Alchemical derivatives have been used in recent years to obtain essentially qualitative information about transformations in which the number of electrons is unchanged. Within the context of Conceptual DFT, we present a systematic approach for combining changes in both the number of electrons and the nuclear charge so that for example one can navigate from one neutral atom to another. A general formalism is presented for transformations involving changes both in or , where Parr's parabolic approach for the dependence is considered as one particular case and the ensemble description in the 0 K limit as the second case. The B3LYP functional in its CAMB3LYP version combined with the aug-cc-pCVQZ basis has been chosen to perform Coupled Perturbed Kohn Sham calculations of the alchemical derivatives. The monotonic behaviour of the alchemical potential is scrutinised. The order of magnitude analysis of the derivatives preludes convergence at third order. These results are injected in two strategies for obtaining transmutation energies from neutral atoms to a neighbouring neutral atom: one road moving along the diagonal, the other one walking along a pure alchemical road after ionisation or electron attachment. Roads involving the anion of the reference atom are much less successful than those involving its cation. The transmutation energy for the cationic pathway displays chemical accuracy when the procedure is carried at third order in . The difficulties inherent to an accurate description of the anion and its response functions are responsible for the shortcomings along the anionic paths. As a direct application Ionization Energies (IE) and Electron Affinities (EA) are evaluated showing an almost perfect agreement with the direct evaluation and a difference with experimental values less than 0.5 eV for the IE. For the first EA reasonable agreement is obtained with direct and experimental values whereas the second EAs for atoms with stable mono-anions show a remarkable agreement with literature data. Besides proof of concept that with the information content of an atom one can get accurate energetics of its neighbours, the results indicate that alchemical derivatives are capable to yield quantitative information when navigating through Chemical Compound Space.
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http://dx.doi.org/10.1039/c9cp03935j | DOI Listing |
J Chem Phys
January 2025
Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany.
We recently introduced the Alchemical Integral Transform (AIT), enabling the prediction of energy differences, and guessed an ansatz to parameterize space r in some alchemical change λ. Here, we present a rigorous derivation of AIT's kernel K and discuss the parameterization r(λ) in n dimensions, i.e.
View Article and Find Full Text PDFJ Mol Model
September 2024
Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370, Wrocław, Poland.
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View Article and Find Full Text PDFThis paper traces the analogy between the making of bread with ferment (leaven or yeast) and theories of metallic transmutation throughout the Middle Ages. For this purpose it surveys several medieval alchemical writings, including Hortulanus's influential . In this work, the ferment, an essential ingredient of the philosophers' stone, is portrayed less as an active agent and more as the passive, nutritive earth () which combines with the soul () in order to yield the stone ().
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September 2024
Scuola Internazionale Superiore di Studi Avanzati, SISSA, Via Bonomea 265, Trieste 34136, Italy.
N6-Methyladenosine (mA) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable mA readers, functions through its highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the mechanism of recognition of mA by the YTHDC1 protein.
View Article and Find Full Text PDFJ Phys Chem B
September 2024
Department of Chemical Engineering, University of Louisville, Louisville, Kentucky 40292, United States.
Pinholin S68 is a viral integral membrane protein whose function is to form nanoscopic "pinholes" in bacterial cell membranes to induce cell lysis as part of the viral replication cycle. Pinholin can transition from an inactive to an active conformation by exposing a transmembrane domain (TMD1) to the extracellular fluid. Upon activation, several copies of the protein assemble via interactions among a second transmembrane domain (TMD2) to form a single pore, thus hastening cell lysis and viral escape.
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