1
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Turan HT, Meuwly M. Local Hydration Control and Functional Implications Through S-Nitrosylation of Proteins: Kirsten Rat Sarcoma Virus (K-RAS) and Hemoglobin (Hb). J Phys Chem B 2023; 127:1526-1539. [PMID: 36757772 DOI: 10.1021/acs.jpcb.2c07371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification (PTM) that can affect the function of proteins. As such, PTMs extend and diversify protein function and thus characterizing consequences of PTM at a molecular level is of great interest. Although PTMs can be detected through various direct/indirect methods, they lack the capability to investigate the modifications with molecular detail. In the present work local and global structural dynamics, their correlation, the hydration structure, and the infrared spectroscopy for WT and S-nitrosylated Kirsten rat sarcoma virus (K-RAS) and hemoglobin (Hb) are characterized from molecular dynamics simulations. It is found that attaching NO to Cys118 in K-RAS rigidifies the protein in the Switch-I region which has functional implications, whereas for Hb, nitrosylation at Cys93 at the β1 chain increases the flexibility of secondary structural motives for Hb in its T0 and R4 conformational substates. Solvent water access decreased by 40% after nitrosylation in K-RAS, similar to Hb for which, however, local hydration of the R4SNO state is yet lower than for T0SNO. Finally, S-nitrosylation leads to detectable peaks for the NO stretch frequency, but the congested IR spectral region will make experimental detection of these bands difficult. Overall, S-nitrosylation in these two proteins is found to influence hydration, protein flexibility, and conformational dynamics which are all eventually involved in protein regulation and function at a molecular level.
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Affiliation(s)
- Haydar Taylan Turan
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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2
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Turan HT, Meuwly M. Spectroscopy, Dynamics, and Hydration of S-Nitrosylated Myoglobin. J Phys Chem B 2021; 125:4262-4273. [PMID: 33724027 DOI: 10.1021/acs.jpcb.0c10353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
S-Nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation in the condensed phase are investigated for the methyl-capped cysteine model system and for myoglobin. Using conventional point charge and physically more realistic multipolar force fields for the -SNO group, it is found that the SN- and NO-stretch and the SNO-bend vibrations can be located and distinguished from the other protein modes for simulations of MbSNO at 50 K. The finding of stable cis- and trans-MbSNO agrees with experimental findings on other proteins as is the observation of buried -SNO. For MbSNO the observed relocation of the EF loop in the simulations by ∼3 Å is consistent with the available X-ray structure, and the conformations adopted by the -SNO label are in good overall agreement with the X-ray structure. Despite the larger size of the -SNO group compared with -SH, MbSNO recruits more water molecules in the first two hydration shells due to stronger electrostatic interactions. Similarly, when comparing the hydration between the A- and H-helices, they differ by up to 30% between WT and MbSNO. This suggests that local hydration can also be significantly modulated through nitrosylation.
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Affiliation(s)
- Haydar Taylan Turan
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland
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3
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Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk. J Phys Chem B 2019; 123:9846-9861. [PMID: 31647873 DOI: 10.1021/acs.jpcb.9b03258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular mechanics with proton transfer (MMPT) force field is combined with multistate adiabatic reactive molecular dynamics (MS-ARMD) to describe proton transport in the condensed phase. Parametrization for small protonated water clusters based on electronic structure calculations at the MP2/6-311+G(2d,2p) level of theory and refinement by comparing with infrared spectra for a protonated water tetramer yields a force field which faithfully describes the minimum energy structures of small protonated water clusters. In protonated water clusters up to (H2O)100H+, the proton hopping rate is around 100 hops/ns. This rate converges for 21 ≤ n ≤ 31, and no further speedup in bulk water is found. This indicates that bulklike behavior requires the solvation of a Zundel motif by ∼25 water molecules, which corresponds to the second solvation sphere. For smaller cluster sizes, the number of available states (i.e., the number of proton acceptors) is too small and slows down proton-transfer rates. The cluster simulations confirm that the excess proton is typically located on the surface. The free-energy surface as a function of the weights of the two lowest states and a configurational parameter suggests that the "special pair" plays a central role in rapid proton transport. The barriers between this minimum-energy structure and the Zundel and Eigen minima are sufficiently low (∼1 kcal/mol, consistent with recent experiments and commensurate with a hopping rate of ∼100/ns or 1 every 10 ps), leading to a highly dynamic environment. These findings are also consistent with recent experiments which find that Zundel-type hydration geometries are prevalent in bulk water.
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4
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Antipov SV, Bhattacharyya S, El Hage K, Xu ZH, Meuwly M, Rothlisberger U, Vaníček J. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061509. [PMID: 29376107 PMCID: PMC5758379 DOI: 10.1063/1.4996559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.
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Affiliation(s)
- Sergey V Antipov
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Swarnendu Bhattacharyya
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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5
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Xu ZH, Meuwly M. Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate. J Phys Chem A 2017; 121:5389-5398. [PMID: 28597659 DOI: 10.1021/acs.jpca.7b02234] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics and infrared spectroscopic signatures of proton transfer in protonated oxalate (p-Oxa) are studied using classical and quantum dynamics. The intermolecular interactions are described by a force field suitable to follow proton transfer. This allows to carry out multiple extended classical molecular dynamics (MD) and ring polymer MD simulations from which the infrared spectrum is determined. Simulations at 600 K sample the quantum mechanical ground state probability distribution and best reproduce the experimentally observed maximum absorption wavelength and part of the line shape. Comparison with the experimentally measured spectrum provides an estimate for the barrier height for proton transfer which can not be determined directly from experiment. A barrier of 4.2 kcal/mol is found to best reproduce the position and width of the infrared absorption of the transferring proton in p-Oxa and also leads to an infrared (IR) spectrum in good agreement with experiment for the deuterated species d-Oxa. A novel means to capture the two resonance forms of oxalate depending on the localization of the excess proton on either CO moiety is found to yield improved results for the spectroscopy in the framework region between 1000 and 2000 cm-1.
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Affiliation(s)
- Zhen-Hao Xu
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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6
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Pitsevich G, Malevich A, Kozlovskaya E, Mahnach E, Doroshenko I, Pogorelov V, Pettersson LGM, Sablinskas V, Balevicius V. MP4 Study of the Anharmonic Coupling of the Shared Proton Stretching Vibration of the Protonated Water Dimer in Equilibrium and Transition States. J Phys Chem A 2017; 121:2151-2165. [PMID: 28187260 DOI: 10.1021/acs.jpca.7b00536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure and harmonic and anharmonic IR spectra of the protonated water dimer (PWD) were calculated in C1, C2, and Cs symmetry at the MP4/acc-pVTZ level of theory. We found that structure and IR spectra are practically identical in C2 and C1 symmetry, demonstrating that an equilibrium C1 configuration of the PWD is not realized. Anharmonic coupling of the shared proton stretching vibration with all other modes in the PWD in C2 and Cs symmetry was the focus of this investigation. For this purpose, 28 two-dimensional potential energy surfaces (2D PES) were built at the MP4/acc-pVTZ level of theory and the corresponding vibrational Schrödinger equations were solved using the DVR method. Differences in the coupling of the investigated mode with other modes in the C2 and Cs configurations, along with some factors that determine the red- or blue-shift of the stretching vibration frequency, were analyzed. We obtained a rather reasonable value of the stretching frequency of the bridging proton (1058.4 cm-1) unperturbed by Fermi resonance. The Fermi resonance between the fundamental vibration ν7 and the combined vibration ν2 + ν6 of the same symmetry was analyzed through anharmonic second-order perturbation theory calculations, as well as by 3D PES constructed using Q2, Q6, and Q7 as normal coordinates. A significant (up to 50%) transfer of intensity from the fundamental vibration to the combined one was found. We have estimated the frequency of the bridging proton stretching vibration in the Cs configuration of the PWD based on calculations of the intrinsic anharmonicity and anharmonic double modes interactions at the MP4/acc-pVTZ level of theory (1261 cm-1).
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Affiliation(s)
- G Pitsevich
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - A Malevich
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - E Kozlovskaya
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - E Mahnach
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - I Doroshenko
- Taras Shevchenko National University of Kyiv , Volodymyrska str., 64\13, 01601, Kyiv, Ukraine
| | - V Pogorelov
- Taras Shevchenko National University of Kyiv , Volodymyrska str., 64\13, 01601, Kyiv, Ukraine
| | - Lars G M Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University , S-106 91 Stockholm, Sweden
| | - V Sablinskas
- Faculty of Physics, Vilnius University , Sauletekio al. 9-3, LT-10222 Vilnius, Lithuania
| | - V Balevicius
- Faculty of Physics, Vilnius University , Sauletekio al. 9-3, LT-10222 Vilnius, Lithuania
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7
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Mackeprang K, Xu ZH, Maroun Z, Meuwly M, Kjaergaard HG. Spectroscopy and dynamics of double proton transfer in formic acid dimer. Phys Chem Chem Phys 2016; 18:24654-62. [PMID: 27545453 DOI: 10.1039/c6cp03462d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We present the isolated gas phase infrared spectra of formic acid dimer, (HCOOH)2, and its deuterated counterpart formic-d acid, (DCOOH)2, at room temperature. The formic acid dimer spectrum was obtained by spectral subtraction of a spectrum of formic acid vapor recorded at low pressure from that recorded at a higher pressure. The spectra of formic acid vapor contain features from both formic acid monomer and formic acid dimer, but at low and high pressures of formic acid, the equilibrium is pushed towards the monomer and dimer, respectively. A similar approach was used for the formic-d acid dimer. Building on the previous development of the Molecular Mechanics with Proton Transfer (MMPT) force field for simulating proton transfer reactions, molecular dynamics (MD) simulations were carried out to interpret the experimental spectra in the OH-stretching region. Within the framework of MMPT, a combination of symmetric single and double minimum potential energy surfaces (PESs) provides a good description of the double proton transfer PES. In a next step, potential morphing together with electronic structure calculations at the B3LYP and MP2 level of theory was used to align the computed and experimentally observed spectral features in the OH-stretching region. From this analysis, a barrier for double proton transfer between 5 and 7 kcal mol(-1) was derived, which compares with a CCSD(T)/aug-cc-pVTZ calculated barrier of 7.9 kcal mol(-1). Such a combination of experimental and computational techniques for estimating barriers for proton transfer in gas phase systems is generic and holds promise for further improved PESs and energetics of these important systems. Additional MD simulations at the semi-empirical DFTB level of theory agree quite well for the center band position but underestimate the width of the OH-stretching band.
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Affiliation(s)
- Kasper Mackeprang
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
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8
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Soloviov M, Meuwly M. Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin. J Chem Phys 2016; 143:105103. [PMID: 26374062 DOI: 10.1063/1.4929527] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, the Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe-ON and Fe-NO state is significantly affected whether or not this co-ordinate is explicitly included. Although the Fe-ON conformation is metastable when considering only the bound (2)A state, it may disappear once the (4)A state is included. This explains the absence of the Fe-ON state in previous experimental investigations of MbNO.
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Affiliation(s)
- Maksym Soloviov
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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9
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Schmid FFF, Meuwly M. Direct Comparison of Experimental and Calculated NMR Scalar Coupling Constants for Force Field Validation and Adaptation. J Chem Theory Comput 2015; 4:1949-58. [PMID: 26620337 DOI: 10.1021/ct800241d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to measure scalar coupling constants across hydrogen bonds ((3h)JNC') from high-resolution NMR experiments allows the characterization of detailed structural properties of biomolecules. To analyze those, a parametrized model based on the linear combination of atomic orbitals relates H-bond geometries with the measured (3h)JNC' coupling magnitude. In the present study the dependence of calculated (3h)JNC' coupling constants on force field parameters is assessed. It is shown that increased polarity of the hydrogen bond improves the calculated (3h)JNC' coupling constants and shifts the conformational ensemble sampled from the molecular dynamics (MD) simulations toward the experimentally measured one. Increased charges lead to more narrow distance and angle distributions and improve the agreement between calculated and measured (3h)JNC' couplings. However, different secondary structures are better represented by different magnitudes of electrostatic interactions-different atomic partial charges in the present work-as indicated by root-mean square deviations (rsmds) between observed and calculated coupling constants (3h)JNC'. The parametrization of the empirical formula is found to be meaningful and robust, but the parameter values are not universal across different proteins and different secondary structural elements (α-helices, β-sheets and loops). Using standard and slightly increased CHARMM charges, predictions for the as-yet unknown scalar coupling constants for the V54A and I6A mutants of protein G are made.
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Affiliation(s)
- Franziska F-F Schmid
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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10
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Huang J, Meuwly M. Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins. J Chem Theory Comput 2015; 6:467-76. [PMID: 26617302 DOI: 10.1021/ct9005695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bonds (H bonds) are fundamental for the stability, structure, and dynamics of chemically and biologically relevant systems. One of the direct means to detect H bonds in proteins is NMR spectroscopy. As H bonds are dynamic in nature, atomistic simulations offer a meaningful way to characterize and analyze properties of hydrogen bonds, provided a sufficiently accurate interaction potential is available. Here, we use explicit H-bond potentials to investigate scalar coupling constants (h3)JNC' and characterize the conformational ensemble for increasingly accurate intermolecular potentials. By considering a range of proteins with different overall topology a general procedure to improve the hydrogen-bonding potential ("morphing potentials") based on experimental information is derived. The robustness of this approach is established through explicit simulations in full solvation and comparison with experimental results. The H-bond potentials used here lead to more directional H bonds than conventional electrostatic representations employed in molecular mechanics potentials. It is found that the optimized potentials lead to H-bond geometries in remarkable agreement with previous ab initio and knowledge-based approaches to H bonds in model systems and in proteins. This suggests that, by combining theory, computation, and experimental data, H-bonding potentials can be improved and are potentially useful to better study coupling, energy transfer, and allosteric communication in proteins.
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Affiliation(s)
- Jing Huang
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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11
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Howard DL, Kjaergaard HG, Huang J, Meuwly M. Infrared and Near-Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone. J Phys Chem A 2015; 119:7980-90. [DOI: 10.1021/acs.jpca.5b01863] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daryl L. Howard
- Australian Synchrotron, 800 Blackburn
Road, Clayton, Victoria 3168, Australia
- Department
of Chemistry, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand
| | - Henrik G. Kjaergaard
- Department
of Chemistry, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Jing Huang
- Department
of Pharmaceutical Science, University of Maryland, Baltimore, Maryland 21201, United States
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
- Department
of Chemistry, Brown University, Providence, Rhode Island 01912, United States
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12
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Spura T, Elgabarty H, Kühne TD. “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer. Phys Chem Chem Phys 2015; 17:14355-9. [DOI: 10.1039/c4cp05192k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.
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Affiliation(s)
- Thomas Spura
- Department of Chemistry
- University of Paderborn
- D-33098 Paderborn
- Germany
| | - Hossam Elgabarty
- Institute for Physical Chemistry
- University of Mainz
- D-55128 Mainz
- Germany
| | - Thomas D. Kühne
- Department of Chemistry
- University of Paderborn
- D-33098 Paderborn
- Germany
- Institute for Physical Chemistry
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13
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Huang J, Häussinger D, Gellrich U, Seiche W, Breit B, Meuwly M. Hydrogen-Bond and Solvent Dynamics in Transition Metal Complexes: A Combined Simulation and NMR-Investigation. J Phys Chem B 2012; 116:14406-15. [DOI: 10.1021/jp309412r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jing Huang
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland, and
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland, and
| | - Urs Gellrich
- Institute
für Organische
Chemie und Biochemie, Albert-Ludwigs-Unversität, Freiburg, Germany
| | - Wolfgang Seiche
- Institute
für Organische
Chemie und Biochemie, Albert-Ludwigs-Unversität, Freiburg, Germany
| | - Bernhard Breit
- Institute
für Organische
Chemie und Biochemie, Albert-Ludwigs-Unversität, Freiburg, Germany
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland, and
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14
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Cazade PA, Huang J, Yosa J, Szymczak JJ, Meuwly M. Atomistic simulations of reactive processes in the gas- and condensed-phase. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.694694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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16
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Lee MW, Plattner N, Meuwly M. Structure, spectroscopy and dynamics of layered H2O and CO2 ices. Phys Chem Chem Phys 2012; 14:15464-74. [PMID: 23072896 DOI: 10.1039/c2cp41904a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Myung Won Lee
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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17
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Lutz S, Tubert-Brohman I, Yang Y, Meuwly M. Water-assisted proton transfer in ferredoxin I. J Biol Chem 2011; 286:23679-87. [PMID: 21531725 DOI: 10.1074/jbc.m111.230003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The role of water molecules in assisting proton transfer (PT) is investigated for the proton-pumping protein ferredoxin I (FdI) from Azotobacter vinelandii. It was shown previously that individual water molecules can stabilize between Asp(15) and the buried [3Fe-4S](0) cluster and thus can potentially act as a proton relay in transferring H(+) from the protein to the μ(2) sulfur atom. Here, we generalize molecular mechanics with proton transfer to studying proton transfer reactions in the condensed phase. Both umbrella sampling simulations and electronic structure calculations suggest that the PT Asp(15)-COOH + H(2)O + [3Fe-4S](0) → Asp(15)-COO(-) + H(2)O + [3Fe-4S](0) H(+) is concerted, and no stable intermediate hydronium ion (H(3)O(+)) is expected. The free energy difference of 11.7 kcal/mol for the forward reaction is in good agreement with the experimental value (13.3 kcal/mol). For the reverse reaction (Asp(15)-COO(-) + H(2)O + [3Fe-4S](0)H(+) → Asp(15)-COOH + H(2)O + [3Fe-4S](0)), a larger barrier than for the forward reaction is correctly predicted, but it is quantitatively overestimated (23.1 kcal/mol from simulations versus 14.1 from experiment). Possible reasons for this discrepancy are discussed. Compared with the water-assisted process (ΔE ≈ 10 kcal/mol), water-unassisted proton transfer yields a considerably higher barrier of ΔE ≈ 35 kcal/mol.
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Affiliation(s)
- Stephan Lutz
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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18
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Yang Y, Meuwly M. A generalized reactive force field for nonlinear hydrogen bonds: hydrogen dynamics and transfer in malonaldehyde. J Chem Phys 2010; 133:064503. [PMID: 20707571 DOI: 10.1063/1.3447701] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using molecular dynamics (MD) simulations, the spectroscopy and dynamics of malonaldehyde is investigated. To this end, the recently proposed molecular mechanics with proton transfer (MMPT) potential is generalized to nonlinear hydrogen bonds. The calculated properties for malonaldehyde in both gas and condensed phases, including equilibrium geometries, infrared spectra, tunneling splittings, and hydrogen transfer rates, compare well with previous experimental and computational works. In particular, by using a harmonic bath averaged (HBA) Hamiltonian, which is based on a reaction path Hamiltonian, it is possible to estimate the tunneling splitting in an efficient manner. It is found that a zero point corrected barrier of 6.7 kcal/mol and effective masses of 1.234 (i.e., 23.4% larger than the mass of a physical H-atom) and 1.117 (for the physical D-atom) are consistent with the measured splittings of 21.6 and 2.9 cm(-1), respectively. The HBA Hamiltonian also yields a pair of hydrogen transfer fundamentals at 1573 and 1267 cm(-1), similar to results obtained with a reaction surface Hamiltonian on a MP2/6-31G(**) potential energy surface. This amounts to a substantial redshift of more than 1000 cm(-1) which can be rationalized by comparison with weakly (HCO(+): rare gas) and strongly (H(2)O-H(+)-OH(2)) proton-bound systems. Hydrogen transfer rates in vacuum and water were determined from the validated MMPT potential and it is found that the solvent enhances the rate by a factor of 5 at 300 K. The rates of 2.4/ns and 10/ns are commensurate with previous density functional tight binding ab initio MD studies.
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Affiliation(s)
- Yonggang Yang
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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Kaminski S, Gaus M, Phatak P, von Stetten D, Elstner M, Mroginski MA. Vibrational Raman Spectra from the Self-Consistent Charge Density Functional Tight Binding Method via Classical Time-Correlation Functions. J Chem Theory Comput 2010. [DOI: 10.1021/ct900660x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steve Kaminski
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany, Universität Karlsruhe, Institut für Theoretische Chemie, Kaiserstrasse 12, D-76131 Karlsruhe, Germany, and Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405
| | - Michael Gaus
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany, Universität Karlsruhe, Institut für Theoretische Chemie, Kaiserstrasse 12, D-76131 Karlsruhe, Germany, and Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405
| | - Prasad Phatak
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany, Universität Karlsruhe, Institut für Theoretische Chemie, Kaiserstrasse 12, D-76131 Karlsruhe, Germany, and Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405
| | - David von Stetten
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany, Universität Karlsruhe, Institut für Theoretische Chemie, Kaiserstrasse 12, D-76131 Karlsruhe, Germany, and Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405
| | - Marcus Elstner
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany, Universität Karlsruhe, Institut für Theoretische Chemie, Kaiserstrasse 12, D-76131 Karlsruhe, Germany, and Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany, Universität Karlsruhe, Institut für Theoretische Chemie, Kaiserstrasse 12, D-76131 Karlsruhe, Germany, and Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405
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Lammers S, Lutz S, Meuwly M. Reactive force fields for proton transfer dynamics. J Comput Chem 2008; 29:1048-63. [PMID: 18072179 DOI: 10.1002/jcc.20864] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A force field-inspired method based on fitted, high-quality multidimensional potential energy surfaces to follow proton transfer (PT) reactions in molecular dynamics simulations is presented. In molecular mechanics with proton transfer (MMPT) a system is partitioned into a region where proton transfer takes place and the remaining degrees of freedom which are treated with a conventional force field. The implementation of the method and applications to specific chemically and biologically relevant scenarios are presented. MMPT is developed in view of two primary areas in mind: to follow the molecular dynamics of proton transfer in the condensed phase on realistic time scales and to adapt the shape (morphing) of the potential energy surface for specific applications. MMPT is applied to PT in protonated ammonia dimer, double proton transfer in 2-pyridone-2-hydroxypyridine, and the first step of PT from a protein side-chain towards a buried [3Fe4S] cluster in ferredoxin I. Specific findings of the work include the fundamental role of the N-N vibration as the gating mode for PT in NH4+...NH3 and the qualitative understanding of PT from the protein to a metastable active-site water molecule in Ferredoxin I.
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Affiliation(s)
- Sven Lammers
- Chemistry Department, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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