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Cummins PL, Kannappan B, Gready JE. Revised mechanism of carboxylation of ribulose-1,5-biphosphate by rubisco from large scale quantum chemical calculations. J Comput Chem 2018; 39:1656-1665. [PMID: 29756365 DOI: 10.1002/jcc.25343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/06/2023]
Abstract
Here, we describe a computational approach for studying enzymes that catalyze complex multi-step reactions and apply it to Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5-step carboxylase reaction, the substrate Ribulose-1,5-bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2 . Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation. However, details of the roles and protonation states of active-site residues, and sources of protons and water, remain highly speculative. Large-scale computations on active-site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi-empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO2 complex and associated active-site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO2 ; both hydration and CC bond scission require early protonation of CO2 in the RuBP.CO2 complex; CC bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3-gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis-Menten-like complex corresponding to the empirical Km (=Kc ) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Peter L Cummins
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Babu Kannappan
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
| | - Jill E Gready
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, 0200, Australia
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Goyal P, Qian HJ, Irle S, Lu X, Roston D, Mori T, Elstner M, Cui Q. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B 2014; 118:11007-27. [PMID: 25166899 PMCID: PMC4174991 DOI: 10.1021/jp503372v] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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Bergonzo C, Galindo-Murillo R, Cheatham TE. Molecular modeling of nucleic acid structure: energy and sampling. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; 54:7.8.1-7.8.21. [PMID: 24510800 DOI: 10.1002/0471142700.nc0708s54] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.
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Affiliation(s)
- Christina Bergonzo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
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Cojocaru C, Rotaru A, Harabagiu V, Sacarescu L. Molecular structure and electronic properties of pyridylindolizine derivative containing phenyl and phenacyl groups: Comparison between semi-empirical calculations and experimental studies. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.08.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sparta M, Shirvanyants D, Ding F, Dokholyan NV, Alexandrova AN. Hybrid dynamics simulation engine for metalloproteins. Biophys J 2013; 103:767-76. [PMID: 22947938 DOI: 10.1016/j.bpj.2012.06.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 06/08/2012] [Accepted: 06/18/2012] [Indexed: 11/15/2022] Open
Abstract
Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins' structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca(2+) form of the enzyme catechol O-methyl transferase, which, unlike the native Mg(2+) form, is catalytically inactive. The Mg(2+) site is ochtahedral, but the Ca(2+) is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight.
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Affiliation(s)
- Manuel Sparta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
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Alonso H, Cummins PL, Gready JE. Methyltetrahydrofolate:corrinoid/iron−sulfur Protein Methyltransferase (MeTr): Protonation State of the Ligand and Active-Site Residues. J Phys Chem B 2009; 113:14787-96. [DOI: 10.1021/jp900181g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Peter L. Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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Pentikäinen U, Shaw KE, Senthilkumar K, Woods CJ, Mulholland AJ. Lennard−Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases. J Chem Theory Comput 2009; 5:396-410. [DOI: 10.1021/ct800135k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulla Pentikäinen
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Katherine E. Shaw
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Kittusamy Senthilkumar
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Christopher J. Woods
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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Lomas JS, Maurel F. Water and alcohol(s): what's the difference? A proton NMR and DFT study of hetero-association with pyridine. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1351] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Geerke DP, Thiel S, Thiel W, van Gunsteren WF. QM–MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians. Phys Chem Chem Phys 2008; 10:297-302. [DOI: 10.1039/b713197f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Lin H, Truhlar DG. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. J Phys Chem A 2007; 109:3991-4004. [PMID: 16833721 DOI: 10.1021/jp0446332] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Special care is needed in carrying out combined quantum mechanical and molecular mechanical (QM/MM) calculations if the QM/MM boundary passes through a covalent bond. The present paper discusses the importance of correctly handling the MM partial point charges at the QM/MM boundary, and in particular, it contributes in two aspects: (1) Two schemes, namely, the redistributed charge (RC) scheme and the redistributed charge and dipole (RCD) scheme, are introduced to handle link atoms in QM/MM calculations. In both schemes, the point charge at the MM boundary atom that is replaced by the link atom is redistributed to the midpoint of the bonds that connect the MM boundary atom and its neighboring MM atoms. These redistributed charges serve as classical mimics for the auxiliary orbitals associated with the MM host atom in the generalized hybrid orbital (GHO) method. In the RCD scheme, the dipoles of these bonds are preserved by further adjustment of the values of the redistributed charges. The treatments are justified as classical analogues of the QM description given by the GHO method. (2) The new methods are compared quantitatively to similar methods that were suggested by previous work, namely, a shifted-charge scheme and three eliminated-charge schemes. The comparisons were carried out for a series of molecules in terms of proton affinities and geometries. Point charges derived from various charge models were tested. The results demonstrate that it is critical to preserve charge and bond dipole and that it is important to use accurate MM point charges in QM/MM boundary treatments. The RCD scheme was further applied to study the H atom transfer reaction CH3 + CH3CH2CH2OH --> CH4 + CH2CH2CH2OH. Various QM levels of theory were tested to demonstrate the generality of the methodology. It is encouraging to find that the QM/MM calculations obtained a reaction energy, barrier height, saddle-point geometry, and imaginary frequency at the saddle point in quite good agreement with full QM calculations at the same level. Furthermore, analysis based on energy decomposition revealed the quantitatively similar interaction energies between the QM and the MM subsystems for the reactant, for the saddle point, and for the product. These interaction energies almost cancel each other energetically, resulting in negligibly small net effects on the reaction energy and barrier height. However, the charge distribution of the QM atoms is greatly affected by the polarization effect of the MM point charges. The QM/MM charge distribution agrees much better with full QM results than does the unpolarized charge distribution of the capped primary subsystem.
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Affiliation(s)
- Hai Lin
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
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11
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Zhang Y, Lin H, Truhlar DG. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. J Chem Theory Comput 2007; 3:1378-98. [DOI: 10.1021/ct7000107] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Zhang
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Hai Lin
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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12
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Cummins PL, Rostov IV, Gready JE. Calculation of a Complete Enzymic Reaction Surface: Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase. J Chem Theory Comput 2007; 3:1203-11. [DOI: 10.1021/ct600313b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Ivan V. Rostov
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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Vchirawongkwin V, Hofer TS, Randolf BR, Rode BM. Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water. J Comput Chem 2007; 28:1057-67. [PMID: 17279549 DOI: 10.1002/jcc.20486] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Classical molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) MD simulations have been performed to investigate the structural and dynamical properties of the Tl(III) ion in water. A six-coordinate hydration structure with a maximum probability of the Tl-O distance at 2.21 A was observed, which is in good agreement with X-ray data. The librational and vibrational spectra of water molecules in the first hydration shell are blue-shifted compared with those of pure liquid water, and the Tl-O stretching force constant was evaluated as 148 Nm(-1). Both structural and dynamical properties show a distortion of the first solvation shell structure. The second shell ligands' mean residence time was determined as 12.8 ps. The Tl(III) ion can be classified as "structure forming" ion; the calculated hydration energy of -986 +/- 9 kcal mol agrees well with the experimental value of -986 kcal mol.
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Affiliation(s)
- Viwat Vchirawongkwin
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Lin H, Zhao Y, Tishchenko O, Truhlar DG. Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations. J Chem Theory Comput 2006; 2:1237-54. [DOI: 10.1021/ct600171u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hai Lin
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Yan Zhao
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Oksana Tishchenko
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
| | - Donald G. Truhlar
- Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Chemistry Department, University of Colorado at Denver and Health Science Center, Denver, Colorado 80217-3364
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Nagaoka M, Nagae Y, Koyano Y, Oishi Y. Transition-State Characterization of the Ammonia Ionization Process in Aqueous Solution via the Free-Energy Gradient Method. J Phys Chem A 2006; 110:4555-63. [PMID: 16571063 DOI: 10.1021/jp056115c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the ionization process of ammonia in aqueous solution, the transition-state (TS) structure was fully optimized for the first time on the free-energy surface (FES) by applying the free-energy gradient (FEG) method combined with a hybrid quantum mechanical and molecular mechanical molecular dynamics (QM/MM-MD) method. In aqueous solution, the ionization process was found to proceed by way of a clear TS (R(N1-H5) = 1.512 A), which does not exist in the gas phase. The free-energy (FE) of activation for ionization obtained was 14.7 kcal/mol, within the classical approximation, via the QM/MM-MD FEG method, and is found to be in good agreement with 9.57 kcal/mol estimated from the TS theory using the experimental value of the rate constant. Apart from the dynamic correction, it is indicated that the theoretical value would be improved to be 10.28 kcal/mol if the electronic-state calculation could be executed at the B3LYP/6-31G(d) level of theory.
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Affiliation(s)
- Masataka Nagaoka
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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Stevenson SA, Blanchard GJ. Dynamics of 4-benzylamino-7-nitrobenzofurazan in the 1-propanol/water binary solvent system. Evidence for composition-dependent solvent organization. J Phys Chem A 2006; 110:3426-31. [PMID: 16526621 DOI: 10.1021/jp057039g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the fluorescence lifetime and rotational diffusion dynamics of 4-benzylamino-7-nitrobenzofurazan (BBD) in a series of 1-propanol/water binary solvent systems. The fluorescence lifetime of BBD increases monotonically with increasing 1-propanol concentration. The rotational diffusion dynamics of BBD also vary with solution 1-propanol content, but this variation is not monotonic. Comparison of the BBD rotational diffusion time constant to solution viscosity and 1-propanol composition reveals the presence of a solution composition dependence of solvent-solute interactions, with a relative decrease in solvent-solute interaction strength for solvent system compositions where the 1-propanol/water azeotrope is known to exist. These data point collectively to the existence of microscopic heterogeneity in these binary solvent systems.
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Affiliation(s)
- Sarah A Stevenson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, USA
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Pu J, Gao J, Truhlar DG. Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. Chemphyschem 2005; 6:1853-65. [PMID: 16086343 PMCID: PMC4481131 DOI: 10.1002/cphc.200400602] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Indexed: 11/06/2022]
Abstract
The generalized hybrid orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary hybrid orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham orbitals are satisfied by carrying out the hybridization in terms of a set of Löwdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.
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Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
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Cummins PL, Gready JE. Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation. J Comput Chem 2005; 26:561-8. [PMID: 15726569 DOI: 10.1002/jcc.20192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree-Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical PM3 method to model the QM region, the application of this PQA/MM method is illustrated by calculation of the relative protonation free energy of the conserved OD2 (Asp27) and the N5 (dihydrofolate) proton acceptor sites in the active site of Escherichia coli dihydrofolate reductase (DHFR) with the bound nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. For a number of choices for the QM region, the relative protonation free energy was calculated as the sum of contributions from the QM region and the interaction between the QM and MM regions via the thermodynamic integration (TI) method. The results demonstrate the importance of including the whole substrate molecule in the QM region, and the overall protein (MM) environment in determining the relative stabilities of protonation sites in the enzyme active site. The PQA/MM free energies obtained by TI were also compared with those estimated by a less computationally demanding nonperturbative method based on the linear response approximation (LRA). For some choices of QM region, the total free energies calculated using the LRA method were in very close agreement with the PQA/MM values. However, the QM and QM/MM component free energies were found to differ significantly between the two methods.
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Affiliation(s)
- Peter L Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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Rode BM, Schwenk CF, Tongraar A. Structure and dynamics of hydrated ions—new insights through quantum mechanical simulations. J Mol Liq 2004. [DOI: 10.1016/j.molliq.2003.09.016] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Pu J, Gao J, Truhlar DG. Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics. J Phys Chem A 2004. [DOI: 10.1021/jp036755k] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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Vener MV, Leontyev IV, Basilevsky MV. Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular–continuum approach. J Chem Phys 2003. [DOI: 10.1063/1.1605945] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nagae Y, Oishi Y, Naruse N, Nagaoka M. Hydrated structure of ammonia–water molecule pair via the free energy gradient method: Realization of zero gradient and force balance on free energy surfaces. J Chem Phys 2003. [DOI: 10.1063/1.1610436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Computational methods for the study of enzymic reaction mechanisms. II. An overlapping mechanically embedded method for hybrid semi-empirical-QM/MM calculations. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00303-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Loferer MJ, Loeffler HH, Liedl KR. A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems. J Comput Chem 2003; 24:1240-9. [PMID: 12820132 DOI: 10.1002/jcc.10283] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.
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Affiliation(s)
- Markus J Loferer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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27
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Kritayakornupong C, Rode BM. Molecular dynamics simulations of Hg2+ in aqueous solution includingN-body effects. J Chem Phys 2003. [DOI: 10.1063/1.1553761] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Tongraar A, Michael Rode B. The hydration structures of F−and Cl−investigated by ab initio QM/MM molecular dynamics simulations. Phys Chem Chem Phys 2003. [DOI: 10.1039/b209240a] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Titmuss SJ, Cummins PL, Rendell AP, Bliznyuk AA, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis. J Comput Chem 2002; 23:1314-22. [PMID: 12214314 DOI: 10.1002/jcc.10122] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.
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Affiliation(s)
- Stephen J Titmuss
- Computational Proteomics and Therapy Design Group, Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601, Australia
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30
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An iterative procedure to determine Lennard-Jones parameters for their use in quantum mechanics/molecular mechanics liquid state simulations. Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00785-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Cummins PL, Greatbanks SP, Rendell AP, Gready JE. Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase. J Phys Chem B 2002. [DOI: 10.1021/jp021070q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Stephen P. Greatbanks
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Alistair P. Rendell
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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32
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Laio A, VandeVondele J, Rothlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations. J Chem Phys 2002. [DOI: 10.1063/1.1462041] [Citation(s) in RCA: 521] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Hirao H, Nagae Y, Nagaoka M. Transition-state optimization by the free energy gradient method: Application to aqueous-phase Menshutkin reaction between ammonia and methyl chloride. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01131-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Tongraar A, Sagarik K, Rode BM. Effects of Many-Body Interactions on the Preferential Solvation of Mg2+ in Aqueous Ammonia Solution: A Born−Oppenheimer ab Initio QM/MM Dynamics Study. J Phys Chem B 2001. [DOI: 10.1021/jp012103p] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Kritsana Sagarik
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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35
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Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: energy and sampling. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2001; Chapter 7:Unit-7.8. [PMID: 18428876 PMCID: PMC4029503 DOI: 10.1002/0471142700.nc0708s04] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT 7.5) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.
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36
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Cichos F, Brown R, Bopp PA. Coupled molecular dynamics/semiempirical simulation of organic solutes in polar liquids. I. Naphthalene in acetonitrile. J Chem Phys 2001. [DOI: 10.1063/1.1351875] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Castillo R, Andrés J, Moliner V. Quantum Mechanical/Molecular Mechanical Study on the Favorskii Rearrangement in Aqueous Media. J Phys Chem B 2001. [DOI: 10.1021/jp003264g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- R. Castillo
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - V. Moliner
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
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Tongraar A, Rode BM. A Born−Oppenheimer Ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation on Preferential Solvation of Na+ in Aqueous Ammonia Solution. J Phys Chem A 2000. [DOI: 10.1021/jp003395h] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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40
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Orozco M, Luque FJ. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem Rev 2000; 100:4187-4226. [PMID: 11749344 DOI: 10.1021/cr990052a] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, E-08028 Barcelona, Spain, and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal s/n, E-08028 Barcelona, Spain
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41
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Luque FJ, Reuter N, Cartier A, Ruiz-López MF. Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods. J Phys Chem A 2000. [DOI: 10.1021/jp001974g] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. J. Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain
| | - N. Reuter
- Unité de Recherche CNRS-UHP 7565, Laboratoire de Chimie Théorique, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - A. Cartier
- Unité de Recherche CNRS-UHP 7565, Laboratoire de Chimie Théorique, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - M. F. Ruiz-López
- Unité de Recherche CNRS-UHP 7565, Laboratoire de Chimie Théorique, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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42
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Chalmet S, Ruiz-López MF. New approaches to the description of short-range repulsion interactions in hybrid quantum/classical systems. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00992-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Svanberg M, Pettersson JBC, Bolton K. Coupled QM/MM Molecular Dynamics Simulations of HCl Interacting with Ice Surfaces and Water Clusters − Evidence of Rapid Ionization. J Phys Chem A 2000. [DOI: 10.1021/jp0012698] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcus Svanberg
- Department of Chemistry, Physical Chemistry, Göteborg University, SE-412 96 Göteborg, Sweden, School of Engineering, University of Borås, SE-501 90 Borås, Sweden, and School of Environmental Sciences, Göteborg University, SE-412 96 Göteborg, Sweden
| | - Jan B. C. Pettersson
- Department of Chemistry, Physical Chemistry, Göteborg University, SE-412 96 Göteborg, Sweden, School of Engineering, University of Borås, SE-501 90 Borås, Sweden, and School of Environmental Sciences, Göteborg University, SE-412 96 Göteborg, Sweden
| | - Kim Bolton
- Department of Chemistry, Physical Chemistry, Göteborg University, SE-412 96 Göteborg, Sweden, School of Engineering, University of Borås, SE-501 90 Borås, Sweden, and School of Environmental Sciences, Göteborg University, SE-412 96 Göteborg, Sweden
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44
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Cummins PL, Gready JE. Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase. J Phys Chem B 2000. [DOI: 10.1021/jp993153l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| | - Jill E. Gready
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
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45
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Titmuss SJ, Cummins PL, Bliznyuk AA, Rendell AP, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00215-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Cummins PL, Gready JE. QM/MM and SCRF studies of the ionization state of 8-methylpterin substrate bound to dihydrofolate reductase: existence of a low-barrier hydrogen bond. J Mol Graph Model 2000; 18:42-9. [PMID: 10935206 DOI: 10.1016/s1093-3263(00)00034-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Using combined semiempirical quantum mechanics and molecular mechanics (QM/MM) and ab initio self-consistent reaction field (SCRF) calculations, we determined that a low-barrier hydrogen bond (LBHB) is formed when the mechanism-based substrate 8-methylpterin binds to dihydrofolate reductase (DHFR). The substrate initially was assumed bound either in the ion-pair form corresponding to N3-protonated substrate hydrogen (H) bonded to the unprotonated (carboxylate) of the conserved Glu30 residue in the active site, or in the neutral-pair form corresponding to unprotonated substrate H bonded to the neutral (carboxylic acid) from of Glu30. The free energy of interaction of these H-bonded systems with the protein/solvent surroundings was computed using a coordinate-coupled free energy perturbation (FEP) method implemented within the molecular dynamics (MD) simulation scheme and using a semiempirical (PM3) QM/MM force field. The free energy obtained from the QM/MM force-field simulations corresponds most closely with the corresponding free energy component obtained from HF/6-31G* SCRF calculations using a value of 2 for the dielectric constant (epsilon) for the solvated protein. Calculations were performed at levels ranging from HF/6-31G to MP2/6-31G* to B3LYP/6-31 + G**, with varying dielectric constants. The energy-minimized path for motion of the proton in the H bond along a one-dimensional reaction coordinate was calculated at HF/6-31G, HF/6-31G* (epsilon = 1) and B3LYP/6-31G* (epsilon = 2) levels. These calculations identified a second neutral-pair complex, involving the 2-amino group of substrate, which also interacts with Glu30, which is lower in energy than the ion-pair form. A harmonic vibrational analysis shows that the first vibrational state appears to lie near or above the TS connecting potential energy minima corresponding to the two neutral-pair configurations, thus indicating an LBHB. Consequently, the H-bonded system will have a significant probability of being found in the ion-pair form, in agreement with experimental spectral studies indicating an enzyme-bound cation and suggesting that the LBHB would activate substrate towards hydride-ion transfer from NADPH.
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Affiliation(s)
- P L Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra, Australia
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47
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Marini GW, Liedl KR, Rode BM. Investigation of Cu2+ Hydration and the Jahn−Teller Effect in Solution by QM/MM Monte Carlo Simulations. J Phys Chem A 1999. [DOI: 10.1021/jp992015t] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gerhard W. Marini
- Department of Theoretical Chemistry, Institute for General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of Theoretical Chemistry, Institute for General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- Department of Theoretical Chemistry, Institute for General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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48
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Antes I, Thiel W. Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods. J Phys Chem A 1999. [DOI: 10.1021/jp991771w] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iris Antes
- Organisch-chemisches Institut, Universität Zürich,Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Walter Thiel
- Organisch-chemisches Institut, Universität Zürich,Winterthurerstrasse 190, 8057 Zürich, Switzerland
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49
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Tongraar A, Rode BM. Preferential Solvation of Li+ in 18.45 Aqueous Ammonia: A Born−Oppenheimer ab Initio Quantum Mechanics/Molecular Mechanics MD Simulation. J Phys Chem A 1999. [DOI: 10.1021/jp991580t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute for General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52 a, A-6020 Innsbruck, Austria
| | - Bernd M. Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute for General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52 a, A-6020 Innsbruck, Austria
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50
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Cummins PL, Gready JE. Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(19990730)20:10<1028::aid-jcc5>3.0.co;2-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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