1
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Vennelakanti V, Li GL, Kulik HJ. Why Nonheme Iron Halogenases Do Not Fluorinate C-H Bonds: A Computational Investigation. Inorg Chem 2023; 62:19758-19770. [PMID: 37972340 DOI: 10.1021/acs.inorgchem.3c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Grace L Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Priyadarsini A, Mallik BS. Structure and rotational dynamics of water around hydrogen peroxide. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Biswas A, Mallik BS. Conformational dynamics of aqueous hydrogen peroxide from first principles molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:28286-28296. [PMID: 33295373 DOI: 10.1039/d0cp05451h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We performed first principles molecular dynamics simulations of a relatively dilute aqueous hydrogen peroxide (H2O2) solution to examine its structural alterations and relevant dynamics upon solvation. The internal rotation of the OH groups about the O-O bond facilitates the flexible structure of H2O2. Structural calculations reveal dihedral angle fluctuations in the aqueous solution. Water molecules make stronger hydrogen bonds through the hydrogen atom of the solute than the oxygen atom leading to distinct hydrogen bonding configurations inside the first solvation shell. Time-dependent dihedral angle alterations result in conformational changes and the normalized dihedral angle distribution plot displays characteristic peaks at ∼100-120° and ∼230°, illustrating various conformational states. Within the simulation time, flexibility-induced interconversion of hydrogen peroxide gives rise to several cisoid and transoid conformers. In this study, we examine the relative population of the associated conformational states and the lifetime of the cisoid and transoid conformers from the torsion angle variations. We also determine the free energy landscape of the rotational isomerization process in H2O2 and explore two distinct energy barriers during such interconversion.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy - 502285, Telangana, India.
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4
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Shi H, Gong LD, Liu C, Lu LN, Yang ZZ. ABEEM/MM OH - Models for OH -(H 2O) n Clusters and Aqueous OH -: Structures, Charge Distributions, and Binding Energies. J Phys Chem A 2020; 124:5963-5978. [PMID: 32520555 DOI: 10.1021/acs.jpca.0c03941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH--water system were proposed. The difference between these two models is whether there is charge transfer between OH- and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH-(H2O)n (n = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods. The results demonstrate that two ABEEM/MM models can search out all stable structures just as the QM methods, and the structures and charge distributions agree well with those from the QM calculations. The structures, the charge transfer, and the strength of hydrogen bonds in the first hydration shell are closely related to the coordination number of OH-. Molecular dynamics simulations on the aqueous OH- solution are performed at 298 and 278 K using ABEEM/MM-I model. The MD results show that the populations of three-, four-, and five-coordinated OH- are 29.6%, 67.1%, and 3.4% at 298 K, respectively, and those of two-, three-, four-, and five-coordinated OH- are 10.8%, 44.9%, 39.2%, and 4.9% at 278 K, respectively; the average hydrogen bond lengths and the hydrogen bond angle in the first shell increase with the temperature decreasing.
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Affiliation(s)
- Hua Shi
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.,School of Marine Science and Environment, Dalian Ocean University, Dalian 116023, People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
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5
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Li H, Wang D, Zhao X, Lu LN, Liu C, Gong LD, Zhao DX, Yang ZZ. Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method. J Comput Chem 2019; 40:1141-1150. [PMID: 30375671 DOI: 10.1002/jcc.25734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 11/06/2022]
Abstract
Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states. The Ru-N-O angle of the triplet ruthenium nitrosyl complexes is in the range of 132.0°-138.2°. However, all the ruthenium nitrosyl complexes at the singlet state show an almost linear Ru-N-O angle. The nitrosylation reaction happens prior to the hydrolysis reaction for the first-step hydrolysates. The activation free energies of the nitrosylation reactions show that the H2 O-NO exchange reaction of [RuCl4 (Im)(H2 O)] in the singlet spin sate is the most likely one. Comparing with the activation free energies of the hydrolysis reactions of the ruthenium nitrosyl complexes, the results indicate that the rate of the DMSO-H2 O exchange reaction of [RuCl3 (NO)(Im)(DMSO)] is faster than that of [RuCl3 (H2 O)(Im)(DMSO)] in both the triplet spin state and the singlet spin state. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Hui Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China.,Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Di Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Xin Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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6
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Trumm M. On the isotropy of induced multipole moments in heavy ion complexes. J Comput Chem 2017; 39:373-379. [DOI: 10.1002/jcc.25121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/09/2017] [Accepted: 11/07/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Trumm
- Institute for nuclear waste disposal (INE), Karlsruhe Institute of Technology (KIT), Postfach 3640; Karlsruhe D-76021 Germany
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7
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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8
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Fast calculation of molecular total energy with ABEEMσπ/MM method – For some series of organic molecules and peptides. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Mohorič T, Hribar-Lee B, Vlachy V. Effects of the translational and rotational degrees of freedom on the hydration of simple solutes. J Chem Phys 2015; 140:184510. [PMID: 24832291 DOI: 10.1063/1.4875280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations with separate thermostats for rotational and translational motion were used to study the effect of these degrees of freedom on the structure of water around model solutes. To describe water molecules we used the SPC/E model. The simplest solute studied here, the hydrophobe, was represented as a Lennard-Jones particle. Since direct interaction between the hydrophobe and water molecules has no angular dependence the influence of the increase of the rotational temperature on the solvation of a hydrophobe is only indirect. In the next step the central solute was assumed to be charged with either a positive or a negative charge to mimic an ion in water. Hence, depending on the charge of the ion, the neighboring water molecules assumed different angular distributions. The principal conclusions of this work are: (i) an increase of the translational temperature always decreases the height of the first peak in the solute-water radial distribution function; (ii) an increase of the rotational temperature yields an increase in the first peak in the solute-water radial distribution function for hydrophobes and cations; (iii) in contrast to this, the solvation peak decreases around ions with sufficiently large negative charge; and (iv) an increase of the rotational temperature affects cations in an opposite way to anions. For this reason complex molecules with a small net charge may not be very sensitive to variation of the rotational temperature.
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Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
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10
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Yang ZZ, Wang JJ, Zhao DX. Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field. J Comput Chem 2014; 35:1690-706. [DOI: 10.1002/jcc.23676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/01/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Jian-Jiang Wang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
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11
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Turchenkov DA, Boronovsky SE, Nartsissov YR. Model of ion diffusion in synaptic cleft based on stochastical integration of langevin equation at dielectric friction approximation. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913060195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Lu LN, Liu C, Gong LD. Microhydration of alanine in gas phase studied by quantum chemical method and ABEEMσπ/MM fluctuating charge model. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Development and applications of the ABEEM fluctuating charge molecular force field in the ion-containing systems. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4787-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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14
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Mg2+/Ca2+ binding to DNA bases: a quantum chemical method and ABEEMσπ/MM fluctuating charge model study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1098-x] [Citation(s) in RCA: 4] [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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Trumm M, Martínez YOG, Réal F, Masella M, Vallet V, Schimmelpfennig B. Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: The case of the halide ions F−, Cl−, and Br−. J Chem Phys 2012; 136:044509. [DOI: 10.1063/1.3678294] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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16
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Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11458-011-0259-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Liu C, Zhao DX, Yang ZZ. Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system. J Comput Chem 2011; 33:379-90. [PMID: 22170234 DOI: 10.1002/jcc.21975] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 09/15/2011] [Accepted: 09/28/2011] [Indexed: 11/11/2022]
Abstract
The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.
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Affiliation(s)
- Cui Liu
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, China
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18
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LIU CUI, ZHAO DONGXIA, YANG ZHONGZHI. ABEEMσπ FLUCTUATING CHARGE FORCE FIELD APPLIED TO ALANINE DIPEPTIDE AND ALANINE DIPEPTIDE–WATER SYSTEMS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610005530] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Atom-bond electronegativity equalization method at σπ level fused into molecular mechanics (ABEEMσπ/MM) divides the bond regions into σ and π bond regions on the basis of previous ABEEM/MM. It may suitably reflect intramolecular and intermolecular interaction and polarization. The fitting function k H-bond in the hydrogen bond (HB) interaction region increases the capability of ABEEMσπ/MM to simulate the hydration. Hydration of alanine dipeptide (AD) in aqueous solution is determined by the intramolecular and intermolecular HBs and the competition among the molecular packing effects. The acceptor molecule in HB complex contains at least one pair of lone pair electrons, sometimes contains π bonds, whose orientations directly effect the orientation of HBs. Therefore, ABEEMσπ/MM has obviously predominance to discuss the AD and AD–water systems, which contain many lone pair electrons, π bonds, and abundant HB nets. Properties of six AD conformers, clusters AD +( H2O )1–4 obtained from ABEEMσπ/MM agree well with the results of experiments, ab initio and other force fields. Structural and dynamical properties of the hydration water molecules have just embodied that the ABEEMσπ/MM gives correct hydration description relative to other force fields.
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Affiliation(s)
- CUI LIU
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian City, Liaoning Province 116029, P. R. China
| | - DONG-XIA ZHAO
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian City, Liaoning Province 116029, P. R. China
| | - ZHONG-ZHI YANG
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian City, Liaoning Province 116029, P. R. China
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GUAN QINGMEI, HAN YAN, YANG ZHONGZHI. MOLECULAR DYNAMICS STUDIES ON Fe2+, Co2+, AND Ni2+ AQUEOUS SOLUTIONS BASED ON ABEEM/MM FLUCTUATING CHARGE MODEL. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608004519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), the intermolecular potential for transition metal ion Fe 2+, Co 2+, and Ni 2+ cations in water has been derived. Parameters for the effective interaction between a cation and a water molecule were determined by reproducing the ab initio results. Many structural and dynamic properties of Fe 2+(aq.), Co 2+(aq.), and Ni 2+(aq.) were studied using these potential parameters. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of alkali metal and alkaline-earth metal cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of transition metal cations in water.
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Affiliation(s)
- QING-MEI GUAN
- Department of Chemistry, Fuyang Teachers College, Fuyang 236041, PR China
| | - YAN HAN
- Department of Chemistry, Fuyang Teachers College, Fuyang 236041, PR China
| | - ZHONG-ZHI YANG
- Department of Chemistry, Liaoning Normal University, Dalian 116029, PR China
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QI SHIFEI, WANG XIAONAN, YANG ZHONGZHI. INSIGHT INTO MECHANISM OF FORMATION OF C8 ADDUCTS IN CARCINOGENIC REACTIONS OF ARYLNITRENIUM IONS WITH PURINE NUCLEOSIDES II: AB INITIO, DFT, AND ABEEM/MM-MD SIMULATION STUDIES OF CHEMICAL REACTIONS CONCERNING N9-SUBSTITUTED PURINE BASES WITH 4-BIPHENYLYLNITRENIUM ION. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609005222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Theoretical insight into the mechanism of C8 adducts formation in a series of complicated carcinogenic reactions has been provided in a previous work. However, two important issues involved in this mechanism still need to be elucidated in detail. Hence, in this paper, we first present a new theoretical model to study the direct formation mechanism of C8 adduct. It is found that this model can well reflect the actual interactions in the real carcinogenic reactions. Thus, a better theoretical model to simulate other properties of these complicated reactions is found using ab initio and density functional theory (DFT) methods. Second, we simulate the formation process of C8 adduct in this new theoretical model using ABEEM/MM-MD method. According to the MD study, we approve that the higher aqueous-phase activation energy for transition state in this kind of reaction contributes to weaker interactions between central sites of reaction and water compared with those for reactants. This study once more supports the mechanism of formation of C8 adducts in the actual carcinogenic reactions where arylnitrenium ions directly attack at C8 positions of nucleoside bases in DNA.
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Affiliation(s)
- SHI-FEI QI
- School of Chemistry and Materials Science, Shanxi Normal University, Linfen, 041004, P. R. China
| | - XIAO-NAN WANG
- School of Chemistry and Materials Science, Shanxi Normal University, Linfen, 041004, P. R. China
| | - ZHONG-ZHI YANG
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, P. R. China
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21
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Zhao DX, Yu L, Gong LD, Liu C, Yang ZZ. Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model. J Chem Phys 2011; 134:194115. [DOI: 10.1063/1.3590718] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Caleman C, Hub JS, van Maaren PJ, van der Spoel D. Atomistic simulation of ion solvation in water explains surface preference of halides. Proc Natl Acad Sci U S A 2011; 108:6838-6842. [PMCID: PMC3084043 DOI: 10.1073/pnas.1017903108] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
Water is a demanding partner. It strongly attracts ions, yet some halide anions—chloride, bromide, and iodide—are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl-, Br-, and I- have shallow minima near the surface. We demonstrate that these minima derive from more favorable water–water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion–water energy, whereas F- is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.
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Affiliation(s)
- Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany; and
| | - Jochen S. Hub
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-75 124 Uppsala, Sweden
| | - Paul J. van Maaren
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-75 124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-75 124 Uppsala, Sweden
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23
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Qi SF, Wang XN, Yang ZZ, Xu XH. Evidence of direct formation of C8 adducts in carcinogenic reactions of arylnitrenium ions with purine nucleosides: Theoretical study of C8 deprotonation process. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.01.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Yu CY, Yang ZZ. A Systemic Investigation of Hydrogen Peroxide Clusters (H2O2)n (n = 1−6) and Liquid-State Hydrogen Peroxide: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics and Molecular Dynamics. J Phys Chem A 2011; 115:2615-26. [DOI: 10.1021/jp111284t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chun-Yang Yu
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, China
| | - Zhong-Zhi Yang
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, China
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25
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Chen SL, Zhao DX, Yang ZZ. An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method. J Comput Chem 2010; 32:338-48. [PMID: 20662079 DOI: 10.1002/jcc.21625] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Shu-Ling Chen
- School of Chemistry and chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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26
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Chen S, Yang Z. Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMδπ/MM). CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Qian P, Lu LN, Yang ZZ. Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model. CAN J CHEM 2009. [DOI: 10.1139/v09-134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.
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Affiliation(s)
- Ping Qian
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, P.R.China
- Chemistry and Chemical Engineering Falculty, Liaoning Normal University, Dalian 116029, P.R.China
| | - Li-Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, P.R.China
- Chemistry and Chemical Engineering Falculty, Liaoning Normal University, Dalian 116029, P.R.China
| | - Zhong-Zhi Yang
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, P.R.China
- Chemistry and Chemical Engineering Falculty, Liaoning Normal University, Dalian 116029, P.R.China
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28
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Zwolak M, Lagerqvist J, Di Ventra M. Quantized ionic conductance in nanopores. PHYSICAL REVIEW LETTERS 2009; 103:128102. [PMID: 19792463 PMCID: PMC2989414 DOI: 10.1103/physrevlett.103.128102] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Indexed: 05/19/2023]
Abstract
Ionic transport in nanopores is a fundamentally and technologically important problem in view of its occurrence in biological processes and its impact on novel DNA sequencing applications. Using molecular dynamics simulations we show that ion transport may exhibit strong nonlinearities as a function of the pore radius reminiscent of the conductance quantization steps as a function of the transverse cross section of quantum point contacts. In the present case, however, conductance steps originate from the break up of the hydration layers that form around ions in aqueous solution. We discuss this phenomenon and the conditions under which it should be experimentally observable.
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Affiliation(s)
- Michael Zwolak
- Theoretical Division, MS-B213, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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29
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Wang FF, Gong LD, Zhao DX. Studies on the torsions of nucleic acids using ABEEMσπ/MM method. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Lopes PEM, Roux B, MacKerell AD. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc 2009; 124:11-28. [PMID: 20577578 PMCID: PMC2888514 DOI: 10.1007/s00214-009-0617-x] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.
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Affiliation(s)
- Pedro E. M. Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21230, USA
| | - Benoit Roux
- Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago 929 E. 57th St. Chicago, IL 60637
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21230, USA
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31
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Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0592-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11426-008-0129-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Vaillancourt FH, Yeh E, Vosburg DA, Garneau-Tsodikova S, Walsh CT. Nature's inventory of halogenation catalysts: oxidative strategies predominate. Chem Rev 2007; 106:3364-78. [PMID: 16895332 DOI: 10.1021/cr050313i] [Citation(s) in RCA: 402] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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34
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Geerke DP, van Gunsteren WF. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters. J Phys Chem B 2007; 111:6425-36. [PMID: 17508737 DOI: 10.1021/jp0706477] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The lack of an explicit description of electronic polarization in nonpolarizable force fields usually results in an incomplete transferability of force-field parameter sets when applied in simulations of the system of interest in either a polar or an apolar environment. For example, the use of nonpolarizable parameter sets optimized to reproduce experimental data on properties of pure liquids of polar compounds commonly yields too low solubilities in water for the corresponding compounds. The reason is that the fixed charge distributions calibrated for the pure liquid might correspond to too low molecular dipole moments in case of hydration. In the current study, we quantitatively show that explicit inclusion of electronic polarization can improve the transferability of biomolecular force-field parameter sets. With this aim, free energies of polarization, DeltaGpola, have been calculated, with DeltaGpola corresponding to the free energy difference between identical systems described by a polarizable and a nonpolarizable model. Using a nonpolarizable model and a polarizable one (based on the charge-on-spring approach) for dimethyl ether (DME), which were both parametrized to reproduce experimental values for pure liquid properties, small values were found for DeltaGpola for the pure liquid or when a DME solute was solvated in the apolar solvent cyclohexane. For the solute hydrated in water, however, DeltaGpola was found to be of the same order of magnitude as the discrepancy between the free energy of hydration from simulation using a nonpolarizable solute model and the experimental value. Thus, introducing polarizabilities clearly improves the transferability of the parameter set. Additionally, in calculations of an anion solvated in DME, DeltaGpola for the solvent adopted relatively large values. From an estimation of the errors in the calculated free energy differences, it was furthermore shown that the calculation of DeltaGpola offers an effective and accurate method to obtain differences in solvation (or excess) free energies between systems described by polarizable and nonpolarizable models when compared to a direct calculation of solvation (or excess) free energies.
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Affiliation(s)
- Daan P Geerke
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH, CH-8093 Zürich, Switzerland
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35
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Application of the ABEEM/MM model in studying the properties of the water clusters (H2O) n (n=7−10). ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11426-007-0003-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Yang ZZ, Qian P. A study of N-methylacetamide in water clusters: Based on atom-bond electronegativity equalization method fused into molecular mechanics. J Chem Phys 2006; 125:64311. [PMID: 16942290 DOI: 10.1063/1.2210940] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.
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Affiliation(s)
- Zhong-Zhi Yang
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, People's Republic of China.
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37
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Correa A, Cavallo L. Dynamic Properties of Metallocenium Ion Pairs in Solution by Atomistic Simulations. J Am Chem Soc 2006; 128:10952-9. [PMID: 16910692 DOI: 10.1021/ja062407v] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a molecular dynamics study of the dynamics and energetic of the [H(2)Si(Cp)(2)ZrMe(+)][MeB(C(6)F(5))(3)(-)], IP1, and [Me(2)Si(Cp)(2)ZrMe(+)][B(C(6)F(5))(4)(-)], IP2, ion pairs in benzene. The metrical parameters obtained for the IP1 ion pair are in excellent agreement with the NMR data reported for the strictly related [Me(2)Si(Cp)(2)ZrMe(+)][MeB(C(6)F(5))(3)(-)] ion pair (J. Am. Chem. Soc. 2004, 126, 1448). This validates the molecular modeling protocol we developed. Simulation of the IP2 ion pair suggests that the counterion oscillates between two geometries characterized by a different coordination pattern of the F atoms to the Zr cation. In one case the B(C(6)F(5))(4)(-) coordinates to the metal with two F atoms of the same aryl ring, whereas in the other case two F atoms of different aryl rings are involved in the coordination. Strong solvent reorganization occurs around IP1 and IP2, as well as around the two isolated cations. In the case of the two ion pairs solvent is never coordinated directly to the metal, whereas in the absence of the counterion one benzene molecule is coordinated to the metal through a cation-pi interaction. Free energy calculations result in ion pair free energies of separation of 36.8 and 23.3 kcal/mol for IP1 and IP2, respectively. Simulations with the Zr-B distance fixed at values > 7 A have been also performed. This mimics the situation occurring after counterion displacement by an inserting monomer molecule during olefin polymerization by the title catalysts.
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Affiliation(s)
- Andrea Correa
- Dipartimento di Chimica, Università di Salerno, Via Salvador Allende, Baronissi (SA), I-84081, Italy
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38
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Vareková RS, Koca J. Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J Comput Chem 2006; 27:396-405. [PMID: 16381078 DOI: 10.1002/jcc.20344] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The most common way to calculate charge distribution in a molecule is ab initio quantum mechanics (QM). Some faster alternatives to QM have also been developed, the so-called "equalization methods" EEM and ABEEM, which are based on DFT. We have implemented and optimized the EEM and ABEEM methods and created the EEM SOLVER and ABEEM SOLVER programs. It has been found that the most time-consuming part of equalization methods is the reduction of the matrix belonging to the equation system generated by the method. Therefore, for both methods this part was replaced by the parallel algorithm WIRS and implemented within the PVM environment. The parallelized versions of the programs EEM SOLVER and ABEEM SOLVER showed promising results, especially on a single computer with several processors (compact PVM). The implemented programs are available through the Web page http://ncbr.chemi.muni.cz/~n19n/eem_abeem.
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Affiliation(s)
- R Svobodová Vareková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic
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