Lone-pair–pi interactions: analysis of the physical origin and
biolological implications

J 2016

Lone-pair–pi interactions: analysis of the physical origin and biolological implications

NOVOTNÝ, Jan, Sophia BAZZI, Radek MAREK a Jiří KOZELKA

Základní údaje

Originální název

Lone-pair–pi interactions: analysis of the physical origin and biolological implications

Autoři

NOVOTNÝ, Jan (203 Česká republika, domácí), Sophia BAZZI (364 Írán, domácí), Radek MAREK (203 Česká republika, domácí) a Jiří KOZELKA (250 Francie, garant, domácí)

Vydání

Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 1463-9076

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

DOI: 10.1039/C6CP01524G

Impakt faktor

Impact factor: 4.123

Kód RIV

RIV/00216224:14310/16:00087988

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1039/C6CP01524G

UT WoS

000379939100089

Klíčová slova anglicky

lone-pair-pi interaction; anion-pi; DFT; energy decomposition analysis

Štítky

AKR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 9. 2019 14:45, prof. RNDr. Radek Marek, Ph.D.

Anotace

V originále

Lone-pair-pi (lp-pi) interactions have been suggested to stabilize DNA and protein structures, and to participate in the formation of DNA-protein complexes. To elucidate their physical origin, we have carried out a theoretical multi-approach analysis of two biologically relevant model systems, the water-indole and water-uracil complexes, which we compared with the structurally similar chloride-tetracyanobenzene (TCB) complex previously shown to contain a strong charge-transfer (CT) binding component. We demonstrate that the CT component in lp-pi interactions between water and indole/uracil is significantly smaller than that stabilizing the Cl-TCB reference system. The strong lp(Cl-)-pi(TCB)* orbital interaction is characterized by a small energy gap and an efficient lp-pi* overlap. In contrast, in lp-pi interactions between water and indole or uracil, the corresponding energy gap is larger and the overlap less efficient. As a result, water-uracil and water-indole interactions are weak forces composed by smaller contributions from electrostatics, polarization, dispersion, and charge transfer. In addition, indole exhibits a negative electrostatic potential at its pi-face, making lp-pi interactions less favorable than O-H···pi hydrogen bonding. Consequently, some of the water-tryptophan contacts observed in X-ray structures of proteins and previously interpreted as lp-pi interactions [Luisi et al., Proteins 2004, 57, 1-8], might in fact arise from O-H···pi hydrogen bonding.

Návaznosti

GA14-14654S, projekt VaV

Název: Studium fyzikální podstaty interakcí lone-pair-pi v biomolekulárních systémech. Role interakcí lone-pair-pi při stabilizaci proteinu Engrailed (Akronym: Lone-pair-pi interactions)

Investor: Grantová agentura ČR, Towards the physical basis of lone-pair-pi interactions. Do lone-pair-pi interactions stabilize the structure of the Engrailed homeodomain?

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

NOVOTNÝ, Jan, Sophia BAZZI, Radek MAREK a Jiří KOZELKA. Lone-pair–pi interactions: analysis of the physical origin and biolological implications. Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2016, roč. 18, č. 28, s. 19472-19481. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/C6CP01524G.

@article{1347769,
   author = {Novotný, Jan and Bazzi, Sophia and Marek, Radek and Kozelka, Jiří},
   article_number = {28},
   doi = {http://dx.doi.org/10.1039/C6CP01524G},
   keywords = {lone-pair-pi interaction; anion-pi; DFT; energy decomposition analysis},
   language = {eng},
   issn = {1463-9076},
   journal = {Physical Chemistry Chemical Physics},
   title = {Lone-pair–pi interactions: analysis of the physical origin and biolological implications},
   url = {http://dx.doi.org/10.1039/C6CP01524G},
   volume = {18},
   year = {2016}
}

TY  - JOUR
ID  - 1347769
AU  - Novotný, Jan - Bazzi, Sophia - Marek, Radek - Kozelka, Jiří
PY  - 2016
TI  - Lone-pair–pi interactions: analysis of the physical origin and biolological implications
JF  - Physical Chemistry Chemical Physics
VL  - 18
IS  - 28
SP  - 19472-19481
EP  - 19472-19481
PB  - Royal Society of Chemistry
SN  - 14639076
KW  - lone-pair-pi interaction
KW  - anion-pi
KW  - DFT
KW  - energy decomposition analysis
UR  - http://dx.doi.org/10.1039/C6CP01524G
L2  - http://dx.doi.org/10.1039/C6CP01524G
N2  - Lone-pair-pi (lp-pi) interactions have been suggested to stabilize DNA and protein structures, and to participate in the formation of DNA-protein complexes. To elucidate their physical origin, we have carried out a theoretical multi-approach analysis of two biologically relevant model systems, the water-indole and water-uracil complexes, which we compared with the structurally similar chloride-tetracyanobenzene (TCB) complex previously shown to contain a strong charge-transfer (CT) binding component. We demonstrate that the CT component in lp-pi interactions between water and indole/uracil is significantly smaller than that stabilizing the Cl-TCB reference system. The strong lp(Cl-)-pi(TCB)* orbital interaction is characterized by a small energy gap and an efficient lp-pi* overlap. In contrast, in lp-pi interactions between water and indole or uracil, the corresponding energy gap is larger and the overlap less efficient. As a result, water-uracil and water-indole interactions are weak forces composed by smaller contributions from electrostatics, polarization, dispersion, and charge transfer. In addition, indole exhibits a negative electrostatic potential at its pi-face, making lp-pi interactions less favorable than O-H···pi hydrogen bonding. Consequently, some of the water-tryptophan contacts observed in X-ray structures of proteins and previously interpreted as lp-pi interactions [Luisi et al., Proteins 2004, 57, 1-8], might in fact arise from O-H···pi hydrogen bonding.
ER  -

NOVOTNÝ, Jan, Sophia BAZZI, Radek MAREK a Jiří KOZELKA. Lone-pair–pi interactions: analysis of the physical origin and biolological implications. \textit{Physical Chemistry Chemical Physics}. Royal Society of Chemistry, 2016, roč.~18, č.~28, s.~19472-19481. ISSN~1463-9076. Dostupné z: https://dx.doi.org/10.1039/C6CP01524G.

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