2017; 122:3418-3425. [PMID: 29206460 DOI: 10.1021/acs.jpcb.7b10448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper studies single-molecule and collective dynamics of water confined in protein powders by means of molecular dynamics simulations. The single-particle dynamics show a modest retardation compared to the bulk but become highly stretched in the powder, with the stretching exponent of ≃0.2. The collective dynamics of the total water dipole are affected by intermolecular correlations inside water and by cross-correlations between the water and the protein. The dielectric spectrum of water in the powder has two nearly equal-amplitude peaks: a Debye peak with ≃16 ps relaxation time and a highly stretched peak with the relaxation time of ≃13 ns and a stretching exponent of ≃0.12. The slower relaxation component is not seen in the single-molecule correlation functions and can be assigned to elastic protein motions displacing water in the powder. The loss spectrum of the intermediate scattering function reported by neutron-scattering experiments is also highly stretched, with the high-frequency wing scaling according to a power law. Translational dynamics can become much slower in the powder than in the bulk but are overshadowed by the rotational loss in the overall loss spectrum of neutron scattering.
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Affiliation(s)
| | - James E Forsmo
- College of Engineering , Georgia Institute of Technology , 225 North Avenue , Atlanta , Georgia 30332 , United States
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Seyedi S, Matyushov DV. Ergodicity breaking of iron displacement in heme proteins. SOFT MATTER 2017; 13:8188-8201. [PMID: 29082406 DOI: 10.1039/c7sm01561e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.
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Affiliation(s)
- Salman Seyedi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287, USA
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Folpini G, Siebert T, Woerner M, Abel S, Laage D, Elsaesser T. Water Librations in the Hydration Shell of Phospholipids. J Phys Chem Lett 2017; 8:4492-4497. [PMID: 28858510 DOI: 10.1021/acs.jpclett.7b01942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm-1 reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w0 = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm-1 is superimposed on a broad absorption band between 300 and 1000 cm-1. Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm-1 arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces.
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Affiliation(s)
- Giulia Folpini
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Michael Woerner
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Stephane Abel
- Institut de Biologie Intégrative de la Cellule (I2BC), Institut Frédéric Joliot, CEA, CNRS, Univ Paris-Sud Université Paris-Saclay, 91405 Gif-Sur-Yvette Cedex, France
| | - Damien Laage
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
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Chergui M, Thomas JM. From structure to structural dynamics: Ahmed Zewail's legacy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:043802. [PMID: 28868324 PMCID: PMC5562505 DOI: 10.1063/1.4998243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 08/08/2017] [Indexed: 05/19/2023]
Abstract
In this brief tribute to Ahmed Zewail, we highlight and place in the historical context, several of the major achievements that he and his colleagues have made in Femtochemistry (of which he was the principal instigator) and his introduction of ultrafast electron scattering, diffraction, microscopy and spectroscopy. By achieving a sub-picosecond temporal resolution, coupled with a picometer spatial resolution, he revolutionised our understanding of the corpus of chemical, physical, biological and materials science systems.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide and Lausanne Centre for Ultrafast Science (LACUS), ISIC, Faculté des Sciences de Base, Station 6, CH-1015 Lausanne, Switzerland
| | - John Meurig Thomas
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB30FS, United Kingdom
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