scholarly journals Short hydrogen bonds enhance nonaromatic protein-related fluorescence

2021 ◽  
Vol 118 (21) ◽  
pp. e2020389118
Author(s):  
Amberley D. Stephens ◽  
Muhammad Nawaz Qaisrani ◽  
Michael T. Ruggiero ◽  
Gonzalo Díaz Mirón ◽  
Uriel N. Morzan ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Transition Probabilities ◽  
Ab Initio Molecular Dynamics ◽  
Single Amino Acid ◽  
Hydrogen Bond Networks ◽  
Short Hydrogen Bond ◽  
Photoactive Materials ◽  
Dynamics Simulations ◽  
Short Hydrogen Bonds

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

scholarly journals Car–Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone

2014 ◽  
Vol 16 (42) ◽  
pp. 23026-23037 ◽  
Author(s):  
Piotr Durlak ◽  
Zdzisław Latajka
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Path Integral ◽  
Molecular Crystal ◽  
Short Hydrogen Bond ◽  
Deuterated Analogue ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations.

scholarly journals A quantum crystallographic approach to short hydrogen bonds

CrystEngComm ◽  
2021 ◽  
Author(s):  
Lucy K. Saunders ◽  
Anuradha R. Pallipurath ◽  
Matthias J. Gutmann ◽  
Harriott Nowell ◽  
Ningjin Zhang ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Electron Density ◽  
Short Hydrogen Bond ◽  
Atom Position ◽  
Short Hydrogen Bonds ◽  
Bond Characteristics

Mapped electron density and ab initio modelling reveal how H-atom position and molecular environment tune short hydrogen bond characteristics and properties.

scholarly journals Structure and thermal properties

1939 ◽  
Vol 173 (955) ◽  
pp. 427-427 ◽  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Thermal Properties ◽  
Hydrogen Bonds ◽  
Isotope Effect ◽  
Hydrogen Fluoride ◽  
Potassium Phosphate ◽  
Short Hydrogen Bond ◽  
Potassium Hydrogen ◽  
Short Hydrogen Bonds

The effect on the lattice spacings of substituting deuterium for hydrogen has been investigated for pentaerythritol, CuS0 4 5H 2 0, SrCl 2 6H 2 0, furmaric acid, KH 2 P0 4 , NaHS0 4 , urea, and KHF 2 . The main conclusion is that when the crystal structure contains hydroxyl bonds the isotope effect is small, and when it contains hydrogen bonds there is a marked expansion, which disturbs the lattice sufficiently to lead to the separation of potassium phosphate in a new crystal structure. The effect for potassium hydrogen fluoride does not suggest a short hydrogen bond in this compound. Short hydrogen bonds seem to require special resonance forces for their explanation.

scholarly journals Unusual Spectroscopic and Electric Field Sensitivity of a Chromophore with Short Hydrogen Bond: GFP and PYP as Model Systems

2020 ◽  
Author(s):  
Chi-Yun Lin ◽  
Steven Boxer
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Electric Field ◽  
External Electric Field ◽  
Heavy Atom ◽  
Model Systems ◽  
Donor And Acceptor ◽  
Short Hydrogen Bond ◽  
Structural Methods ◽  
Short Hydrogen Bonds

<p> Short hydrogen bonds, with heavy-atom distances less than 2.7 Å, are believed to exhibit proton delocalization and their possible role in catalysis has been widely debated. While spectroscopic and/or structural methods are usually employed to study the degree of proton delocalization, ambiguities still arise and no direct information on the corresponding potential energy surface is obtained. Here we apply an external electric field to perturb the short hydrogen bond(s) within a collection of green fluorescent protein S65T/H148D variants and photoactive yellow protein mutants, where the chromophore participates in the short hydrogen bond(s) and serves as an optical probe of the proton position. As the proton is charged, its position may shift in response to the external electric field, and the chromophore’s electronic absorption can thus reflect the ease of proton transfer. The results suggest that low-barrier hydrogen bonds are not present within these proteins even when proton affinities between donor and acceptor are closely matched. Exploiting the chromophores as pre-calibrated electrostatic probes, the covalency of short hydrogen bonds as a non-electrostatic component was also revealed. No clear evidence was found for a possible contribution of unusually large polarizabilities of short hydrogen bonds due to proton delocalization; a theoretical framework for this interesting phenomenon is developed.<br></p>

scholarly journals Structure and thermal properties associated with some hydrogen bonds in crystals. III. Further examples of the isotope effect

1939 ◽  
Vol 173 (954) ◽  
pp. 417-427 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Thermal Properties ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Isotope Effect ◽  
Resonance Effects ◽  
Short Hydrogen Bond ◽  
Salt Hydrates ◽  
Small Change ◽  
Short Hydrogen Bonds

The conclusion from previous experiments on the isotope effect in crystals (Robertson and Ubbelohde 1939) was that on substituting D for H in hydroxyl bonds (length 2.75-285 A) there was only a small change in the lattice spacings, whereas for the short hydrogen bonds (length ~2.55 A) there was a considerable expansion. From this conclusion it was suggested that resonance effects must contribute an appreciable proportion of the binding energy in short hydrogen bonds. One difficulty in this suggestion arose from the complicated crystal structures used, for which inferences about changes in bond lengths cannot be very direct. The aim of the present experiments was to substantiate the former results by investigating further examples of the isotope effect. In order to have a structurally simple example of the hydroxyl bond, pentaerythritol C(CH 2 OH) 4 was compared with C(CH 2 OD) 4 . The salt hydrates SrCl 2 6H 2 O and CuSO 4 5H 2 O were also compared with the corresponding deuterium compounds. For the short hydrogen bond a comparison was made between KH 2 PO 4 and KD 2 PO 4 . The (unknown) structures of NaHSO 4 and fumaric acid were also investigated. Finally, in order to obtain information on possible “hydrogen bonds” between atoms other than oxygen, urea was compared with CO(ND 2 ) 2 and KHF 2 with KDF 2 . In addition to confirming the previous conclusions, certain fresh facts have emerged about the behaviour of hydrogen bonds in crystals, as is recorded below.

scholarly journals Unusual Spectroscopic and Electric Field Sensitivity of a Chromophore with Short Hydrogen Bond: GFP and PYP as Model Systems

2020 ◽  
Author(s):  
Chi-Yun Lin ◽  
Steven Boxer
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Electric Field ◽  
External Electric Field ◽  
Heavy Atom ◽  
Model Systems ◽  
Donor And Acceptor ◽  
Short Hydrogen Bond ◽  
Structural Methods ◽  
Short Hydrogen Bonds

<p> Short hydrogen bonds, with heavy-atom distances less than 2.7 Å, are believed to exhibit proton delocalization and their possible role in catalysis has been widely debated. While spectroscopic and/or structural methods are usually employed to study the degree of proton delocalization, ambiguities still arise and no direct information on the corresponding potential energy surface is obtained. Here we apply an external electric field to perturb the short hydrogen bond(s) within a collection of green fluorescent protein S65T/H148D variants and photoactive yellow protein mutants, where the chromophore participates in the short hydrogen bond(s) and serves as an optical probe of the proton position. As the proton is charged, its position may shift in response to the external electric field, and the chromophore’s electronic absorption can thus reflect the ease of proton transfer. The results suggest that low-barrier hydrogen bonds are not present within these proteins even when proton affinities between donor and acceptor are closely matched. Exploiting the chromophores as pre-calibrated electrostatic probes, the covalency of short hydrogen bonds as a non-electrostatic component was also revealed. No clear evidence was found for a possible contribution of unusually large polarizabilities of short hydrogen bonds due to proton delocalization; a theoretical framework for this interesting phenomenon is developed.<br></p>

scholarly journals Short hydrogen bonds in the catalytic mechanism of serine proteases

2008 ◽  
Vol 73 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Vladimir Leskovac ◽  
Svetlana Trivic ◽  
Draginja Pericin ◽  
Mira Popovic ◽  
Julijan Kandrac
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Serine Proteases ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Data Bank ◽  
Ground State Structure ◽  
Low Barrier Hydrogen Bonds ◽  
Short Hydrogen Bonds

The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

Hydrogen-Bond Networks: Strengths of Different Types of Hydrogen Bonds and An Alternative to the Low Barrier Hydrogen-Bond Proposal

2013 ◽  
Vol 135 (47) ◽  
pp. 17919-17924 ◽  
Author(s):  
Alireza Shokri ◽  
Yanping Wang ◽  
George A. O’Doherty ◽  
Xue-Bin Wang ◽  
Steven R. Kass
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Networks ◽  
Different Types
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