Charge-patching method for the calculation of electronic structure of polypeptides

Literature Information

Publication Date 2018-08-17
DOI 10.1039/C8CP01803K
Impact Factor 3.676
Authors

Fu Ding, Lin-Wang Wang


View Original

Abstract

Theoretical study of the electronic structures of protein is a fundamental challenge in computational biochemistry due to the large size of the systems. The electronic structure of a protein is important for some of the important protein functionalities, such as photosynthesis. In this study, we explored the charge-patching method to calculate the electronic structure of polypeptides. This method generates the charge densities of the systems by patching the charge motifs calculated from small prototype systems. The method was tested on a range of polypeptides, including the glycine polypeptide in 27-ribbon, α-helix, 310-helix, and β-strand structures. After the charge density profiles of these systems were obtained, the electronic structures of these glycine polypeptides were further calculated based on density functional theory (DFT) using a folded-spectrum method. The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) were analyzed and compared with conventional direct DFT calculations. The charge-patching method results were found to be in good agreement with the directed DFT results.

Related Literature

Contents list

2023-11-29 Front/Back Matter

DOI: 10.1039/D3CP90239K

Correction: UV and VUV-induced fragmentation of tin-oxo cage ions

Jarich Haitjema, Lianjia Wu, Laurent Nahon, Sonia Castellanos

2023-11-27 Correction

DOI: 10.1039/D3CP90231E

Book and software reviews

2002-04-04 News

DOI: 10.1039/B202897M

A Ti3C2Tx@PANI core–shell heterostructure assembled into a 3D porous hydrogel as a free-standing electrode for high-energy supercapacitors

Peng Liao, Jian Song, Zenghui Qiu, Cheng Wen, Xin Zhang, Lin Guo, Haijun Xu

2023-10-30 Paper

DOI: 10.1039/D3CP01965A

High-pressure structural studies and pressure-induced sensitisation of 3,4,5-trinitro-1H-pyrazole

Jack Hemingway, Xiaojiao Liu, Adam A. L. Michalchuk, Carole A. Morrison, Colin R. Pulham

2023-11-09 Paper

DOI: 10.1039/D3CP04526A

Impacts of QM region sizes and conformation numbers on modelling enzyme reactions: a case study of polyethylene terephthalate hydrolase

Mingna Zheng, Yanwei Li, Qingzhu Zhang, Wenxing Wang

2023-10-24 Paper

DOI: 10.1039/D3CP04519F

Enhancement of wide-band trace terahertz absorption spectroscopy based on microstructures: a review

Jining Li, Wenxin Lu

2023-11-09 Review Article

DOI: 10.1039/D3CP04746F

XANES analysis of phosphate glasses melted with Tb4O7 and SnO: evaluating the impact of valence states on structural, thermal, and luminescent properties

José A. Jiménez, Dugan Hayes, Cali Antolini, Benjamin J. Reinhart

2023-11-28 Paper

DOI: 10.1039/D3CP04784A

You might also like

Compound Q&A

Are there alternatives to 1-(4-Chlorophenyl)-N-hydroxymethanimine (CAS: 3848-36-0) in synthesis?

When considering alternatives to 1-(4-Chlorophenyl)-N-hydroxymethanimine (CAS: 3...

3848-36-01-(4-Chlorophenyl)-N...
Compound Q&A

How is 3-(4-Bromophenyl)-5-(2-fluorophenyl)-1,2,4-oxadiazole (CAS: 419553-16-5) typically synthesized?

3-(4-Bromophenyl)-5-(2-fluorophenyl)-1,2,4-oxadiazole is synthesized through a m...

419553-16-53-(4-Bromophenyl)-5-...
Compound Q&A

How is 5-Chloro-2-(4-chlorophenyl)-4-methyl-6-[3-(1-piperidinyl)propoxy]pyrimidine (CAS: 1639220-19-1) typically synthesized?

5-Chloro-2-(4-chlorophenyl)-4-methyl-6-[3-(1-piperidinyl)propoxy]pyrimidine (CAS...

1639220-19-15-Chloro-2-(4-chloro...
Compound Q&A

What industries use 2-Chloro-4-(difluoromethoxy)pyridine (CAS: 1206978-15-5)?

2-Chloro-4-(difluoromethoxy)pyridine is used in the pharmaceutical industry for ...

1206978-15-52-Chloro-4-(difluoro...
Compound Q&A

What regulatory guidelines apply to 3-Chloro-6-methylpyridazine (CAS: 1121-79-5)?

3-Chloro-6-methylpyridazine (CAS: 1121-79-5) is classified under the Globally Ha...

1121-79-53-Chloro-6-methylpyr...
Compound Q&A

Are there alternatives to Methyl 4,5-dimethyl-2-nitrobenzoate in synthesis?

Several alternatives can be used in the synthesis of Methyl 4,5-dimethyl-2-nitro...

90922-74-0Methyl 4,5-dimethyl-...
Compound Q&A

Are there alternatives to (2E,2'E)-3,3'-(1,4-Phenylene)bisacrylaldehyde in synthesis?

Alternatives to (2E,2'E)-3,3'-(1,4-Phenylene)bisacrylaldehyde include other acry...

63405-68-5(2E,2'E)-3,3'-(1,4-P...
Compound Q&A

What is 3-Amino-5-chloropyridin-2-ol hydrochloride (CAS: 1261906-29-9)?

3-Amino-5-chloropyridin-2-ol hydrochloride is an organic compound with the CAS n...

1261906-29-93-Amino-5-chloropyri...
Compound Q&A

What precautions should be taken when handling 6,7-Difluoro-2,3-dihydro-4H-chromen-4-one (CAS: 1092349-93-3)?

When handling 6,7-Difluoro-2,3-dihydro-4H-chromen-4-one, it is essential to wear...

1092349-93-36,7-Difluoro-2,3-dih...

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.