Qualitative Thinking in the Age of Modern Computational Chemistry, or What Lionel Salem Knows

Author(s):  
Roald Hoffmann

The achievements of modern computational chemistry are astounding. It is reasonable today to handle billions of configurations, and to achieve chemical accuracy, kilocalories say, in calculating binding energies and geometries, in ground and transition states of reasonably complex molecules. There is no question that the enterprise of computational theoretical chemistry is successful. Now Lionel Salem and I grew up and developed scientifically in the climate of the very same computer which made all this possible. Russ Pitzer taught me to punch cards; I still miss the sound of the key punch. The extended Hückel method, which several of us developed in the Lipscomb group, would have been impossible without modern computers. But I took a different turn, moving from being a calculator in the framework of semiempirical theory, to being an explainer, the builder of simple molecular orbital models. I was and am still doing calculations, but my abiding interest is in the construction of explanations. And also in thinking up moderately unreasonable things for experimentalists to try. In existing as a scientist, meaning that my work was of continuing interest to other chemists, I was helped in that I moved into whatever part of chemistry I did, just a little ahead of the heavy guns of computational chemistry. So I switched from organic to inorganic molecules just when organic molecules became reasonably calculable. Recently I’ve been less fortunate, for when I moved to solids and surfaces I came back into heavy fire—physicists had been doing calculations on these materials for a long time. And they were (are) hardly likely to believe that one-electron calculations and a chemical viewpoint are of value. I want to make some observations on computational quantum chemistry, perforce influenced by my prejudices. Given the advances in the field, any molecule I can calculate (without geometrical optimization), with the simplest extended Hückel approximation, can be done so much better by most computational chemists. So why don’t I feel threatened; why is there a role for people of my ilk? Or for Lionel. Actually, I do feel threatened and bypassed! But that’s just an emotional reaction, and my aging figures in it.

2020 ◽  
Vol 12 (19) ◽  
pp. 1743-1757
Author(s):  
Anna Pawełczyk ◽  
Lucjusz Zaprutko

At the end of 2019, a novel virus causing severe acute respiratory syndrome to spread globally. There are currently no effective drugs targeting SARS-CoV-2. In this study, based on the analysis of numerous references and selected methods of computational chemistry, the strategy of integrative structural modification of small molecules with antiviral activity into potential active complex molecules has been presented. Proposed molecules have been designed based on the structure of triterpene oleanolic acid and complemented by structures characteristic of selected anti-COVID therapy assisted drugs. Their pharmaceutical molecular parameters and the preliminary bioactivity were calculated and predicted. The results of the above analyses show that among the designed complex substances there are potential antiviral agents directed mainly on SARS-CoV-2.


2011 ◽  
Vol 356-360 ◽  
pp. 707-711 ◽  
Author(s):  
Narisara Suthanyawatchai ◽  
Usa Onthong

The adsorption of hydrogen sulfide (H2S), carbondioxide (CO2) and methane (CH4) on H-FER zeolite was investigated under computational chemistry using ONIOM (HF/6-31G (d,p):UFF) and ONIOM (B3LYP/6-31G (d,p):UFF) method. Compared to the H-FER zeolite induces much stronger binding of H2S, CO2 and CH4 suggesting great enhancements in the adsorption selectivity. The order of binding energies of adsorbed molecules is H2S > CO2 > CH4. It was found that the extended zeolitic framework covering the nanocavity was essential for describing the confinement effect of the zeolite. The results of these calculations show that the zeolite can be used to adsorb H2S bester then CO2 and CH4. Carbondioxide and hydrogen sulfide are pollutant in biogas product from anaerobic digestion of biodegradable materials. There for, zeolite can be use to purified gas before using as fuel.


MRS Advances ◽  
2016 ◽  
Vol 1 (35) ◽  
pp. 2489-2494 ◽  
Author(s):  
Richard T Hoffman ◽  
Alexander P Moore ◽  
Chaitanya S Deo

ABSTRACTA Kinetic Monte Carlo simulation, using a modified version of the SPPARKS code, of simple defects and complex vacancy clusters was run on a bcc lattice. In this simulation the complexity of void formation was varied by introducing a detachment rate for individual vacancies leaving the void and either treating this value as constant for all size voids or having this value be dependent on the size of the void. Molecular Dynamics simulations were used to determine the binding energies of vacancies for voids of varying size. The simulation was then run over long time periods to determine the number of defects in the simulation under irradiation conditions. It was found that the additional complexity of size dependent void detachment rates had little effect on the defect concentrations and thus a constant barrier should be sufficient for simulations of voids in bcc metals.


A technique for calculating the binding energy of any saturated molecule is developed.The method is based on an application of the electrostatic theorem, discussed in earlier parts, to paired-electron orbital wave functions.These wave functions include both molecular-orbital and valence-bond functions as special cases.The resulting numerical computations are sufficiently simple to be carried through without approximation even for complex molecules. The method is applied to the lithium molecule and the lithium hydride molecule, and yields results in good agreement with experiment. The choice of wave functions for calculations on other molecules is discussed.


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