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Listyarini R, Kriesche BM, Hofer TS. Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H 2O. J Chem Theory Comput 2024; 20:3028-3045. [PMID: 38595064 PMCID: PMC11044269 DOI: 10.1021/acs.jctc.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO2. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Bernhard M. Kriesche
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry Center for Chemistry
and Biomedicine, University of Innsbruck Innrain 80-82, A-6020 Innsbruck, Austria
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2
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Listyarini R, Gamper J, Hofer TS. Storage and Diffusion of Carbon Dioxide in the Metal Organic Framework MOF-5─A Semi-empirical Molecular Dynamics Study. J Phys Chem B 2023; 127:9378-9389. [PMID: 37857343 PMCID: PMC10627117 DOI: 10.1021/acs.jpcb.3c04155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/22/2023] [Indexed: 10/21/2023]
Abstract
Metal-organic frameworks (MOFs) have attracted increasing attention due to their high porosity for exceptional gas storage applications. MOF-5 belongs to the family of isoreticular MOFs (IRMOFs) and consists of Zn4O6+ clusters linked by 1,4-benzenedicarboxylate. Due to the large number of atoms in the unit cell, molecular dynamics simulation based on density functional theory has proved to be too demanding, while force field models are often inadequate to model complex host-guest interactions. To overcome this limitation, an alternative semi-empirical approach using a set of approximations and extensive parametrization of interactions called density functional tight binding (DFTB) was applied in this work to study CO2 in the MOF-5 host. Calculations of pristine MOF-5 yield very good agreement with experimental data in terms of X-ray diffraction patterns as well as mechanical properties, such as the negative thermal expansion coefficient and the bulk modulus. In addition, different loadings of CO2 were introduced, and the associated self-diffusion coefficients and activation energies were investigated. The results show very good agreement with those of other experimental and theoretical investigations. This study provides detailed insights into the capability of semi-empirical DFTB-based molecular dynamics simulations of these challenging guest@host systems. Based on the comparison of the guest-guest pair distributions observed inside the MOF host and the corresponding gas-phase reference, a liquid-like structure of CO2 can be deduced upon storage in the host material.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Innrain 80-82A, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Jakob Gamper
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Innrain 80-82A, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Innrain 80-82A, A-6020 Innsbruck, Austria
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3
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Jamal S, Naz Z, Moin ST, Hofer TS. Deciphering Structural and Dynamical Properties of Hydrated Cobalt Porphyrins via Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation. J Phys Chem B 2023. [PMID: 37220311 DOI: 10.1021/acs.jpcb.3c00837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The present study successfully implemented the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism for the investigation of structural and dynamical properties of hydrated cobalt-porphyrin complexes. Considering the significance of cobalt ions in biological systems (for instance, vitamin B12), which reportedly incorporate cobalt ions in a d6, low spin, +3 state chelated in the corrin ring, an analog of porphyrin, the current study is focused on cobalt in the oxidation states +2 and +3 bound to the parent porphyrin lead structures embedded in an aqueous solution. These cobalt-porphyrin complexes were investigated in terms of their structural and dynamical properties at the quantum chemical level. The structural attributes of these hydrated complexes revealed the contrasting features of the water binding to these solutes, including a detailed evaluation of the associated dynamics. The study also yielded notable findings in regard to the respective electronic configurations vs coordination, which suggested that Co(II)-POR possesses a 5-fold square pyramidal coordination geometry in an aqueous solution containing the metal ion coordinating to four nitrogen atoms of the porphyrin ring and one axial water as the fifth ligand. On the other hand, high-spin Co(III)-POR was hypothesized to be more stable due to the smaller size-to-charge ratio of the cobalt ion, but the high-spin complex demonstrated unstable structural and dynamical behavior. However, the corresponding properties of the hydrated Co(III)LS-POR revealed a stable structure in an aqueous solution, thus suggesting the Co(III) ion to be in a low-spin state when bound to the porphyrin ring. Moreover, the structural and dynamical data were augmented by computing the free energy of water binding to the cobalt ions and the solvent-accessible surface area, which provide further information on thermochemical properties of the metal-water interaction and the hydrogen bonding potential of the porphyrin ring in these hydrated systems.
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Affiliation(s)
- Sehrish Jamal
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Zobia Naz
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S Hofer
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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4
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Listyarini RV, Kriesche BM, Hofer TS. The solvation structure of CO2 in dichloromethane – A comparative correlated, semi-empirical and classical MD simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Irregular structure of the hydrated Ag+ in aqueous solution and its Dynamics: An insight from perturbation theory hybrid forces molecular dynamics simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Prasetyo N, Hidayat Y. Lability of the first solvation shell of silver cations in liquid ammonia: A quantum mechanical charge field molecular dynamics simulation study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Saputri WD, Pranowo HD, Hofer TS. Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Theoretical insight on the solvation properties of Zn2+ in pure liquid ammonia: A quantum mechanical molecular charges field molecular dynamics (QMCF-MD) study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Saleh M, Zam ZZ, Hofer TS. Solvent influence on the presence of axial ligand coordination: A QMCF-MD study of the structural and dynamical properties of Pd(II) and Pd(II) tetra-ammine in aqueous solution. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Malloum A, Fifen JJ, Conradie J. Determination of the absolute solvation free energy and enthalpy of the proton in solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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11
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First solvation shell structure and dynamics of solvated Ca2+ in dilute aqueous ammonia by first principle approach: a QMCF MD simulation study. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02678-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Saputri WD, Pranowo HD, Schuler MJ, Hofer TS. Cu 2+ in liquid ammonia-The impact of solvent flexibility and electron correlation in ab initio quantum mechanical charge field molecular dynamics. J Comput Chem 2020; 41:2168-2176. [PMID: 32735755 DOI: 10.1002/jcc.26379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/13/2020] [Indexed: 11/06/2022]
Abstract
The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu2+ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH3 )6 ]2+ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu2+ - NH3 distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu2+ - NH3 interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu2+ - NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Austrian-Indonesian Centre for Computational Chemistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Austrian-Indonesian Centre for Computational Chemistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Manuel J Schuler
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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13
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Saputri WD, Sulaiman SS, Sari FR, Sudiono S, Pranowo HD, Saleh M, Hofer TS. Co3+ and Ir3+ in pure liquid ammonia: Structure and dynamics from ab initio quantum mechanical charge field molecular dynamics. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Xin X, Niu X, Liu W, Wang D. Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy. Chemphyschem 2020; 21:762-769. [PMID: 32154979 DOI: 10.1002/cphc.202000039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/15/2020] [Indexed: 02/03/2023]
Abstract
We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.
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Affiliation(s)
- Xin Xin
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiao Niu
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Wanqi Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong, 250014, China
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15
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Naz Z, Moin ST, Hofer TS. Hydration of Closely Related Manganese and Magnesium Porphyrins in Aqueous Solutions: Ab Initio Quantum Mechanical Charge Field Molecular Dynamics Simulation Study. J Phys Chem B 2019; 123:10769-10779. [PMID: 31738566 DOI: 10.1021/acs.jpcb.9b07639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To the best of our knowledge, the current study based on ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) is the first to explore the difference in the hydration behavior between Mn(II)- and Mg(II)-associated porphyrins (Mn(II)-POR and Mg(II)-POR) in aqueous solution. The simulation study highlights similar and dissimilar characteristics of the structural, dynamical, and thermodynamical properties of these closely related metals bound to porphyrins in aqueous solution. The structural analysis is based on radial and angular distribution functions, coordination number distributions, and angular-radial distributions. Both hydrated systems demonstrate similar pentacoordinated structures formed via the axial coordination of one water molecule to the metal ion in addition to the four nitrogen atoms of the porphyrin ring. However, in the case of Mn(II)-POR, the formation of a distorted square pyramidal geometry was observed. It was envisaged as a weak coordination of the water molecule to the Mn(II) atom and thus higher atomic fluctuation for all atoms in contrast to that for the hydrated Mg(II)-POR. The dynamical data in terms of the mean residence times, velocity autocorrelation function, free energy, and other parameters revealed the difference in the metal binding effect because the Mn(II) atom was observed to inhibit H-bond formation more than the presence of Mg(II) atoms in the core of the porphyrin. The current study thus highlights the significant differences in the structural and dynamical properties of Mn(II)- and Mg(II)-associated porphyrin systems.
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Affiliation(s)
- Zobia Naz
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi 75270 , Pakistan
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi 75270 , Pakistan
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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16
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Saputri WD, Wijaya K, Pranowo HD, Hofer TS. The Jahn-Teller effect in mixed aqueous solution: the solvation of Cu2+ in 18.6% aqueous ammonia obtained from ab initio quantum mechanical charge field molecular dynamics. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-1115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Karna Wijaya
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Thomas S. Hofer
- University of Innsbruck , Theoretical Chemistry Division , Innsbruck , Austria
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17
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Investigation of the preferential solvation and dynamical properties of Cu+ in 18.6% aqueous ammonia solution using ab initio quantum mechanical charge field (QMCF) molecular dynamics and NBO analysis. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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18
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Prasetyo N, Hofer TS. Structure, Dynamics, and Hydration Free Energy of Carbon Dioxide in Aqueous Solution: A Quantum Mechanical/Molecular Mechanics Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) Simulation Study. J Chem Theory Comput 2018; 14:6472-6483. [PMID: 30336013 DOI: 10.1021/acs.jctc.8b00557] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solvation of carbon dioxide in solution represents a key step for the capture and fixation CO2 in nature, which may be further influenced by the formation of (bi)carbonate species and/or the formation of CO2 clusters in solution. The latter processes are strongly dependent on the exact environment of the liquid state (e.g., pH value, solvated ions, etc.) and may interfere with the experimental determination of structural, dynamical, and thermodynamic properties. In this work a hybrid quantum mechanical/molecular mechanical (QM/MM) simulation approach at correlated ab initio level of theory resolution-of-identity second-order Møller-Plesset Perturbation Theory (RI-MP2) has been applied in the framework of thermodynamic integration (TI) to study structure, dynamics, and the hydration free energy of a single carbon dioxide molecule in aqueous solution. A detailed analysis of the individual QM/MM potential energy contributions demonstrate that the overall potential remains highly consistent over the entire sampling phase and that no artificial contributions are influencing the determination of the hydration free energy. The latter value of 0.01 ± 0.92 kcal/mol was found in very good agreement with the values of 0.06 and 0.24 kcal/mol obtained via quasi-chemical theory and experimental measurements, respectively. In order to obtain detailed information about the C- and O C-water interaction, conically restricted regions with respect to the main axis of the CO2 molecule have been employed in structural analysis. The presented data not only provide detailed information about the hydration properties of CO2 but act as a critical validation of the simulation technique, which will be beneficial in the study of nonaqueous solvents such as pure and aqueous NH3 solutions, which have been suggested as potential candidates to capture CO2 from anthropogenic sources.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82A , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara, Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara, Yogyakarta 55281 , Indonesia
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82A , A-6020 Innsbruck , Austria
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19
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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20
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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Hofer TS, Wiedemair MJ. Towards a dissociative SPC-like water model II. The impact of Lennard-Jones and Buckingham non-coulombic forces. Phys Chem Chem Phys 2018; 20:28523-28534. [DOI: 10.1039/c8cp04957b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissociative water potential by Garofalini and coworkers has been re-formulated in the framework of the widely employed Lennard-Jones and Buckingham potentials, enhancing the transferability of the model to third party simulation programs.
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Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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22
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Saleh M, Hofer TS. Square planar or octahedral after all? The indistinct solvation of platinum(ii). Dalton Trans 2018; 47:13032-13045. [DOI: 10.1039/c8dt02169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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23
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Moin ST, Hofer TS. Hydration of iron-porphyrins: ab initio quantum mechanical charge field molecular dynamics simulation study. Phys Chem Chem Phys 2017; 19:30822-30833. [PMID: 29135005 DOI: 10.1039/c7cp04436d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe2+-P and Fe3+-P in water to evaluate their structural, dynamical and energetic properties. Based on the structural data, it was found that Fe2+-P accommodates one water molecule in the first coordination sphere of the Fe2+ ion including the four nitrogen atoms of the porphyrin system coordinating with central metal species. On the other hand, two water molecules were coordinated to Fe3+-P, thus forming a hexa-coordinated species. Comparison of dynamical properties such as the vibrational power spectrum and ligand mean residence times to other metal-free porphyrin systems demonstrate the ions' influence on the hydration structure, enabling a characterisation of the strong interaction of the ions which greatly reduces the hydrogen bonding potential of the complex. The association of water molecules with the metal ions in both solutes was quantified by computing the free energy of binding obtained via the potential of mean force. This further confirmed the strong association of water to the metal ions which was conversely weak as inferred from the energetic data for the Fe2+-P system.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi, Karachi-75270, Pakistan.
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24
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Hitzenberger M, Schuster D, Hofer TS. The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study. Front Chem 2017; 5:76. [PMID: 29109946 PMCID: PMC5660280 DOI: 10.3389/fchem.2017.00076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Erroneous activation of the Hedgehog pathway has been linked to a great amount of cancerous diseases and therefore a large number of studies aiming at its inhibition have been carried out. One leverage point for novel therapeutic strategies targeting the proteins involved, is the prevention of complex formation between the extracellular signaling protein Sonic Hedgehog and the transmembrane protein Patched 1. In 2009 robotnikinin, a small molecule capable of binding to and inhibiting the activity of Sonic Hedgehog has been identified, however in the absence of X-ray structures of the Sonic Hedgehog-robotnikinin complex, the binding mode of this inhibitor remains unknown. In order to aid with the identification of novel Sonic Hedgehog inhibitors, the presented investigation elucidates the binding mode of robotnikinin by performing an extensive docking study, including subsequent molecular mechanical as well as quantum mechanical/molecular mechanical molecular dynamics simulations. The attained configurations enabled the identification of a number of key protein-ligand interactions, aiding complex formation and providing stabilizing contributions to the binding of the ligand. The predicted structure of the Sonic Hedgehog-robotnikinin complex is provided via a PDB file as Supplementary Material and can be used for further reference.
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Affiliation(s)
- Manuel Hitzenberger
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria.,Department of Physics, Theoretical Biophysics (T38), Technical University of Munich, Munich, Germany
| | - Daniela Schuster
- Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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25
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Moin ST, Hofer TS. Zinc- and copper-porphyrins in aqueous solution - two similar complexes with strongly contrasting hydration. MOLECULAR BIOSYSTEMS 2017; 12:2288-2295. [PMID: 27194391 DOI: 10.1039/c6mb00133e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal-water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper-water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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26
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Affiliation(s)
- Martin J. Field
- Dynamo Team/DYNAMOP Group,
UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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27
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Saleh M, Hofer TS. Palladium(ii) in liquid ammonia: an investigation of structural and dynamical properties by applying quantum mechanical charge field molecular dynamics (QMCF-MD). Dalton Trans 2017; 46:9630-9638. [DOI: 10.1039/c7dt01548h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural and dynamical properties of Pd2+ in liquid ammonia have been investigated via quantum mechanical charge field molecular dynamics.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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28
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Wiedemair MJ, Hofer TS. Towards a dissociative SPC-like water model – probing the impact of intramolecular Coulombic contributions. Phys Chem Chem Phys 2017; 19:31910-31920. [DOI: 10.1039/c7cp06191a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modification of the dissociative Garofalini water model towards an SPC-like Coulombic formulation proved to enhance accuracy and transferability of this successful force field approach.
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Affiliation(s)
- Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
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29
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Saleh M, Hofer TS. Structure and dynamics of Ni2+ in liquid ammonia: A quantum mechanical charge field molecular dynamics (QMCF-MD) study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Hofer TS, Tirler AO. Combining 2d-Periodic Quantum Chemistry with Molecular Force Fields: A Novel QM/MM Procedure for the Treatment of Solid-State Surfaces and Interfaces. J Chem Theory Comput 2015; 11:5873-87. [DOI: 10.1021/acs.jctc.5b00548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division,
Institute for General Inorganic and Theoretical Chemistry, Center
for Chemistry and Biomedicine, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Andreas O. Tirler
- Theoretical Chemistry Division,
Institute for General Inorganic and Theoretical Chemistry, Center
for Chemistry and Biomedicine, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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31
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Tirler AO, Persson I, Hofer TS, Rode BM. Is the Hexacyanoferrate(II) Anion Stable in Aqueous Solution? A Combined Theoretical and Experimental Study. Inorg Chem 2015; 54:10335-41. [DOI: 10.1021/acs.inorgchem.5b01701] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas O. Tirler
- Theoretical
Chemistry Division Institute of General, Inorganic and Theoretical
Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Ingmar Persson
- Department of Chemistry and Biotechnology Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Thomas S. Hofer
- Theoretical
Chemistry Division Institute of General, Inorganic and Theoretical
Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- Theoretical
Chemistry Division Institute of General, Inorganic and Theoretical
Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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32
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Tirler AO, Hofer TS. A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics. J Phys Chem B 2015; 119:8613-22. [PMID: 26090779 DOI: 10.1021/acs.jpcb.5b03938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.
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Affiliation(s)
- Andreas O Tirler
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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33
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Canaval LR, Hadisaputra S, Hofer TS. Remarkable conformational flexibility of aqueous 18-crown-6 and its strontium(II) complex-ab initio molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:16359-66. [PMID: 26050993 DOI: 10.1039/c5cp01977j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ab initio QMCF-MD simulations of aqueous 18-crown-6 (18C6) and strontium(II)-18-crown-6 (18C6-Sr) were performed to gather insight into their hydration properties. Strongly different characteristics were found for the two solutes in terms of structure and dynamics such as H-bonding. They, however, have in common that their backbone shows high flexibility in aqueous medium, adopting structures significantly differing from idealized gas phase geometries. In particular, planar oxyethylene units stable in the picosecond range occurred in 18C6, while the strontium complex readily exhibits a bent structure. Detailed analysis of this high flexibility was done via two dimensional root mean square deviation plots as well as the evolution of dihedral angles and angles within the simulation trajectory. The vibrational spectra obtained from the QMCF-MD simulations are in excellent agreement with experimental data and show a pronounced blueshift upon complexation of the strontium(II) ion in 18C6.
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Affiliation(s)
- Lorenz R Canaval
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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34
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Canaval LR, Passler PP, Rode BM. The hydration properties of Gd(III) and Tb(III): An ab initio quantum mechanical molecular dynamics study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Eklund L, Hofer TS, Persson I. Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS. Dalton Trans 2015; 44:1816-28. [PMID: 25473816 PMCID: PMC4281468 DOI: 10.1039/c4dt02580f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2(-), chlorate, ClO3(-), and perchlorate, ClO4(-). In addition, the structures of the hydrated hypochlorite, ClO(-), bromate, BrO3(-), iodate, IO3(-) and metaperiodate, IO4(-), ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO6(3-), ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01-0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.
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Affiliation(s)
- Lars Eklund
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O.Box 7015, SE-750 07 Uppsala, Sweden
| | - Tomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Ingmar Persson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O.Box 7015, SE-750 07 Uppsala, Sweden
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36
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Hofer TS. Probing Proton Transfer Reactions in Molecular Dynamics—A Crucial Prerequisite for QM/MM Simulations Using Dissociative Models. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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37
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Canaval LR, Rode BM. The hydration properties of Eu(II) and Eu(III): An ab initio quantum mechanical molecular dynamics study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.10.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Moin ST, Hofer TS. Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study. Phys Chem Chem Phys 2014; 16:26075-83. [DOI: 10.1039/c4cp03697b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Tirler AO, Hofer TS. Structure and Dynamics of the Uranyl Tricarbonate Complex in Aqueous Solution: Insights from Quantum Mechanical Charge Field Molecular Dynamics. J Phys Chem B 2014; 118:12938-51. [DOI: 10.1021/jp503171g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andreas O. Tirler
- Theoretical
Chemistry Division,
Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical
Chemistry Division,
Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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40
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Canaval LR, Lutz OMD, Weiss AKH, Huck CW, Hofer TS. A Dissociative Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation and Infrared Experiments Reveal Characteristics of the Strongly Hydrolytic Arsenic(III). Inorg Chem 2014; 53:11861-70. [DOI: 10.1021/ic4031156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Lorenz R. Canaval
- Theoretical Chemistry Division, Institute of General,
Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Oliver M. D. Lutz
- Institute for Analytical Chemistry and
Radiochemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division, Institute of General,
Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Christian W. Huck
- Institute for Analytical Chemistry and
Radiochemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General,
Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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41
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Bhattacharjee A, Weiss AKH, Artero V, Field MJ, Hofer TS. Electronic Structure and Hydration of Tetramine Cobalt Hydride Complexes. J Phys Chem B 2014; 118:5551-61. [DOI: 10.1021/jp502651s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anirban Bhattacharjee
- DYNAMO/DYNAMOP,
Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I), 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Alexander K. H. Weiss
- Department
of Theoretical Chemistry, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Inrain 80-82, A-6020 Innsbruck, Austria
| | - Vincent Artero
- Laboratoire
de Chimie et Biologie des Métaux (UMR 5249, CNRS,
CEA, Université Grenoble I), DSV/iRTSV,
CEA-Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I), 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Thomas S. Hofer
- Department
of Theoretical Chemistry, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Inrain 80-82, A-6020 Innsbruck, Austria
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42
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Moin ST, Weiss AK, Rode BM. Ionized CO2 and SO2 in aqueous environment: Ab initio QMCF-MD studies. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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43
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Sakwarathorn T, Pongstabodee S, Vchirawongkwin V, Canaval LR, Tirler AO, Hofer TS. Characteristics of selenate in aqueous solution – An ab initio QMCF-MD study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.01.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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44
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Hofer TS. Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an advanced QM/MM protocol, are discussed and simulation results for various systems ranging from simple ionic hydrates to solvated organic molecules and coordination complexes in solution are presented. A particularly challenging application is the description of proton-transfer reactions in chemical simulations, which is a prerequisite to study acidified and basic systems. The methodical requirements for a combination of the QMCF methodology with a dissociative potential model for the description of the solvent are discussed. Furthermore, the possible extension of QM/MM approaches to solid/liquid interfaces is outlined.
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45
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Spezia R, Jeanvoine Y, Beuchat C, Gagliardi L, Vuilleumier R. Hydration properties of Cm(iii) and Th(iv) combining coordination free energy profiles with electronic structure analysis. Phys Chem Chem Phys 2014; 16:5824-32. [DOI: 10.1039/c3cp54958e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Wiedemair MJ, Weiss AKH, Rode BM. Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation. Phys Chem Chem Phys 2014; 16:7368-76. [DOI: 10.1039/c3cp54986k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Moin ST, Hofer TS. Hydration of porphyrin and Mg–porphyrin: ab initio quantum mechanical charge field molecular dynamics simulations. ACTA ACUST UNITED AC 2014; 10:117-27. [DOI: 10.1039/c3mb70300b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Eklund L, Hofer TS, Weiss AKH, Tirler AO, Persson I. Structure and water exchange of the hydrated thiosulfate ion in aqueous solution using QMCF MD simulation and large angle X-ray scattering. Dalton Trans 2014; 43:12711-20. [DOI: 10.1039/c4dt01010h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Experimental and simulation data of the thiosulfate ion show large similarities in hydration structure and mechanism with the sulfate ion but with weaker hydration of the terminal sulfur atom in thiosulfate.
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Affiliation(s)
- Lars Eklund
- Department of Chemistry and Biotechnology
- Swedish University of Agricultural Sciences
- SE-750 07 Uppsala, Sweden
| | - Tomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck, Austria
| | - Andreas O. Tirler
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck, Austria
| | - Ingmar Persson
- Department of Chemistry and Biotechnology
- Swedish University of Agricultural Sciences
- SE-750 07 Uppsala, Sweden
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49
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Tirler AO, Weiss AKH, Hofer TS. A Comparative Quantum Mechanical Charge Field Study of Uranyl Mono- and Dicarbonate Species in Aqueous Solution. J Phys Chem B 2013; 117:16174-87. [DOI: 10.1021/jp407179s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas O. Tirler
- Theoretical Chemistry Division, Institute
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Alexander K. H. Weiss
- Theoretical Chemistry Division, Institute
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical Chemistry Division, Institute
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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50
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Canaval LR, Sakwarathorn T, Rode BM, Messner CB, Lutz OMD, Bonn GK. Erbium(III) in aqueous solution: an ab initio molecular dynamics study. J Phys Chem B 2013; 117:15151-6. [PMID: 24251538 DOI: 10.1021/jp410284z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Structural and dynamical properties of the erbium(III) ion in water have been obtained by means of ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulations for the ground state and an excited state. The quality of the simulations has been monitored by recording UV/vis and Raman spectra of dilute solutions of ErCl3 and Er(NO3)3 in water and by comparison with EXAFS data from literature. Slight deviations between these data can be mainly attributed to relativistic effects, which are not sufficiently considered by the methodological framework. In both simulations, a mixture of coordination numbers eight and nine and a ligand exchange on the picosecond range are observed. The strength of the Er-ligand bond is considerably lower than that of trivalent transition metal ions but higher than that for La(III) and Ce(III) in aqueous solution. The main difference between ground state and excited state is the ligand exchange rate of the first shell. The second hydration shell is stable in both cases but with significantly different properties.
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Affiliation(s)
- Lorenz R Canaval
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 80-82, A-6020 Innsbruck, Austria
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