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Zhang J, Yan Y, Wang B, Liu L, Li S, Tian Z, Ouyang C, Gu J, Zhang X, Chen Y, Han J, Zhang W. Water dynamics in the hydration shell of hyper-branched poly-ethylenimine. Phys Chem Chem Phys 2022; 24:18393-18400. [PMID: 35880732 DOI: 10.1039/d2cp01944b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We performed THz and GHz dielectric relaxation spectroscopy to investigate the reorientational dynamics of water molecules in the hydration shell of amphiphilic hyper-branched poly-ethylenimine (HPEI). Four Debye equations were employed to describe four types of water in the hydration shell, including bulk-like water, under-coordinated water, slow water (water molecules hydrating the hydrophobic groups and water molecules accepting hydrogen bonds from the NH2 groups) and super slow water (water molecules donating hydrogen bonds to and accepting hydrogen bonds from NH groups). The time scales of undercoordinated and bulk-like water show a slight decline from 0.4 to 0.1 ps and from 8 to 2 ps, respectively. Because of hydrophilic amino groups, HPEI molecules exhibit a strong retardation effect, where the time scales of slow and super slow water increase with concentration from 17 to 39.9 ps and from 88 to 225 ps, respectively.
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Affiliation(s)
- Jiaqi Zhang
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Yuyue Yan
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Bin Wang
- Tianjin Engineering Technology Center of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University, Tianjin 300072, People's Republic of China
| | - Liyuan Liu
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Shaoxian Li
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Zhen Tian
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Chunmei Ouyang
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Jianqiang Gu
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Xueqian Zhang
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Yu Chen
- Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, School of Sciences, Tianjin University, Tianjin 300354, China
| | - Jiaguang Han
- Centre for Terahertz Waves and College of Precision Instrument and Optoeletronics Engineering, Tianjin University, Tinajin 300072, People's Republic of China.
| | - Weili Zhang
- School of Electrical and Computer Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, USA.
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Zhang F, Yu L, Zhang W, Liu L, Wang C. A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly. RSC Adv 2021; 11:28667-28673. [PMID: 35478591 PMCID: PMC9038178 DOI: 10.1039/d1ra05463e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures. Accumulating evidence leads to a hypothesis that the hydrophobicity of a nonpolar patch of a molecule is non-additive and susceptible to the chemical context of a judicious polar patch. However, the quantification of the hydrophobic interaction at the nanoscale remains a central challenge to validate the hypothesis. In this review, we aim to outline the recent efforts made to determine the hydrophobic interaction at a nanoscopic length scale. The advances achieved in the understanding of proximal polar groups perturbing the magnitude of hydrophobic interaction generated by the nonpolar patch are introduced. We will also discuss the influence of chemical heterogeneity on the modulation of amphiphilic peptide/protein assembly and molecular recognition. Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures.![]()
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Affiliation(s)
- Feiyi Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Lei Liu
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
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3
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Ma S, Hwang S, Lee S, Acree WE, No KT. Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model. J Chem Inf Model 2018; 58:761-772. [PMID: 29561152 DOI: 10.1021/acs.jcim.7b00410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described as compared to that of the G-SFED model.
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Affiliation(s)
- Songling Ma
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea.,Bioinformatics and Molecular Design Research Center , Seoul 120-749 , Korea
| | - Sungbo Hwang
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea
| | - Sehan Lee
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea.,Gulf Ecology Division , U.S. Environmental Protection Agency , Gulf Breeze , Florida 32561 , United States
| | - William E Acree
- Department of Chemistry , University of North Texas , 1155 Union Circle Drive #305070 , Denton , Texas 76230-5017 , United States
| | - Kyoung Tai No
- Department of Biotechnology , Yonsei University , Seoul 120-749 , Korea.,Bioinformatics and Molecular Design Research Center , Seoul 120-749 , Korea
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4
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Wang C, Ma CKD, Yeon H, Wang X, Gellman SH, Abbott NL. Nonadditive Interactions Mediated by Water at Chemically Heterogeneous Surfaces: Nonionic Polar Groups and Hydrophobic Interactions. J Am Chem Soc 2017; 139:18536-18544. [DOI: 10.1021/jacs.7b08367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chenxuan Wang
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chi-Kuen Derek Ma
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Hongseung Yeon
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Xiaoguang Wang
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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5
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Farrokhpour H, Manassir M. A Simple Method for Estimating the Absolute Solvation Free Energy of Monovalent Ions in Different Solvents. J Phys Chem A 2014; 119:160-71. [DOI: 10.1021/jp509177g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hossein Farrokhpour
- Chemistry
Department, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Mohammad Manassir
- Chemistry
Department, Isfahan University of Technology, 84156-83111, Isfahan, Iran
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6
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A generalized G-SFED continuum solvation free energy calculation model. Proc Natl Acad Sci U S A 2013; 110:E662-7. [PMID: 23378634 DOI: 10.1073/pnas.1221940110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An empirical continuum solvation model, solvation free energy density (SFED), has been developed to calculate solvation free energies of a molecule in the most frequently used solvents. A generalized version of the SFED model, generalized-SFED (G-SFED), is proposed here to calculate molecular solvation free energies in virtually any solvent. G-SFED provides an accurate and fast generalized framework without a complicated description of a solution. In the model, the solvation free energy of a solute is represented as a linear combination of empirical functions of the solute properties representing the effects of solute on various solute-solvent interactions, and the complementary solvent effects on these interactions were reflected in the linear expansion coefficients with a few solvent properties. G-SFED works well for a wide range of sizes and polarities of solute molecules in various solvents as shown by a set of 5,753 solvation free energies of diverse combinations of 103 solvents and 890 solutes. Octanol-water partition coefficients of small organic compounds and peptides were calculated with G-SFED with accuracy within 0.4 log unit for each group. The G-SFED computation time depends linearly on the number of nonhydrogen atoms (n) in a molecule, O(n).
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7
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Rubinson KA, Meuse CW. Deep hydration: Poly(ethylene glycol) Mw 2000–8000 Da probed by vibrational spectrometry and small-angle neutron scattering and assignment of ΔG° to individual water layers. POLYMER 2013. [DOI: 10.1016/j.polymer.2012.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Ratkova EL. A semiempirical model for estimating the hydration free energy of neutral nonpolar compounds. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412100196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Ma SL, Joung JY, Lee S, Cho KH, No KT. PXR ligand classification model with SFED-weighted WHIM and CoMMA descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:485-504. [PMID: 22591167 DOI: 10.1080/1062936x.2012.665385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Understanding which type of endogenous and exogenous compounds serve as agonists for the nuclear pregnane X receptor (PXR) would be valuable for drug discovery and development, because PXR regulates a large number of genes related to xenobiotic metabolism. Although several models have been proposed to classify human PXR activators and non-activators, models with better predictability are necessary for practical purposes in drug discovery. Grid-weighted holistic invariant molecular (G-WHIM) and comparative molecular moment analysis (G-CoMMA) type 3D descriptors that contain information about the solvation free energy of target molecules were developed. With these descriptors, prediction models built using decision tree (DT)-, support vector machine (SVM)-, and Kohonen neural network (KNN)-based models exhibited better predictability than previously proposed models. Solvation free energy density-weighted G-WHIM and G-CoMMA descriptors reveal new insights into PXR ligand classification, and incorporation with machine learning methods (DT, SVM, KNN) exhibits promising results, especially SVM and KNN. SVM- and KNN-based models exhibit accuracy around 0.90, and DT-based models exhibit accuracy around 0.8 for both the training and test sets.
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Affiliation(s)
- S L Ma
- Department of Biotechnology, Yonsei University, Seoul, Korea
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10
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Joung JY, Nam KY, Cho KH, No KT. Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors. J Chem Inf Model 2012; 52:984-95. [DOI: 10.1021/ci200501p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jong Young Joung
- Department
of Biotechnology, Yonsei University, Seoul
120-749, Republic of Korea
- Bioinformatics & Molecular Design Research Center, Seoul 120-749, Republic of Korea
| | - Ky-Youb Nam
- Bioinformatics & Molecular Design Research Center, Seoul 120-749, Republic of Korea
| | - Kwang-Hwi Cho
- School of Systems Biomedical Science and CAMD Research Center, Soongsil University, Seoul 156-743, Republic of Korea
| | - Kyoung Tai No
- Department
of Biotechnology, Yonsei University, Seoul
120-749, Republic of Korea
- Translational Research Center for Protein Function Control, Seoul 120-749,
Republic of Korea
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11
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Lee S, Cho KH, Acree WE, No KT. Development of Surface-SFED Models for Polar Solvents. J Chem Inf Model 2012; 52:440-8. [DOI: 10.1021/ci2004913] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sehan Lee
- Department of Biotechnology,
Yonsei University, Seoul, 120-749, Korea
| | - Kwang-Hwi Cho
- Department of Bioinformatics,
Soongsil University, Seoul, 156-743, Korea
| | - William E. Acree
- Department of Chemistry, University
of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76230-5017,
United
States
| | - Kyoung Tai No
- Department of Biotechnology,
Yonsei University, Seoul, 120-749, Korea
- Bioinformatics and
Molecular
Design Research Center, Seoul, 120-749, Korea
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12
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Lee S, Cho KH, Lee CJ, Kim GE, Na CH, In Y, No KT. Calculation of the solvation free energy of neutral and ionic molecules in diverse solvents. J Chem Inf Model 2010; 51:105-14. [PMID: 21133372 DOI: 10.1021/ci100299m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvation free energy density (SFED) model was modified to extend its applicability and predictability. The parametrization process was performed with a large, diverse set of solvation free energies that included highly polar and ionic molecules. The mean absolute error for 1200 solvation free energies of the 379 neutral molecules in 9 organic solvents and water was 0.40 kcal/mol, and for 90 hydration free energies of ions was 1.7 kcal/mol. Overall, the calculated solvation free energies of a wide range of solute functional groups in diverse solvents were consistent with experimental data.
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Affiliation(s)
- Sehan Lee
- Department of Biotechnology, Yonsei University, Seoul 120-749, Korea
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13
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Ratkova EL, Chuev GN, Sergiievskyi VP, Fedorov MV. An Accurate Prediction of Hydration Free Energies by Combination of Molecular Integral Equations Theory with Structural Descriptors. J Phys Chem B 2010; 114:12068-79. [DOI: 10.1021/jp103955r] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ekaterina L. Ratkova
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Gennady N. Chuev
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Volodymyr P. Sergiievskyi
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Maxim V. Fedorov
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
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14
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Katritzky AR, Kuanar M, Slavov S, Hall CD, Karelson M, Kahn I, Dobchev DA. Quantitative Correlation of Physical and Chemical Properties with Chemical Structure: Utility for Prediction. Chem Rev 2010; 110:5714-89. [DOI: 10.1021/cr900238d] [Citation(s) in RCA: 386] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Minati Kuanar
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Svetoslav Slavov
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - C. Dennis Hall
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Mati Karelson
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Iiris Kahn
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Dimitar A. Dobchev
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
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15
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Parameterization of an empirical model for the prediction of n-octanol, alkane and cyclohexane/water as well as brain/blood partition coefficients. J Comput Aided Mol Des 2008; 23:105-11. [DOI: 10.1007/s10822-008-9243-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 09/02/2008] [Indexed: 11/27/2022]
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16
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Miličević A, Raos N. Estimation of stability constants of copper(II) chelates with triamines and their mixed complexes with amino acids by using topological indices and the overlapping spheres method. Polyhedron 2007. [DOI: 10.1016/j.poly.2007.03.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Theoretical Study on Hydrophobicity of Amino Acids by the Solvation Free Energy Density Model. B KOREAN CHEM SOC 2003. [DOI: 10.5012/bkcs.2003.24.12.1742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Investigation of some amino acids conformations at the interface of binary mixture using the solvation free energy density model. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)01335-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Abstract
A novel empirical model is presented that allows the fast computation of hydration free energies with high accuracy. The linear model is based upon the separation of the free energy of hydration into a cavity and an interaction term. The cavity contribution is modeled as a linear combination of molecular volume and surface terms. The interaction part is derived from the statistical three-dimensional (3D) free energy density and is modeled approximately as a molecular interaction field using the program GRID. A compression scheme is employed to represent this 3D information on the molecular surface by means of a linear combination of surface functions. A set of 81 small organic molecules with known experimental hydration free energies is used to determine the coefficients of the linear model by least squares regression. The fit is statistically significant yielding a correlation coefficient of 0.99, a root mean square error of 0.27 kcal/mol for the 81 molecules belonging to the training set, and 0.63 kcal/mol for an independent test set of 10 molecules.
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Affiliation(s)
- R Jäger
- Institut für Physikalische Chemie, Technische Universität Darmstadt, Germany.
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20
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Czaplewski C, Rodziewicz-Motowidło S, Liwo A, Ripoll DR, Wawak RJ, Scheraga HA. Molecular simulation study of cooperativity in hydrophobic association. Protein Sci 2000; 9:1235-45. [PMID: 10892816 PMCID: PMC2144663 DOI: 10.1110/ps.9.6.1235] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
To investigate the cooperativity of hydrophobic interactions, the potential of mean force of two- and three-molecule methane clusters in water was determined by molecular dynamics simulations using two methods: umbrella-sampling with the weighted histogram analysis method and thermodynamic integration. Two water models, TIP3P and TIP4P, were used, while each methane molecule was modeled as a united atom. It was found that the three-body potential of mean force is not additive, i.e., it cannot be calculated as a sum of two-body contributions, but requires an additional three-body cooperative term. The cooperative term, which amounts to only about 10% of the total hydrophobic association free energy, was found to increase the strength of hydrophobic association; this finding differs from the results of earlier Monte Carlo studies with the free energy perturbation method of Rank and Baker (1997). As in the work of Rank and Baker, the solvent contribution to the potential of mean force was found to be well approximated by the molecular surface of two methane molecules. Moreover, we also found that the cooperative term is well represented by the difference between the molecular surface of the three-methane cluster and those of all three pairs of methane molecules. In addition, it was found that, while there is a cooperative contribution to the hydrophobic association free energy albeit a small one, the errors associated with the use of pairwise potentials are comparable to or larger than this contribution.
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Affiliation(s)
- C Czaplewski
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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21
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Kimura SR, Brower RC, Zhang C, Sugimori M. Surface of active polarons: A semiexplicit solvation method for biomolecular dynamics. J Chem Phys 2000. [DOI: 10.1063/1.481364] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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