NITROSYL IODIDE, INO: MILLIMETER-WAVE SPECTROSCOPY GUIDED BY AB   INITIO   QUANTUM CHEMICAL COMPUTATION

2015 ◽  
Author(s):  
Stephane Bailleux ◽  
Hiroyuki Ozeki ◽  
Shohei Aiba ◽  
Denis Duflot
Keyword(s):  
Ab Initio ◽  
Millimeter Wave ◽  
Quantum Chemical ◽  
Quantum Chemical Computation ◽  
Millimeter Wave Spectroscopy ◽  
Chemical Computation

scholarly journals Ultra-Large-Scale Ab Initio Quantum Chemical Computation of Bio-Molecular Systems: The Case of Spike Protein of SARS-CoV-2 Virus

2020 ◽  
Author(s):  
Wai-Yim Ching ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Binding Domain ◽  
Spike Protein ◽  
Hydrogen Atoms ◽  
Structural Domains ◽  
S Protein ◽  
Quantum Chemical Computation ◽  
Chemical Computation ◽  
Central Helix

<p>The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. <i>Spike (S) glycoprotein</i> of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of <i>ab initio</i> computation of the spike protein, the largest <i>ab initio</i> quantum chemical computation to date on any bio-molecular system, using a <i>divide and conquer strategy</i> by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, <i>ab initio</i> calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic. </p>

scholarly journals Ultra-Large-Scale Ab Initio Quantum Chemical Computation of Bio-Molecular Systems: The Case of Spike Protein of SARS-CoV-2 Virus

2020 ◽  
Author(s):  
Wai-Yim Ching ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Binding Domain ◽  
Spike Protein ◽  
Hydrogen Atoms ◽  
Structural Domains ◽  
S Protein ◽  
Quantum Chemical Computation ◽  
Chemical Computation ◽  
Central Helix

<p>The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. <i>Spike (S) glycoprotein</i> of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of <i>ab initio</i> computation of the spike protein, the largest <i>ab initio</i> quantum chemical computation to date on any bio-molecular system, using a <i>divide and conquer strategy</i> by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, <i>ab initio</i> calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic. </p>

scholarly journals Laboratory Millimeter Wave Spectroscopy of Small Reactive Species

1994 ◽  
Vol 146 ◽  
pp. 417-431
Author(s):  
C. Demuynck ◽  
M. Bogey ◽  
H. Bolvin ◽  
M. Cordonnier ◽  
J.L. Destombes ◽  
...  
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Millimeter Wave ◽  
Radio Astronomy ◽  
Molecular Ions ◽  
Reactive Species ◽  
Oh Radical ◽  
Line Frequency ◽  
Millimeter Wave Spectroscopy ◽  
Strong Motivation

The discovery of a large variety of molecules by radio astronomy has been a very strong motivation for the development of laboratory millimeter wave spectroscopy. Among them, the reactive species, neutral and/or ionic, have been early recognized as playing a very important role in the chemistry of the interstellar and circumstellar medium. While the laboratory spectroscopy of free radicals started relatively early, with the observation of the OH radical by the group of Townes (Dousmanis et al. 1955), the detection of molecular ions proved to be a much more difficult task, and the first millimeter line due to an ion was actually detected by radio astronomy (Buhl &amp; Snyder 1970). It was called “U89.2” until it was tentatively attributed to HCO+by Klemperer (1970) on the basis of both considerations on the chemistry of the interstellar medium, and of ab initio calculations for the prediction of the expected line frequency. This identification was later confirmed by more elaborated ab initio calculations (Wahlgren et al. 1973, Kraemers &amp; Diercksen 1976), and by the observation of a transition attributed to H13CO+(Snyder et al. 1976), but the definite confirmation was the observation of the same transition in a laboratory glow discharge by the group of Woods (Woods et al. 1975).

Millimeter-Wave Spectroscopy, High-Resolution Infrared Spectrum, ab Initio Calculations, and Molecular Geometry of FPS

2001 ◽  
Vol 210 (2) ◽  
pp. 213-223 ◽  
Author(s):  
Helmut Beckers ◽  
Marcel Bogey ◽  
Jürgen Breidung ◽  
Hans Bürger ◽  
Jean Demaison ◽  
...  
Keyword(s):  
High Resolution ◽  
Infrared Spectrum ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Millimeter Wave ◽  
Molecular Geometry ◽  
Millimeter Wave Spectroscopy

scholarly journals De Novo Creation of a Naked-Eye-Detectable Fluorescent Molecule Based on Quantum-Chemical Computation and Machine Learning

2021 ◽  
Author(s):  
Masato Sumita ◽  
Kei Terayama ◽  
Naoya Suzuki ◽  
Shinsuke Ishihara ◽  
Ryo Tamura ◽  
...  
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
De Novo ◽  
Molecular Structures ◽  
Molecular Properties ◽  
Naked Eye ◽  
Quantum Chemical Computation ◽  
Spectrum Measurement ◽  
Chemical Computation ◽  
Molecular Fluorescence

Correlations between molecular properties and structures, such as those between the absorption wavelength and conjugate length, are beneficial for designing materials and controlling their properties. However, determining the molecular structures that correlate with the target molecular properties (such as molecular fluorescence) is not an easy task. In this study, we have used a de novo molecule generator (DNMG) coupled with quantum-chemical computation (QC) to develop new fluorescent molecules, which are garnering significant attention in various disciplines. With massive parallel computation (1024 cores, 5 days), DNMG has produced 3,643 candidate molecules within the density functional theory (DFT; one of QC) framework. Among the generated molecules, we have selected an unreported molecule and synthesized it for photoluminescence spectrum measurement. Our experimental verification demonstrated that DNMG can successfully create a new molecule which emits fluorescence detectable by the naked eye, as predicted by the DFT.

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