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 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 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 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 Effective prediction of short hydrogen bonds in proteins via machine learning method

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Shengmin Zhou ◽  
Yuanhao Liu ◽  
Sijian Wang ◽  
Lu Wang
Keyword(s):  
Machine Learning ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Protein Structures ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Donor And Acceptor ◽  
Wide Range ◽  
Short Hydrogen Bonds

AbstractShort hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.

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 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 Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

2016 ◽  
Vol 18 (29) ◽  
pp. 19746-19756 ◽  
Author(s):  
Suehiro Iwata ◽  
Dai Akase ◽  
Misako Aida ◽  
Sotiris S. Xantheas
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Nearest Neighbor ◽  
Water Clusters ◽  
Hydrogen Donor ◽  
Donor And Acceptor ◽  
Bond Strengths

Comparison of the sum of the characteristic factors for some of the typical hydrogen donor and acceptor pairs with the CT term/kJ mol−1 (the upper value) and the O⋯O distance/in cubic (H2O)8.

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