A modified electronegativity equalization method for fast and accurate calculation of atomic charges in large biological molecules

Literature Information

Publication Date 2009-05-26
DOI 10.1039/B821696G
Impact Factor 3.676
Authors

Yongzhong Ouyang, Fei Ye, Yizeng Liang


View Original

Abstract

To further extend the EEM approach to improve its accuracy, a new approach, in which the different connectivities and hybridized states are introduced to represent the different chemical environments, has been developed. The C, O and N atoms are distinguished between different hybridized states. Different states of hydrogen atoms are defined according to their different connectivities. Furthermore, the sp2 carbons in the aromatic rings are also separated from the other sp2 carbons. Geometries and NPA charges are calculated at the B3LYP/6-31G* level, and the effective electronegativity and hardness values could be calibrated with the help of a training set of 141 organic molecules using the Differential Evolution (DE) algorithm. The quality of the modified EEM charges is evaluated by comparison with the B3LYP/6-31G* charges calculated for a series of polypeptides, not contained in the training set. For further comparison, the atomic parameters of the original EEM without including chemical environments are recalibrated under the same conditions. It is found that the accuracy of the modified EEM method improves significantly as compared to that of the original EEM method.

Related Literature

Atomic-level 2-dimensional chemical mapping and imaging of individual dopants in a phosphor crystal

Guo-zhen Zhu, Andrew P. Knights, Gianluigi A. Botton

2013-05-09 Paper

DOI: 10.1039/C3CP51135A

Towards systematically improvable models for actinides in condensed phase: the electronic spectrum of uranyl in Cs2UO2Cl4 as a test case

André Severo Pereira Gomes, Christoph R. Jacob, Florent Réal, Lucas Visscher, Valérie Vallet

2013-07-12 Paper

DOI: 10.1039/C3CP52090K

Front cover

Cover

DOI: 10.1039/C3CP90110F

Front cover

Cover

DOI: 10.1039/C3CP90115G

Back cover

Cover

DOI: 10.1039/C3CP90092D

An ENDOR and DFT analysis of hindered methyl group rotations in frozen solutions of bis(acetylacetonato)-copper(ii)

Katherine M. Sharples, Emma Carter, Colan E. Hughes, Kenneth D. M. Harris, James A. Platts, Damien M. Murphy

2013-08-05 Paper

DOI: 10.1039/C3CP52464G

Compact large area and high-quality Au film with a hierarchical structure and its application in SERS

Youyi Xia, Tenjiao Li, Jun Chen

2013-05-15 Paper

DOI: 10.1039/C3CP51080H

Temperature dependence of high field 13C dynamic nuclear polarization processes with trityl radicals below 35 Kelvin

Shamon A. Walker, Devin T. Edwards, Ting Ann Siaw, Brandon D. Armstrong

2013-07-24 Paper

DOI: 10.1039/C3CP51628H

You might also like

Compound Q&A

How should waste containing N-Methoxy-N-methyl-1,3-thiazole-5-carboxamide (CAS: 898825-89-3) be handled?

Waste containing N-Methoxy-N-methyl-1,3-thiazole-5-carboxamide (CAS: 898825-89-3...

898825-89-3N-Methoxy-N-methyl-1...
Compound Q&A

How should N-(4-Biphenylyl)dibenzo[b,d]furan-4-amine (CAS: 1318338-47-4) be stored?

N-(4-Biphenylyl)dibenzo[b,d]furan-4-amine should be stored in a tightly sealed c...

1318338-47-4N-(4-Biphenylyl)dibe...
Compound Q&A

What is the market or research trend for 3-Acetamido-5-amino-2,4,6-triiodobenzoic acid (CAS: 1713-07-1)?

The market for 3-Acetamido-5-amino-2,4,6-triiodobenzoic acid (CAS: 1713-07-1) is...

1713-07-13-Acetamido-5-amino-...
Compound Q&A

How should Benzyl 2-O-acetyl-3,4,6-tri-O-benzyl-beta-D-galactopyranoside (CAS: 61820-03-9) be stored?

Benzyl 2-O-acetyl-3,4,6-tri-O-benzyl-beta-D-galactopyranoside (CAS: 61820-03-9) ...

61820-03-9Benzyl 2-O-acetyl-3,...
Compound Q&A

What regulatory guidelines apply to 2-Ethylpiperazine dihydrochloride (CAS: 438050-52-3)?

2-Ethylpiperazine dihydrochloride (CAS: 438050-52-3) is regulated under the Glob...

438050-52-32-Ethylpiperazine di...
Compound Q&A

What regulatory guidelines apply to 1,1'-[1,3-Phenylenebis(methylene)]bis(3-methyl-1H-pyrrole-2,5-dione) (CAS: 119462-56-5)?

1,1'-[1,3-Phenylenebis(methylene)]bis(3-methyl-1H-pyrrole-2,5-dione) (CAS: 11946...

119462-56-51,1'-[1,3-Phenyleneb...
Compound Q&A

Are there alternatives to 5-Fluoro-2-(1-pyrrolidinyl)pyridine (CAS: 1287217-79-1) in synthesis?

Several alternatives can be used in the synthesis of 5-Fluoro-2-(1-pyrrolidinyl)...

1287217-79-15-Fluoro-2-(1-pyrrol...
Compound Q&A

What precautions should be taken when handling 6-Bromoimidazo[1,2-a]pyridin-8-amine (CAS: 676371-00-9)?

When handling 6-Bromoimidazo[1,2-a]pyridin-8-amine, it is important to wear appr...

676371-00-96-Bromoimidazo[1,2-a...
Compound Q&A

Are there alternatives to (2S,4R)-4-(4-Nitrobenzyl)pyrrolidine-2-carboxylic acid hydrochloride (CAS: 1049740-22-8) in synthesis?

Alternatives to (2S,4R)-4-(4-Nitrobenzyl)pyrrolidine-2-carboxylic acid hydrochlo...

1049740-22-8(2S,4R)-4-(4-Nitrobe...

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

Recommended Compounds

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.