scholarly journals Hydrogen bonding and DNA: 66-year retrospective (briefly)

2020 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Double Helix ◽  
Density Functional Method ◽  
Point Mutations ◽  
Functional Method ◽  
Wide Range ◽  
Functional Features ◽  
Hydrogen Bonded

Background: As Yu.P. Blagoi, the memory of who is dedicated to this work, once said: "The molecular structure of DNA — the famous double helix — is stabilized by water molecules and metal ions". The central, key interaction that determines both the double-helix structure of DNA and its functioning (the genetic code, replication, mutagenesis) is hydrogen-bonded interaction. Objectives: Demonstration of the diverse manifestations of the hydrogen bond in the structure and functioning of DNA. Materials and Methods: A computer simulation based on the density functional method was used. Results: This paper identifies a wide range of hydrogen-bonded interactions that determine key aspects of both DNA structures and functional features related to heredity (replication, mutagenesis). Conclusions: The preopeness of DNA base pairs with an embedded water molecule on the exterior hydrogen bond create more favorable conditions for proton transitions between bases along the central hydrogen bond. In this case, the hydrogen bonds of the bases to a lesser extent hinder the transition of the proton due to the smaller electrostatic repulsion (due to a larger distance) between them. Therefore, the preopened pairs are likely to form tautomeric forms of nucleic acid bases and to originate a probable mechanism for the formation of point mutations in DNA. At the same time, the central hydrogen bonds with the imino groups of bases in pairs remain intact.

Density functional studies of fused dodecahedral and irregular-dodecahedral water cages

RSC Advances ◽  
2015 ◽  
Vol 5 (91) ◽  
pp. 74270-74273 ◽  
Author(s):  
V. Shilpi ◽  
Surinder Pal Kaur ◽  
C. N. Ramachandran
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Density Functional Method ◽  
Functional Method ◽  
Functional Studies

The fused cages of dodecahedral and irregular-dodecahedral water cages with the maximum number of t1d hydrogen bonds were studied using the dispersion corrected density functional method.

A THEORETICAL INVESTIGATION OF THE INTERACTIONS BETWEEN CELLULOSE AND 1-BUTYL-3-METHYLIMIDAZOLIUM CHLORIDE

2010 ◽  
Vol 09 (03) ◽  
pp. 611-624 ◽  
Author(s):  
JINXIN GUO ◽  
DONGJU ZHANG ◽  
CHENGBU LIU
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Density Functional Method ◽  
Functional Method ◽  
Chloride Anion ◽  
Cellulose Dissolution ◽  
Hydrogen Atoms ◽  
Imidazolium Cation ◽  
Quantum Chemistry Calculations ◽  
Weak Hydrogen Bonds

To better understand the interactions between cellulose and imidazolium-based ionic liquids (ILs), quantum chemistry calculations have been performed on the systems composed of one cellulose unit with the anion, cation, and the ion pair of 1-butyl-3-methylimidazolium chloride ( [bmim]Cl ) by the density functional method. The relevant geometries, energies, electronic properties and IR characteristics have been systematically discussed. It is found that H-bond interaction is essential for the systems under consideration. The hydroxyls in cellulose bind to chloride anions strongly through H -bonds, which could be predominant to cellulose dissolution in ILs. Chloride anion prefers to occur between two adjacent hydroxyls in cellulose to form bridging OH⋯Cl⋯HO hydrogen bonds. In contrast, weak hydrogen bonds exist between the hydrogen atoms on the imidazolium cation and hydroxyl oxygen atoms of cellulose, which are too much weaker than the hydrogen bonds between the cellulose hydroxyls and chloride anions to be detected by the experiments. The phenomena of cellulose dissolution in ILs should be a result of the joint interactions of chloride anions and [bmim]+ cations with hydroxyls in cellulose.

scholarly journals The Watson-Crick rare tautomer hypothesis of mutations and reality

2020 ◽  
Keyword(s):  
Charge Transfer ◽  
Electron Affinity ◽  
Density Functional ◽  
Density Functional Method ◽  
Point Mutations ◽  
Functional Method ◽  
Mutation Model ◽  
A Charge ◽  
Charge Transfer In Dna ◽  
Adenine Thymine

Background: In their Nature's seminal work (Nature. 1953;171:737), J.D. Watson and F.H.C. Crick noted that the structure of DNA admits a so-called tautomeric model of spontaneous point mutations. This work reported at the conference "Nanobiophysics-2019" (Kiev) as a plenary report, is actually an attempt to answer the following questions: (i) "Yes, the tautomerism of the bases is a very attractive model, but how important is it in mutagenesis?" by Morgan (Morgan AR. Trends Biochem. Sci. 1993;18:160–163); (ii) What reality does the rare tautomeric mutation model describe? The structure [А×Т]WC was selected in the work. Developing the previously proposed mutation model×of the Watson-Crick pair [А×Т]WC due to the shift of the bases in the pair relative to each other and the interconnection hydrogen bonds (Kryachko ES, Sabin JR. Int. J. Quantum Chem. 2003;91:695–710), it is shown that some resultant structures possess the electron affinity that is 1.7 times higher compared to the canonical pair, which is definitely of interest in the view of the numerous phenomena associated with a charge transfer in and attachment of an electron to DNA. Objectives: Answer the questions raised in the Background, and show the realism of the tautomeric [А×Т]WC-mutation model modified in the present work on the example of the Watson-Crick pair [А×Т]WC that is dubbed as a pair-tautomerism model. Materials and Methods: The key method is a computer simulation based on the density functional method. All calculations performed in the present work use the package of programs GAUSSIAN with the density functional method invoking the Becke-Lee-Yang-Parr density functional, B3LYP. Results: The paper shows the existence and stability of paired tautomeric mutations in a pair of adenine-thymine and investigates to what wobble pairs it can lead. It is also shown that, due to the specific structure of the paired tautomeric mutation of the adenine-thymine pair, the mutation possesses a larger electronic affinity in comparison with the pair that it generates, and thus can be observed in reality and through it one can explain a number of phenomena of charge transfer in DNA, which, again, emphasizes its reality. Conclusions: On the one hand, a generalization of the Watson-Crick tautomeric hypothesis, proposed in this work, specifically for the adenine-thymine pair, the name of the paired tautomeric mutation. This mutation refers to dipole-binding-electron systems, which implies their high adiabatic electron affinity. The latter, on the other hand, emphasizes the realism of the proposed mutational model and its possible application to the explanation of the phenomena of charge transfer in DNA and the processes of attachment electron to DNA.

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®).

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