A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

2020 ◽  
Author(s):  
Egle Maximowitsch ◽  
Tatiana Domratcheva
Keyword(s):  
Hydrogen Bond ◽  
Light Adaptation ◽  
Positive Charge ◽  
Pyrrole Ring ◽  
Md Simulations ◽  
Spectral Shift ◽  
Specific Domain ◽  
Study Guides ◽  
Rational Engineering ◽  
Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

scholarly journals A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

2020 ◽  
Author(s):  
Egle Maximowitsch ◽  
Tatiana Domratcheva
Keyword(s):  
Hydrogen Bond ◽  
Light Adaptation ◽  
Positive Charge ◽  
Pyrrole Ring ◽  
Md Simulations ◽  
Spectral Shift ◽  
Specific Domain ◽  
Study Guides ◽  
Rational Engineering ◽  
Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

scholarly journals Cocrystals of Ethenzamide With 2-Nitrobenzoic Acid - Conformational Analysis, MD Simulations And DFT Investigations

2021 ◽  
Author(s):  
Y. Sheena Mary ◽  
Y. Shyma Mary ◽  
Razieh Razavi
Keyword(s):  
Hydrogen Bond ◽  
Conformational Analysis ◽  
Crystal Engineering ◽  
Energy Charge ◽  
Thermodynamic Characteristics ◽  
Md Simulations ◽  
Pharmaceutical Chemistry ◽  
Nitrobenzoic Acid ◽  
Wide Range ◽  
Stability Energy

Abstract In crystal engineering and pharmaceutical chemistry, cocrystals have a wide range of applications. Ethenzamide (EA) is found to form cocrystal with 2-nitrobenzoic acid (NBA). Geometry properties like stability energy, charge distribution, bond length, electronic properties and thermodynamic characteristics have been analyzed. The C-H…O hydrogen bond involves C-H of EA and oxygen of NBA. Configuration with the angle, N3-C4-C5-C6 gives the lowest energy conformation. Partition coefficient value suggests that EA-NBA has pharmaceutics behavior. RMSD values show the simulation’s relative stability and the complexes, remained stable throughout.

THE STUDY OF HYDROGEN BONDING AND RELATED PHENOMENA BY SPECTROSCOPIC METHODS: PART VIII. THE ULTRAVIOLET AND INFRARED SPECTRA OF SOME 2,4-DINITRODIPHENYLAMINES

1964 ◽  
Vol 42 (12) ◽  
pp. 2674-2683 ◽  
Author(s):  
A. Balasubramanian ◽  
J. B. Capindale ◽  
W. F. Forbes
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Spectral Data ◽  
Intramolecular Hydrogen Bond ◽  
Infrared Spectra ◽  
Positive Charge ◽  
Spectroscopic Methods ◽  
Amino Group ◽  
Strong Type ◽  
Intramolecular Hydrogen

The ultraviolet spectra of a number of 2,4-dinitrodiphenylamines suggest that these compounds are generally non-planar in a number of different solvents. The infrared and ultraviolet spectral data in different solvents also suggest that an intramolecular hydrogen bond is present in these molecules, at least in inert solvents. There is evidence that a p-nitro substituent is necessary to increase the positive charge on the amino group sufficiently to permit it to form this fairly strong type of hydrogen bond.

Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol revisited

2004 ◽  
Vol 76 (1) ◽  
pp. 247-254 ◽  
Author(s):  
H. Torii
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Pressure Dependence ◽  
Md Simulations ◽  
Liquid Structure ◽  
Present Calculation ◽  
Number Density ◽  
Transition Dipole ◽  
Liquid Systems

Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol is examined with the combination of molecular dynamics (MD) simulations and the intermolecular resonant vibrational interactions determined by the transition dipole coupling (TDC) mechanism (MD/TDC method). It is shown that the observed decrease of the Raman noncoincidence νNCE of the CO stretching band with increasing density reported in the literature is quantitatively reproduced by the present calculation. As the density increases, the hydrogen bonds get slightly shorter, but molecules belonging to different hydrogen-bond chains get closer to each other to a greater extent. This anisotropic change in the liquid structure is the reason for the behavior of νNCE. It is also shown that the concentration dependence of νNCE in the methanol/CCl4 binary mixtures reported in a previous study, and the pressure dependence of νNCE in methanol may be described in a consistent way as a function of the number density of methanol in the liquid systems.

scholarly journals 4-Methoxybenzoyl-meso-octamethylcalix[2]pyrrolidino[2]pyrrole: an acyl chloride derivative of a partially reduced calix[4]pyrrole

2012 ◽  
Vol 68 (4) ◽  
pp. o929-o930 ◽  
Author(s):  
Guillaume Journot ◽  
Reinhard Neier ◽  
Helen Stoeckli-Evans
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Pyrrole Ring ◽  
Acyl Chloride ◽  
Compound C ◽  
Centroid Distance

In the title compound, C36H50N4O2, the two pyrrolidine rings have envelope conformations. The conformation of the macrocycle is stabilized by N—H...N hydrogen bonds and a C—H...N interaction. The benzoyl ring is inclined to an adjacent pyrrole ring by 6.76 (9)°, with a centroid-to-centroid distance of 3.6285 (10) Å. In the crystal, apart from a C—H...O and a C—H...π interaction, molecules are linkedviaan N—H...O hydrogen bond, leading to the formation of helical chains propagating along [010].

An abnormally weak hydrogen bond in a diol with a O° dihedral angle. Breakdown of the OH....OH spectral shift-dihedral angle relationship

1972 ◽  
Vol 13 (30) ◽  
pp. 3039-3042
Author(s):  
T.M. Gorrie ◽  
E.M. Engler ◽  
R.C. Bingham ◽  
P.v.R. Schleyer
Keyword(s):  
Hydrogen Bond ◽  
Dihedral Angle ◽  
Spectral Shift ◽  
Weak Hydrogen Bond

1,7-Dideaza-2′-deoxy-6-nitronebularine: a pyrrolo[2,3-b]pyridine nucleoside with an intramolecular hydrogen bond stabilizing thesynconformation

2013 ◽  
Vol 69 (8) ◽  
pp. 892-895
Author(s):  
Haozhe Yang ◽  
Simone Budow ◽  
Henning Eickmeier ◽  
Hans Reuter ◽  
Frank Seela
Keyword(s):  
Hydrogen Bond ◽  
Intramolecular Hydrogen Bond ◽  
Torsion Angle ◽  
Pyridine Ring ◽  
Pyrrole Ring ◽  
Three Dimensional ◽  
Sugar Residue ◽  
Adjacent Layer ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The title compound [systematic name: 1-(2-deoxy-β-D-erythro-pentofuranosyl)-4-nitro-1H-pyrrolo[2,3-b]pyridine], C12H13N3O5, forms an intramolecular hydrogen bond between the pyridine N atom as acceptor and the 5′-hydroxy group of the sugar residue as donor. Consequently, the N-glycosylic bond exhibits asynconformation, with a χ torsion angle of 61.6 (2)°, and the pentofuranosyl residue adopts a C2′-endoenvelope conformation (2E,S-type), withP= 162.1 (1)° and τm= 36.2 (1)°. The orientation of the exocyclic C4′—C5′ bond is +sc(gauche,gauche), with a torsion angle γ = 49.1 (2)°. The title nucleoside forms an ordered and stacked three-dimensional network. The pyrrole ring of one layer faces the pyridine ring of an adjacent layer. Additionally, intermolecular O—H...O and C—H...O hydrogen bonds stabilize the crystal structure.

Ionic hydrogen bond donor organocatalyst for fast living ring-opening polymerization

2016 ◽  
Vol 7 (2) ◽  
pp. 339-349 ◽  
Author(s):  
Xu Zhi ◽  
Jingjing Liu ◽  
Zhenjiang Li ◽  
Huiying Wang ◽  
Xin Wang ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Ring Opening ◽  
Positive Charge ◽  
Ring Opening Polymerization ◽  
Hydrogen Bond Donor

A positive charge enhanced H-bond donor combined with H-bond acceptor as a bifunctional organocatalyst enables fast living ring-opening polymerization of lactide.

scholarly journals Selectivity of cations and nonelectrolytes for acetylcholine-activated channels in cultured muscle cells.

1978 ◽  
Vol 71 (4) ◽  
pp. 397-410 ◽  
Author(s):  
L Y Huang ◽  
W A Catterall ◽  
G Ehrenstein
Keyword(s):  
Hydrogen Bond ◽  
Positive Charge ◽  
Binding Capacity ◽  
High Mobility ◽  
Muscle Cells ◽  
The Other ◽  
Organic Cations ◽  
Hydrogen Binding ◽  
Alkali Cations ◽  
Charged Site

The selectivity of acetylcholine (A-Ch)-activated channels for alkali cations, organic cations, and nonelectrolytes in cultured muscle cells has been studied. To test the effect of size, charge, and hydrogen-binding capacity of permeant molecules on their permeability, we have obtained the selectivity sequences of alkali cations, compared the permeability of pairs of permeant molecules with similar size and shape but differing in charge, and studied the permeability of amines of different hydrogen bonding capacity. ACh-activated channels transport alkali cations of small hydration radii and high mobility. The molecules with positive charge and (or) a hydrogen-bond donating moiety are more permeable than the ones without. On the other hand, several nonelectrolytes, i.e., ethylene glycol, formamide, and urea, do have a small, but measurable, permeability through the channels. These results are consistent with a model that ACh-activated channel is a water-filled pore containing dipoles or hydrogen bond accepting groups and a negative charged site with a pK of 4.8.

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