Journal Article10.1016/S0009-2614(01)01416-6
Fragment molecular orbital method: use of approximate electrostatic potential
Tatsuya Nakano,Tsuguchika Kaminuma,Toshiyuki Sato,Kaori Fukuzawa,Yutaka Akiyama,Masami Uebayasi,Kazuo Kitaura +6 more
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TL;DR: The fragment molecular orbital (FMO) method as discussed by the authors has been proposed to reproduce ab initio total energies and geometries of molecules in good accuracy, but the most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation.
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About: This article is published in Chemical Physics Letters. The article was published on 17 Jan 2002. The article focuses on the topics: Fragment molecular orbital & Ab initio.
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Citations
Cyclosporin A: Conquering Conformational Complexity and Chameleonicity
Satoshi Ono,Matthew R. Naylo,Chad E. Townsend,Chieko Okumura,Okimasa Okada,Hsiau-Wei Lee,R. Scott Lokey +6 more
TL;DR: In this paper , the chameleonic behavior of cyclosporin A (CsA) was investigated through conformational ensembles employing multicanonical molecular dynamics simulations that could sample the wide range of conformational space including cis and trans isomers of N-methylated amino acids.
N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation
TL;DR: The sequence context of a given modification within an mRNA plays a large role in determining how (and if) the modification impacts the number and distribution of proteoforms synthesized by the ribosome.
The ABINIT-MP Program
Yuji Mochizuki,Yuji Mochizuki,Tatsuya Nakano,Kota Sakakura,Yoshio Okiyama,Hiromasa Watanabe,Koichiro Kato,Yoshinobu Akinaga,Shinya Sato,Jun-inchi Yamamoto,Katsumi Yamashita,Tadashi Murase,Takeshi Ishikawa,Yuto Komeiji,Yuji Kato,Naoki Watanabe,Takashi Tsukamoto,Hirotoshi Mori,Koji Okuwaki,Shigenori Tanaka,Akifumi Kato,Chiduru Watanabe,Kaori Fukuzawa,Kaori Fukuzawa +23 more
- 01 Jan 2021
TL;DR: The ABINIT-MP program as mentioned in this paper is an original code for the fragment molecular orbital (FMO) calculations and has several unique features such as a variety of efficient correlated methods and hybrid parallelism.
Anion–Anion Interactions in the Crystal Packing of Functionalized Methanide Anions: An Experimental and Computational Study
Anthony S. R. Chesman,Jennifer L. Hodgson,Ekaterina I. Izgorodina,Aron Urbatsch,David R. Turner,Glen B. Deacon,Stuart Robert Batten +6 more
TL;DR: Examination of the crystal structures of (Me4N)(dcnm) and Me4N(nbdm) was carried out by as discussed by the authors, showing that the crystal structure of dcnm and nbdm is similar to that of dicyanonitrosomethanide.
Fragment molecular orbital calculations on large scale systems containing heavy metal atom
Takeshi Ishikawa,Yuji Mochizuki,Tatsuya Nakano,Shinji Amari,Hirotoshi Mori,Hiroaki Honda,Takatoshi Fujita,Hiroaki Tokiwa,Shigenori Tanaka,Yuto Komeiji,Kaori Fukuzawa,Kiyoshi Tanaka,Eisaku Miyoshi +12 more
TL;DR: In this article, a fully quantum treatment of large scale systems containing heavy metal atoms was realized by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme.
References
Fragment molecular orbital method: an approximate computational method for large molecules
TL;DR: In this paper, an approximate molecular orbital (MO) method was proposed to calculate the total energy of a molecule by assigning the electrons of the molecules to fragments and calculating the MOs of fragments and fragment pairs.
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Fragment molecular orbital method: application to polypeptides
Tatsuya Nakano,Tsuguchika Kaminuma,Toshiyuki Sato,Yutaka Akiyama,Masami Uebayasi,Kazuo Kitaura +5 more
TL;DR: In this article, the fragment molecular orbital method (FMO) was applied to the model peptides of (Gly)n and (Ala)n (n=5-20), [Met5]enkephalin (YGGFM), and the synthetic designed peptide ALPHA-1 (acetyl-ELLKKLLEELKG) and the calculated total energies compare well with those from the conventional ab initio MO method.
358
Fragment molecular orbital method: analytical energy gradients
TL;DR: In this article, the fragment molecular orbital (FMO) method with the analytical energy gradient at the HF level of theory has been incorporated into the G aussian 94 (G94) package.
210
Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.
TL;DR: The 0.75 Å crystal structure of a racemic mixture of the 12‐residue designed peptide “Alpha‐1” (Acetyl‐ELLKKLLEELKG) is reported, the L‐enantiomer of which is described in the accompanying paper.
Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Christian Jelsch,Martha M. Teeter,Victor S. Lamzin,Virginie Pichon-Pesme,Robert H. Blessing,Claude Lecomte +5 more
TL;DR: The charge density distribution of a protein has been refined experimentally and the resulting electron density maps of redistributed valence electrons compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide.