Zobrazeno 1 - 10
of 130
pro vyhledávání: '"W. A. Sokalski"'
Publikováno v:
The Journal of Physical Chemistry. B
Catalytic fields representing the topology of the optimal molecular environment charge distribution that reduces the activation barrier have been used to examine alternative reaction variants and to determine the role of conserved catalytic residues
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::840e7cd77ba4c0b65d627698afda492a
https://doi.org/10.1021/acs.jpcb.1c05256
https://doi.org/10.1021/acs.jpcb.1c05256
Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields
Autor:
Wiktor Beker, W. Andrzej Sokalski
Publikováno v:
Journal of Chemical Theory and Computation
Currently developed protocols of theozyme design still lead to biocatalysts with much lower catalytic activity than enzymes existing in nature, and, so far, the only avenue of improvement was the in vitro laboratory-directed evolution (LDE) experimen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::65038324d2a3dff8fa1be0b9012bfd06
https://pubmed.ncbi.nlm.nih.gov/32282205
https://pubmed.ncbi.nlm.nih.gov/32282205
Publikováno v:
Structural Chemistry. 27:429-438
We explore the idea of supplementing partial atomic charges with cumulative multipole moments for modeling electrostatic effects during chemical reactions. To this end, we investigate the first stage of alkaline hydrolysis of O,O-dimethyl phosphorofl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f5a518546d5338076e6ed9db1ee5455
https://doi.org/10.1007/s11224-016-0741-x
https://doi.org/10.1007/s11224-016-0741-x
Publikováno v:
Journal of Molecular Modeling
Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has bee
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6763f3b695259237195106775b94de5
http://europepmc.org/articles/PMC5741779
http://europepmc.org/articles/PMC5741779
Publikováno v:
Chemphyschem : a European journal of chemical physics and physical chemistry. 18(12)
Representative Lewis acid-Lewis base complexes linked by tetrel, pnicogen, chalcogen, and halogen bonds have been studied within the quantum theory of atoms in molecules (QTAIM) approach and the hybrid variation-perturbation theory (HVPT) to analyze
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::035c17ae6d10fcd897ad578f43f4d65f
https://pubmed.ncbi.nlm.nih.gov/28346740
https://pubmed.ncbi.nlm.nih.gov/28346740
Publikováno v:
Beker, W L, Van der Kamp, M W, Mulholland, A J & Sokalski, W A 2017, ' Rapid estimation of catalytic efficiency by cumulative atomic multipole moments : application to ketosteroid isomerase mutants ', Journal of Chemical Theory and Computation, vol. 13, no. 2, pp. 945-955 . https://doi.org/10.1021/acs.jctc.6b01131
We propose a simple atomic multipole electrostatic model to rapidly evaluate the effects of mutation on enzyme activity and test its performance on wild-type and mutant ketosteroid isomerase. The predictions of our atomic multipole model are similar
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::13f4fb0601efda07eb1bb37b0c0ebcac
https://research-information.bris.ac.uk/en/publications/6e12275f-90ad-4985-9354-6ad96f9b8734
https://research-information.bris.ac.uk/en/publications/6e12275f-90ad-4985-9354-6ad96f9b8734
Publikováno v:
The Journal of Physical Chemistry B. 118:7277-7289
The fundamental mechanism of organophosphate hydrolysis is the subject of a growing interest resulting from the need for safe disposal of phosphoroorganic pesticides. Herein, we present a detailed ab initio study of the gas-phase mechanisms of alkali
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5bd0739d4e56fe901189be079dee3dba
https://doi.org/10.1021/jp503382j
https://doi.org/10.1021/jp503382j
Autor:
W. Andrzej Sokalski, Borys Szefczyk
Publikováno v:
The Journal of Physical Chemistry B. 118:2147-2156
The intermolecular interaction energy in a popular ionic liquid, [BMIM][PF6] is analyzed using the Hybrid Variation-Perturbation Theory approach. The analysis is performed on a sample of configurations from molecular dynamics simulation, instead of m
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::385fdcc56d3838db541c66fe99889c77
https://doi.org/10.1021/jp411363d
https://doi.org/10.1021/jp411363d
Autor:
Wiktoria Jedwabny, Edyta Dyguda-Kazimierowicz, Rebecca C. Wade, W. Andrzej Sokalski, Joanna Panecka-Hofman
Publikováno v:
Journal of Computer-Aided Molecular Design
There is a need for improved and generally applicable scoring functions for fragment-based approaches to ligand design. Here, we evaluate the performance of a computationally efficient model for inhibitory activity estimation, which is composed only
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::daeb6d450dfea255e47e800ea9917657
https://pubmed.ncbi.nlm.nih.gov/28688090
https://pubmed.ncbi.nlm.nih.gov/28688090
Publikováno v:
Chemical Physics Letters. 552:156-161
Based on the hybrid variational-perturbation decomposition scheme we show that the electrostatic and delocalization energy terms are the most stabilizing components of the interaction energy of the charge-inverted hydrogen-bond (CIHB). It is shown th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::75b46cc6252f30ecb8f179e59c1148d5
https://doi.org/10.1016/j.cplett.2012.09.061
https://doi.org/10.1016/j.cplett.2012.09.061