From Single Hydrogen Bonds to Extended Hydrogen-Bond Wires: Low-Dimensional Model Systems for Vibrational Spectroscopy of Associated Liquids

2013 ◽  
Vol 52 (37) ◽  
pp. 9634-9654 ◽  
Author(s):  
Martin Olschewski ◽  
Stephan Knop ◽  
Jörg Lindner ◽  
Peter Vöhringer
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Vibrational Spectroscopy ◽  
Model Systems ◽  
Dimensional Model ◽  
Bond Wires ◽  
Low Dimensional

scholarly journals Hydrogen bond simulation in molecular crystals of tyrosine

2019 ◽  
Vol 58 (6) ◽  
pp. 73-77
Author(s):  
Tatiana G. Volkova ◽  
◽  
Irina O. Talanova ◽  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Biologically Active ◽  
Model Systems ◽  
Significant Difference ◽  
Molecular Associate ◽  
Order Of Magnitude ◽  
Chemical Simulation

The problem of the study of hydrogen bonds in biomolecules and living systems is important. Among the drugs, doctors emphasize substances of natural origin involved in metabolic processes. Such compounds include amino acids, peptides, vitamins, enzymes, macro- and microelements, and other biologically active substances, many of which are capable of forming hydrogen bonds. Amino acids and their derivatives are drugs of metabolic pharmacotherapy, characterized by low toxicity and severity of side effects. They also have virtually no allergenic effect, which makes them promising for the creation of drugs or their modifications. The instability of the hydrogen bond can significantly affect the state of pharmaceutical drug containing, for example, amino acids, during their storage, transportation or technological processing. One of the methods for studying the nature and determining the strength of hydrogen bonds is quantum chemical simulation. The calculation of the interaction energy in the studied molecular associate and its decomposition have been carried out according to Morocuma’s method (HF/6-31G (PC GAMESS). The evaluation of such energy components as electrostatic, exchange repulsion, polarization, charge transfer, mixing is given. The main contribution to the interaction energy comes from the electrostatic component. All the studied models have the same distribution of the components of the interaction energy in order of magnitude. Significant difference in the interaction energy in two model systems was noted, that could be explained by different geometry of hydrogen bonds. The comparison of received data made it possible to conclude that there are three types of hydrogen bonds in the molecular tyrosine crystal, which differ from each other in energy and geometry.

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 Surface resonances on transition metals as low-dimensional model systems

2007 ◽  
Vol 9 (10) ◽  
pp. 386-386 ◽  
Author(s):  
M Minca ◽  
S Penner ◽  
E Dona ◽  
A Menzel ◽  
E Bertel ◽  
...  
Keyword(s):  
Transition Metals ◽  
Model Systems ◽  
Dimensional Model ◽  
Low Dimensional

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>

Hydrogen bonds in N-(3-chloro-2-benzo[b]thienocarbonyl)- and N-(2-benzo[b]thienocarbonyl)-N'-monosubstituted thioureas

1987 ◽  
Vol 52 (11) ◽  
pp. 2673-2679 ◽  
Author(s):  
Oľga Hritzová ◽  
Peter Kutschy ◽  
Ján Imrich ◽  
Thomas Schöffmann
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Strong Hydrogen Bond ◽  
Cyclic Form ◽  
Thiourea Derivatives

N-(3-Chloro-2-benzo[b]thienocarbonyl)-N'-monosubstituted thiourea derivatives undergo photocyclizations with lower yields than those obtained from analogous N',N'-disubstituted derivatives. This decreased reactivity is caused by the existence of a six-membered cyclic form with the very strong hydrogen bond NH···O=C. The possibility of formation of various conformers has been found with N-(2-benzo[b]thienocarbonyl)-N'-monosubstituted thiourea derivatives as a consequence of the rotation around the C(2)-C(O) connecting line.

Crystal structure of tofacitinib dihydrogen citrate (Xeljanz®), (C16H21N6O)(H2C6H5O7)

2021 ◽  
pp. 1-8
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Acid Group ◽  
Dimensional Network ◽  
Van Der Waals Contacts ◽  
Citrate Anion

The crystal structure of tofacitinib dihydrogen citrate (tofacitinib citrate) has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Tofacitinib dihydrogen citrate crystallizes in space group P212121 (#19) with a = 5.91113(1), b = 12.93131(3), c = 30.43499(7) Å, V = 2326.411(6) Å3, and Z = 4. The crystal structure consists of corrugated layers perpendicular to the c-axis. Within the layers, cation⋯anion and anion⋯anion hydrogen bonds link the fragments into a two-dimensional network parallel to the ab-plane. Between the layers, there are only van der Waals contacts. A terminal carboxylic acid group in the citrate anion forms a strong charge-assisted hydrogen bond to the ionized central carboxylate group. The other carboxylic acid acts as a donor to the carbonyl group of the cation. The citrate hydroxy group forms an intramolecular charge-assisted hydrogen bond to the ionized central carboxylate. Two protonated nitrogen atoms in the cation act as donors to the ionized central carboxylate of the anion. These hydrogen bonds form a ring with the graph set symbol R2,2(8). The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

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