Prírodovedecká fakultaUniverzita Komenského v Bratislave

Prednáška Properties of proteins and nano materials calculated with the fragment molecular orbital (FMO) method

Pozvánka na prednášku

2019-08-02-pozvanka.pdf

2019-08-02-seminar-abstract.pdf

Properties of proteins and nano materials calculated with the fragment molecular orbital (FMO) method

D. G. Fedorov

Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan

Vážení kolegovia,
dovoľujeme si Vás srdečne pozvať na prednášku Dr. Fedorova, ktorá sa uskutoční v prednáškovej miestnosti AMOS na Prírodovedeckej Fakute UK dňa 2. 8. 2019 o 10:30.

Prednáška je orientovaná na širšiu vedeckú komunitu z oblasti výskumu štruktúry a funkcie proteínov, príp. iných bio-makromolekúl. Cieľovú skupinu poslucháčov možno rozdeliť do dvoch kategórií. Jedna sú teoretickí chemici, biofizici, ktorí sa oboznámia s najnovším stavom v oblasti vývoja a implementácie pokročílých výpočtových FMO metód aplikovateľných na štúdium vlastností a interakcií v a medzi proteínmi. Druhou, sú biochemici a/alebo štrukturálni/molekulárni biológovia pracujúci s proteínmi. Títo sa rovnako dozvedia čo všetko je v súčasnosti už možné študovať presnými ab initio metódami, alebo ako teroretické výsledky môžu priniesť jasnejšiu interpretáciu experimentálnych pozorovaní. Veríme, že je jednoduchšie nadobudnúť predstavu o možnostiach tejto “state of the art” metódy výpočtovej chémie formou seminára, ako pracným samoštúdiom. Rovnako veríme, že takouto formou je možné napomôcť plodnejšej spolupráci teoretických a expetimentálnych skupín v oblasti biomolekúl a otvárať dvere pre nové smery vývoja teoretických metód, tak, ako je to už roky praxou pri štúdiu malých molekúl.

Tešíme sa na Vašu účasť!

Za organizátorov

Vladimir Sladek, PhD.
Inst. of Chemistry - Centre for Glycomics
Slovak Academy of Sciences
Dubravska cesta 9
845 38 Bratislava, Slovakia
E-mail: sladek.vladimirsavba.sk
Tel.: ++421 2 594 10 322

Invitation to the lecture

Properties of proteins and nano materials calculated with the fragment molecular orbital (FMO) method

D. G. Fedorov

Research Center for Computational Design of Advanced Functional Materials  CD-FMat), National Institute of Advanced Industrial Science and Technology  (AIST), Tsukuba, Japan

Dear colleagues,
it is a pleasure to invite you cordially to the lecture by Dr. Fedorov, which will be  held in the seminar room AMOS at the Faulty of Natural Sciences UK on the 2nd of August 2019 at 10:30.

The lecture is intended for the broader scientific community who’s research is  oriented on structural and/or functional study of proteins and other large biomolecules.

The target audience may be split into two subcategories. Firstly, theoretical chemists, biophysicists etc. might be interested to learn about the current state of the development and implementation of the FMO method – a method tailored for the study of structure, energetics and interactions of large molecules at the level of electronic structure theory. Secondly, biochemists and structural/molecular biologists working with proteins can benefit form this lecture too. These specialists can broaden their perspective on what can at present be studied with ab initio methods in their field and establish links to experimental observations. We believe that is is more effective to attain basic knowledge of the possibilities of this state of the art method (FMO) rather than by laborious self-education. Finally, we hope that sharing experimental expectations in the field of proteomics with theoreticians can induce new directions in the method development.

We are awaiting you at the talk!

Abstract

Properties of proteins and nano materials calculated with the fragment molecular orbital method

Dmitri G. Fedorov

CD-FMat, AIST, Tsukuba, Japan

By fragmenting large molecular systems into pieces called fragments and computing the properties of fragments and interactions between them, one can perform quantum-mechanical calculations very efficiently and also obtain very rich insight into their properties. The two types of systems in the title are only two important examples, and other systems can be treated as well.

The fragment molecular orbital method (FMO) is based a series expansion of properties such as energy or electron density. In the series, the starting point is the electronic state of isolated fragments, to which the polarization, charge transfer and other physically well-defined contributions are added.

By enhancing the series expansion with a decomposition analysis, it is possible to evaluate the polarization, electrostatic interaction, charge transfer (CT), exchange-repulsion, dispersion, solvent screening and other properties. As an example, the total electron density of a cyclic water trimer can be decomposed as isolated polarization pairwise charge transfer CT coupling

The interaction energies between fragments provide useful insight into molecular recognition of drug ligand molecules by amino acid residues in proteins. FMO can also be used to compute electronic excited states, IR and Raman spectra, and other properties.

Geometry optimizations and MD simulations of large molecular systems can be performed.

For nano materials, density of states can be computed from a series expansion of the Fock matrix.

The FMO program is distributed free of charge inside GAMESS package. Several GUIs are also available (Facio, FU and others).

D. G. Fedorov. The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications. WIREs: Comp. Mol. Sc. 7 (2017) e1322.