AI Article Synopsis
Article Abstract
The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/jcc.20645 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Hydrophenoxylation of alkynes by gold catalysts: a mini review.
J Mol Model
September 2024
Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003, Girona, Catalonia, Spain.
Context: The field of chemistry has significantly evolved, with catalysis playing a crucial role in transforming chemical processes. From Valerius' use of sulfuric acid in the sixteenth century to modern advancements, catalysis has driven innovations across various industries. The introduction of gold as a catalyst marked a pivotal shift, expanding its applications beyond ornamentation to homogeneous catalysis.
View Article and Find Full Text PDF5-(Pyridin-3-yl)-3,4-dihydro-2-furan-1-ium (NNKFI): a computational study of its physico-chemical properties.
R Soc Open Sci
September 2024
Department of Chemistry and Biochemistry, University of Southern Indiana, Evansville, IN 47712, USA.
Recent work on the diazonium ion metabolite of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKDI) suggests that 5-(pyridin-3-yl)-3,4-dihydro-2-furan-1-ium (NNKFI) may form from NNKDI via an intramolecular reaction. NNKDI is an important carcinogen whose role as an alkylating agent has received significant attention. While there is some experimental evidence supporting NNKFI's production , it has not yet been directly observed.
View Article and Find Full Text PDFAssessment of the usefulness of β-cyclodextrin in the removal of progesterone from the environment.
Sci Total Environ
November 2024
Institute of Technology and Life Sciences - National Research Institute, Falenty, 3 Hrabska Avenue, 05-090 Raszyn, Poland. Electronic address:
The paper presents the results and interpretation of theoretical calculations for the progesterone-β-cyclodextrin (P@β-CD; G4MP2) and progesterone-β-cyclodextrin-β-cyclodextrin (P@β-CD-β-CD; G2) systems. The geometry of the progesterone molecule was optimized on basis of the DFT theory using the B3LYP, PBE1PBE and M06-2X functionals, for selected Pople basis sets [6-31G, 6-31++G, 6-31++G(d,p), 6-311G, 6-311++G, 6-311++G(d,p)] and the Dunning basis set (aug-cc-pVDZ). Presented results of theoretical calculations provide insight into the mechanism of formation of supramolecular systems of progesterone and β-cyclodextrin, allowing us to understand the impact of differences in the polarizability of specific fragments of the "guest" molecule, through the analysis of the Mulliken population distribution, on the tendency for equilibrium inclusion by "host" molecules characterized by selective affinity towards hydrophilic and hydrophobic molecular systems.
View Article and Find Full Text PDFFirst-Principles Investigations of Novel Guanidine-Based Dyes.
ACS Omega
March 2024
Environment and Sustainability Institute (ESI), Faculty of Environment, Science and Economy, University of Exeter, Penryn Campus, TR10 9FE Cornwall, U.K.
In the pursuit of finding efficient D-π-A organic dyes as photosensitizers for dye-sensitized solar cells (DSSCs), first-principles calculations of guanidine-based dyes [-] were executed using density functional theory (DFT). The various electronic and optical properties of guanidine-based organic dyes with different D-π-A structural modifications were investigated. The structural modification of guanidine-based dyes largely affects the properties of molecules, such as excitation energies, the oscillator strength dipole moment, the transition dipole moment, and light-harvesting efficiencies.
View Article and Find Full Text PDFA physical organic strategy to predict and interpret stabilities of chemical bonds in energetic compounds for the discovery of thermal-resistant properties.
J Mol Model
February 2024
School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, 621010, People's Republic of China.
Context: The in-depth understanding about the stability of chemical bonds in energetic compounds plays a central role for molecular design and safety-related evaluations. Most energetic compounds contain nitro as explosophores, and nitro cleavage is fundamental for thermal and mechanical stability. However, the quantum chemistry approach to accurately predict energy and temperature properties related to bond stability is challenging, due to the tradeoff between computational costs and deviations.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!