1
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Segreto N, Schwarz TM, Dietrich CA, Stender P, Schuldt R, Schmitz G, Kästner J. Understanding the Underlying Field Evaporation Mechanism of Pure Water Tips in High Electrical Fields. J Phys Chem A 2022; 126:5663-5671. [PMID: 35972399 DOI: 10.1021/acs.jpca.2c04163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the field evaporation process of frozen water in atom probe tomography (APT) by density functional simulations. In previous experiments, a strong tailing effect was observed for peaks caused by the molecular structure (H2O)nH+, in contrast to other peaks. In purely field-induced and thermally assisted evaporation simulations, we found that chains of protonated water molecules were pulled out of the dielectric surface by up to 6 Å, which are stable over a wide range of field strengths. Therefore, the resulting water clusters experience only part of the acceleration after evaporation compared to molecules evaporating directly from the surface and, thus, exhibit an energy deficit, which explains the tailing effect. Our simulations provide new insight into the complex evaporation behavior of water in high electrical fields and reveal possibilities for adapting the existing reconstruction algorithms.
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Affiliation(s)
- Nico Segreto
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Tim M Schwarz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Carolin A Dietrich
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Patrick Stender
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Robin Schuldt
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guido Schmitz
- Institute for Materials Science, Chair of Materials Physics, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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2
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Lu T, Chen Q. Ultrastrong Regulation Effect of the Electric Field on the All‐Carboatomic Ring Cyclo[18]Carbon**. Chemphyschem 2021; 22:386-395. [DOI: 10.1002/cphc.202000903] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/18/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Tian Lu
- Beijing Kein Research Center for Natural Sciences Beijing 100022 P. R. China
| | - Qinxue Chen
- Beijing Kein Research Center for Natural Sciences Beijing 100022 P. R. China
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3
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Dutta Dubey K, Stuyver T, Kalita S, Shaik S. Solvent Organization and Rate Regulation of a Menshutkin Reaction by Oriented External Electric Fields are Revealed by Combined MD and QM/MM Calculations. J Am Chem Soc 2020; 142:9955-9965. [PMID: 32369357 PMCID: PMC7304904 DOI: 10.1021/jacs.9b13029] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Indexed: 01/01/2023]
Abstract
When and how do external electric fields (EEFs) lead to catalysis in the presence of a (polar or nonpolar) solvent? This is the question that is addressed here using a combination of molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical calculations with EEF, and quantum mechanical/(local) electric field calculations. The paper focuses on a model reaction, the Menshutkin reaction between CH3I and pyridine in three solvents of varying polarity. Using MD simulations, we find that the EEF causes the solvent to undergo organization; the solvent molecules gradually align with the applied field as the field strength increases. The collective orientation of the solvent molecules modifies the electrostatic environment around the Menshutkin species and induces a global electric field pointing in the opposite direction of the applied EEF. The combination of these two entangled effects leads to partial or complete screening of the EEF, with the extent of screening being proportional to the polarity/polarizability of the solvent. Nevertheless, we find that catalysis of the Menshutkin reaction inevitably emerges once the EEF exceeds the opposing field of the organizing solvent, i.e., once polarization of the Menshutkin complex is observed to set in. Overall, our analysis provides a lucid and pictorial interpretation of the behavior of solutions in the presence of EEFs and indicates that EEF-mediated catalysis should, in principle, be feasible in bulk setups, especially for nonpolar and mildly polar solvents. By application of the charge-transfer paradigm, it is shown that the emergence of OEEF catalysis in solution can be generalized to other reactions as well.
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Affiliation(s)
- Kshatresh Dutta Dubey
- Department
of Chemistry & Center for Informatics, Shiv Nadar University, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Thijs Stuyver
- Institute
of Chemistry, Edmond J. Safra Campus at Givat Ram, The Hebrew University, Jerusalem 9190400, Israel
- Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Surajit Kalita
- Department
of Chemistry & Center for Informatics, Shiv Nadar University, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Sason Shaik
- Institute
of Chemistry, Edmond J. Safra Campus at Givat Ram, The Hebrew University, Jerusalem 9190400, Israel
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4
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Xu T, Lang X, Fan S, Wang Y, Chen J. The effect of electric fields in methane hydrate growth and dissociation: A molecular dynamics simulation. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Vibrational, energetic-dynamical and dissociation properties of water clusters in static electric fields: Non-equilibrium molecular-dynamics insights. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Hashim R, Sugimura A, Nguan HS, Rahman M, Zimmermann H. Anhydrous octyl-glucoside phase transition from lamellar to isotropic induced by electric and magnetic fields. J Chem Phys 2018; 146:084702. [PMID: 28249421 DOI: 10.1063/1.4976979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A static deuterium nuclear magnetic resonance (2HNMR) technique (magnetic field, B = 7.05 T) was employed to monitor the thermotropic lamellar phase of the anhydrous 1:1 mixture sample of octyl-b-D-glucoside (βOG) and that of partially deuterium labelled at the alpha position on the chain, i.e.,βOG-d2 In the absence of an electric field, the 2H NMR spectrum of the mixture gives a typical quadrupolar doublet representing the aligned lamellar phase. Upon heating to beyond the clearing temperature at 112 °C, this splitting converts to a single line expected for an isotropic phase. Simultaneous application of magnetic and electric fields (E = 0.4 MV/m) at 85 °C in the lamellar phase, whose direction was set to be parallel or perpendicular to the magnetic field, resulted in the change of the doublet into a single line and this recovers to the initial doublet with time for both experimental geometries. This implies E- and B-field-induced phase transitions from the lamellar to an isotropic phase and a recovery to the lamellar phase again with time. Moreover, these phase transformations are accompanied by a transient current. A similar observation was made in a computational study when an electric field was applied to a water cluster system. Increasing the field strength distorts the water cluster and weakens its hydrogen bonds leading to a structural breakdown beyond a threshold field-strength. Therefore, we suggest the observed field-induced transition is likely due to a structure change of the βOG lamellar assembly caused by the field effect and not due to Joule heating.
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Affiliation(s)
- Rauzah Hashim
- Centre of Fundamental and Frontier Science of Self-Assembly, Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Akihiko Sugimura
- School of Information Systems Engineering, Osaka Sangyo University, 3-1-1 Nakagaito, Daito-Shi, Osaka 574-8530, Japan
| | - Hock-Seng Nguan
- Centre of Fundamental and Frontier Science of Self-Assembly, Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Matiur Rahman
- Centre of Fundamental and Frontier Science of Self-Assembly, Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Herbert Zimmermann
- Department of Biophysics, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
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7
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Tibbetts KM, Feng XJ, Rabitz H. Exploring experimental fitness landscapes for chemical synthesis and property optimization. Phys Chem Chem Phys 2017; 19:4266-4287. [DOI: 10.1039/c6cp06187g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The topology of experimental fitness landscapes for chemical optimization objectives is assessed through svr-based HDMR modeling.
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8
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Miliordos E, Aprà E, Xantheas SS. A New, Dispersion-Driven Intermolecular Arrangement for the Benzene–Water Octamer Complex: Isomers and Analysis of their Vibrational Spectra. J Chem Theory Comput 2016; 12:4004-14. [DOI: 10.1021/acs.jctc.6b00668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evangelos Miliordos
- Physical
Sciences Division, Pacific Northwest National Laboratory, 902 Battelle
Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Edoardo Aprà
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Sotiris S. Xantheas
- Physical
Sciences Division, Pacific Northwest National Laboratory, 902 Battelle
Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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9
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Sen S, Boda M, Venkat Lata S, Naresh Patwari G. Internal electric fields in small water clusters [(H2O)n; n = 2-6]. Phys Chem Chem Phys 2016; 18:16730-7. [PMID: 27270616 DOI: 10.1039/c6cp02803a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by the donor O-H of a particular water molecule due to the hydrogen bonding network. The red-shifts in O-H stretching frequencies show a spread of about ±100 cm(-1) against the corresponding electric fields. Deviations from linearity were marked in the region of 100-160 MV cm(-1), which can be attributed to the strain in the hydrogen bonding network, especially for structures with DDAA and DDA motifs. The linear Stark effect holds up to 200 MV cm(-1) of internal electric field for the average red-shifts in the O-H stretching frequencies, with a Stark tuning rate of 2.4 cm(-1) (MV cm(-1))(-1), suggesting the validity of the classical model in small water clusters.
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Affiliation(s)
- Saumik Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manjusha Boda
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - S Venkat Lata
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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10
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Cole WTS, Farrell JD, Wales DJ, Saykally RJ. Structure and torsional dynamics of the water octamer from THz laser spectroscopy near 215 μm. Science 2016; 352:1194-7. [PMID: 27257252 DOI: 10.1126/science.aad8625] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/02/2016] [Indexed: 11/02/2022]
Affiliation(s)
- William T S Cole
- Department of Chemistry, University of California, Berkeley, CA 94705, USA
| | - James D Farrell
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - David J Wales
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Richard J Saykally
- Department of Chemistry, University of California, Berkeley, CA 94705, USA.
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11
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Luis D, López-Lemus J, Maspoch ML, Franco-Urquiza E, Saint-Martin H. Methane hydrate: shifting the coexistence temperature to higher temperatures with an external electric field. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1139704] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- D.P. Luis
- CONACYT Research Fellow-Centro de Ingeniería y Desarrollo Industrial, Querétaro, México
| | - J. López-Lemus
- Facultad de ciencias, Universidad Autónoma del Estado de México, Toluca, México
| | - M. Ll. Maspoch
- Centre Català del Plàstic, Universitat Politècnica de Catalunya, Terrassa, Spain
| | - E.A. Franco-Urquiza
- CONACYT Research Fellow-Centro de Ingeniería y Desarrollo Industrial, Querétaro, México
| | - H. Saint-Martin
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México,
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12
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English NJ, Waldron CJ. Perspectives on external electric fields in molecular simulation: progress, prospects and challenges. Phys Chem Chem Phys 2016; 17:12407-40. [PMID: 25903011 DOI: 10.1039/c5cp00629e] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, the application of a wide variety of external electric fields in molecular simulation shall be discussed, including time-varying and electromagnetic, as well as the utility and potential impact and prospects for exploitation of such simulations for real-world and industrial end use. In particular, non-equilibrium molecular dynamics will be discussed, as well as challenges in addressing adequate thermostatting and scaling field amplitudes to more experimentally relevant levels. Attention shall be devoted to recent progress and advances in external fields in ab initio molecular simulation and dynamics, as well as elusive challenges thereof (and, to some extent, for molecular dynamics from empirical potentials), such as timescales required to observe low-frequency and intensity field effects. The challenge of deterministic molecular dynamics in external fields in sampling phase space shall be discussed, along with prospects for application of fields in enhanced-sampling simulations. Finally, the application of external electric fields to a wide variety of aqueous, nanoscale and biological systems will be discussed, often motivated by the possibility of exploitation in real-world applications, which serve to underpin our molecular-level understanding of field effects in terms of microscopic mechanisms, and possibly with a view to control thereof.
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Affiliation(s)
- Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
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13
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Luis DP, Herrera-Hernández EC, Saint-Martin H. A theoretical study of the dissociation of the sI methane hydrate induced by an external electric field. J Chem Phys 2015; 143:204503. [PMID: 26627964 DOI: 10.1063/1.4936214] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations in the equilibrium isobaric-isothermal (NPT) ensemble were used to examine the strength of an external electric field required to dissociate the methane hydrate sI structure. The water molecules were modeled using the four-site TIP4P/Ice analytical potential and methane was described as a simple Lennard-Jones interaction site. A series of simulations were performed at T = 260 K with P = 80 bars and at T = 285 K with P = 400 bars with an applied electric field ranging from 1.0 V nm(-1) to 5.0 V nm(-1). For both (T,P) conditions, applying a field greater than 1.5 V nm(-1) resulted in the orientation of the water molecules such that an ice Ih-type structure was formed, from which the methane was segregated. When the simulations were continued without the external field, the ice-like structures became disordered, resulting in two separate phases: gas methane and liquid water.
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Affiliation(s)
- D P Luis
- CONACYT Research Fellow-Centro de Ingeniería y Desarrollo Industrial, Av. Playa Pie de la Cuesta No. 702, Desarrollo San Pablo, Querétaro, Querétaro 76125, Mexico
| | - E C Herrera-Hernández
- CONACYT Research Fellow-Centro de Ingeniería y Desarrollo Industrial, Av. Playa Pie de la Cuesta No. 702, Desarrollo San Pablo, Querétaro, Querétaro 76125, Mexico
| | - H Saint-Martin
- Instituto de Ciencias Físicas, Universidad Autónoma de México, Apartado Postal 48-3, Cuernavaca, Morelos 62251, Mexico
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14
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Bai Y, He HM, Li Y, Li ZR, Zhou ZJ, Wang JJ, Wu D, Chen W, Gu FL, Sumpter BG, Huang J. Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties. J Phys Chem A 2015; 119:2083-90. [DOI: 10.1021/jp511460c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yang Bai
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Hui-Min He
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Ying Li
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Zhi-Ru Li
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Zhong-Jun Zhou
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Jia-Jun Wang
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Di Wu
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Wei Chen
- State
Key Laboratory of Theoretical and Computational Chemistry Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Feng-Long Gu
- Center
for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, P. R. China
| | - Bobby G. Sumpter
- Center for Nanophase Materials Sciences and Computer Science & Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6493, United States
| | - Jingsong Huang
- Center for Nanophase Materials Sciences and Computer Science & Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6493, United States
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15
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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16
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Qian Z, Fu Z, Wei G. Influence of electric fields on the structure and structure transition of water confined in a carbon nanotube. J Chem Phys 2014. [DOI: 10.1063/1.4871625] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Rühle V, Kusumaatmaja H, Chakrabarti D, Wales DJ. Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules. J Chem Theory Comput 2013; 9:4026-34. [PMID: 26592398 DOI: 10.1021/ct400403y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present new methodology for exploring the energy landscapes of molecular systems, using angle-axis variables for the rigid-body rotational coordinates. The key ingredient is a distance measure or metric tensor, which is invariant to global translation and rotation. The metric is used to formulate a generalized nudged elastic band method for calculating pathways, and a full prescription for normal-mode analysis is described. The methodology is tested by mapping the potential energy and free energy landscape of the water octamer, described by the TIP4P potential.
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Affiliation(s)
- Victor Rühle
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Halim Kusumaatmaja
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Department of Physics, Durham University , South Road, Durham DH1 3LE, United Kingdom
| | - Dwaipayan Chakrabarti
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - David J Wales
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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18
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Rai D, Kulkarni AD, Gejji SP, Bartolotti LJ, Pathak RK. Exploring electric field induced structural evolution of water clusters, (H2O)n [n = 9–20]: Density functional approach. J Chem Phys 2013; 138:044304. [DOI: 10.1063/1.4776214] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Richardson JO, Wales DJ, Althorpe SC, McLaughlin RP, Viant MR, Shih O, Saykally RJ. Investigation of Terahertz Vibration–Rotation Tunneling Spectra for the Water Octamer. J Phys Chem A 2013; 117:6960-6. [DOI: 10.1021/jp311306a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jeremy O. Richardson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge,
CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge,
CB2 1EW, United Kingdom
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge,
CB2 1EW, United Kingdom
| | - Ryan P. McLaughlin
- Department of Chemistry, University of California, Berkeley, California 94720,
United States
| | - Mark R. Viant
- Department of Chemistry, University of California, Berkeley, California 94720,
United States
| | - Orion Shih
- Department of Chemistry, University of California, Berkeley, California 94720,
United States
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720,
United States
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20
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Structure of the floating water bridge and water in an electric field. Proc Natl Acad Sci U S A 2012; 109:16463-8. [PMID: 23010930 DOI: 10.1073/pnas.1210732109] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The floating water bridge phenomenon is a freestanding rope-shaped connection of pure liquid water, formed under the influence of a high potential difference (approximately 15 kV). Several recent spectroscopic, optical, and neutron scattering studies have suggested that the origin of the bridge is associated with the formation of anisotropic chains of water molecules in the liquid. In this work, high energy X-ray diffraction experiments have been performed on a series of floating water bridges as a function of applied voltage, bridge length, and position within the bridge. The two-dimensional X-ray scattering data showed no direction-dependence, indicating that the bulk water molecules do not exhibit any significant preferred orientation along the electric field. The only structural changes observed were those due to heating, and these effects were found to be the same as for bulk water. These X-ray scattering measurements are supported by molecular dynamics (MD) simulations which were performed under electric fields of 10(6) V/m and 10(9) V/m. Directional structure factor calculations were made from these simulations parallel and perpendicular to the E-field. The 10(6) V/m model showed no significant directional-dependence (anisotropy) in the structure factors. The 10(9) V/m model however, contained molecules aligned by the E-field, and had significant structural anisotropy.
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21
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Wales DJ, Carr JM. Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations. J Chem Theory Comput 2012; 8:5020-34. [PMID: 26593194 DOI: 10.1021/ct3004832] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.
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Affiliation(s)
- David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Joanne M Carr
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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22
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Abstract
The evolution of many systems is dominated by rare activated events that occur on timescale
ranging from nanoseconds to the hour or more. For such systems, simulations must leave aside the
full thermal description to focus specifically on mechanisms that generate a configurational change.
We present here the activation relaxation technique (ART), an open-ended saddle point search
algorithm, and a series of recent improvements to ART nouveau and kinetic ART, an ART-based
on-the-fly off-lattice self-learning kinetic Monte Carlo method.
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Acosta-Gutiérrez S, Hernández-Rojas J, Bretón J, Llorente JMG, Wales DJ. Physical properties of small water clusters in low and moderate electric fields. J Chem Phys 2012; 135:124303. [PMID: 21974518 DOI: 10.1063/1.3640804] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Likely candidates for the lowest minima of water clusters (H(2)O)(N) for N ≤ 20 interacting with a uniform electric field strength in the range E ≤ 0.6 V/Å have been identified using basin-hopping global optimization. Two water-water model potentials were considered, namely TIP4P and the polarizable Dang-Chang potential. The two models produce some consistent results but also exhibit significant differences. The cluster internal energy and dipole moment indicate two varieties of topological transition in the structure of the global minimum as the field strength is increased. The first takes place at low field strengths (0.1 V/Å<E < 0.2 V/Å) and reorganizes the hydrogen-bonds to orient the water permanent dipoles along the field. The second type of transition occurs at larger field strengths (0.3 V/Å<E < 0.5 V/Å) and corresponds to an extensive structural reorganization, where several hydrogen-bonds break as the cluster stretches along the field direction, the larger clusters (N > 10) usually forming helical structures.
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Affiliation(s)
- S Acosta-Gutiérrez
- Departamento de Física Fundamental II and IUdEA, Universidad de La Laguna, 38205 Tenerife, Spain
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24
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What is the best density functional to describe water clusters: evaluation of widely used density functionals with various basis sets for (H2O) n (n = 1–10). Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0989-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Rai D, Kulkarni AD, Gejji SP, Pathak RK. Methanol clusters (CH3OH)n, n = 3–6 in external electric fields: Density functional theory approach. J Chem Phys 2011; 135:024307. [DOI: 10.1063/1.3605630] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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27
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Neela YI, Mahadevi AS, Sastry GN. Hydrogen Bonding in Water Clusters and Their Ionized Counterparts. J Phys Chem B 2010; 114:17162-71. [DOI: 10.1021/jp108634z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Y. Indra Neela
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
| | - A. Subha Mahadevi
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
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28
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Luis D, López-Lemus J, Mayorga M. Electrodissociation of clathrate-like structures. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927021003628889] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Bandyopadhyay P. Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H2O)20 and (H2O)50. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.01.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Asare E, Musah AR, Curotto E, Freeman DL, Doll JD. The thermodynamic and ground state properties of the TIP4P water octamer. J Chem Phys 2009; 131:184508. [DOI: 10.1063/1.3259047] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Mukherjee B, Maiti PK, Dasgupta C, Sood AK. Jump Reorientation of Water Molecules Confined in Narrow Carbon Nanotubes. J Phys Chem B 2009; 113:10322-30. [DOI: 10.1021/jp904099f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Biswaroop Mukherjee
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, and Condensed Matter Theory Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Prabal K. Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, and Condensed Matter Theory Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Chandan Dasgupta
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, and Condensed Matter Theory Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - A. K. Sood
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, Department of Physics, Indian Institute of Science, Bangalore 560 012, India, and Condensed Matter Theory Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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32
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Is high electric field capable of selectively inducing a covalent-like bond between polar and non-polar molecular species? Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0570-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Calvo F, Dugourd P. Folding of gas-phase polyalanines in a static electric field: alignment, deformations, and polarization effects. Biophys J 2008; 95:18-32. [PMID: 18223004 PMCID: PMC2426642 DOI: 10.1529/biophysj.107.124685] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 12/28/2007] [Indexed: 11/18/2022] Open
Abstract
Monte Carlo simulations of the temperature-induced unfolding of small gas-phase polyalanines in a static, homogeneous electric field are reported, based on the AMBER ff96 force field. The peptides exhibit a structural transition from the native alpha-helix state to entropically favored beta-sheet conformations, before eventually turning to extended coil at higher temperatures. Upon switching the electric field, the molecules undergo preferential alignment of their dipole moment vector toward the field axis and a shift of the alpha-beta transition to higher temperatures. At higher field strengths (>10(8) V/m) the molecules stretch and the alpha-beta and beta-coil transitions merge. A simple three-state model is shown to account for the observed behavior. Under even higher fields, density functional theory calculations and a polarizable force field both show that electronic rearrangements tend to further increase the dipole moment, polarization effects being approximately half in magnitude with respect to stretching effect. Finally a tentative (temperature, field-strength) phase diagram is sketched.
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Affiliation(s)
- F Calvo
- Centre National de la Recherche Scientifique, Laboratoire de Spectrometrie Ionique et Moleculaire, Université de Lyon, Université Lyon 1, Villeurbanne, France.
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34
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Nguyen QC, Ong YS, Soh H, Kuo JL. Multiscale approach to explore the potential energy surface of water clusters (H2O)nn <or= 8. J Phys Chem A 2008; 112:6257-61. [PMID: 18572899 DOI: 10.1021/jp802118j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a multiscale method to explore the energy landscape of water clusters. An asynchronous genetic algorithm is employed to explore the potential energy surface (PES) of OSS2 and TTM2.1-F models. Local minimum structures are collected on the fly, and the ultrafast shape recognition algorithm was used to remove duplicate structures. These structures are then refined at the B3LYP/6-31+G* level. The number of distinct local minima we found (21, 76, 369, 1443, and 3563 isomers for n = 4-8, respectively) reflects the complexity of the PES of water clusters.
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Affiliation(s)
- Quoc Chinh Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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35
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Curotto E, Freeman DL, Doll JD. A stereographic projection path integral study of the coupling between the orientation and the bending degrees of freedom of water. J Chem Phys 2008; 128:204107. [DOI: 10.1063/1.2925681] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Rai D, Kulkarni AD, Gejji SP, Pathak RK. Water clusters (H2O)n, n=6–8, in external electric fields. J Chem Phys 2008; 128:034310. [DOI: 10.1063/1.2816565] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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