scholarly journals A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3111
Author(s):  
Massimiliano Aschi ◽  
Giorgia Toto Brocchi ◽  
Gustavo Portalone
Keyword(s):  
Proton Transfer ◽  
Crystal Packing ◽  
Computational Study ◽  
Theoretical Calculations ◽  
Bromine Atom ◽  
Lone Pair ◽  
Organic Salts ◽  
Dna And Rna ◽  
Molecular Salts ◽  
Derivatives Of

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the Nimino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C–Br…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).

scholarly journals Computational Study on Substituteds-Triazine Derivatives as Energetic Materials

2012 ◽  
Vol 9 (2) ◽  
pp. 583-592 ◽  
Author(s):  
Vikas D. Ghule ◽  
S. Radhakrishnan ◽  
Pandurang M. Jadhav ◽  
Surya P. Tewari
Keyword(s):  
Thermal Stability ◽  
Energetic Materials ◽  
Density Functional ◽  
Crystal Packing ◽  
Computational Study ◽  
Heats Of Formation ◽  
Dissociation Energies ◽  
The Density Functional Theory ◽  
Triazine Derivatives ◽  
Derivatives Of

s-Triazine is the essential candidate of many energetic compounds due to its high nitrogen content, enthalpy of formation and thermal stability. The present study explores s-triazine derivatives in which different -NO2, -NH2and -N3substituted azoles are attached to the triazine ring via C-N linkage. The density functional theory is used to predict geometries, heats of formation and other energetic properties. Among the designed compounds, -N3derivatives show very high heats of formation. The densities for designed compounds were predicted by using the crystal packing calculations. Introduction of -NO2group improves density as compared to -NH2and -N3, their order of increasing density can be given as NO2>N3>NH2. Analysis of the bond dissociation energies for C-NO2, C-NH2and C-N3bonds indicates that substitutions of the -N3and -NH2group are favorable for enhancing the thermal stability ofs-triazine derivatives. The nitro and azido derivatives of triazine are found to be promising candidates for the synthetic studies.

scholarly journals Charge density analysis of metformin chloride, a biguanide anti-hyperglycemic agent

2017 ◽  
Vol 73 (1) ◽  
pp. 10-22 ◽  
Author(s):  
Rajendran Niranjana Devi ◽  
Christian Jelsch ◽  
Samuel Israel ◽  
Emmanuel Aubert ◽  
Chellam Anzline ◽  
...  
Keyword(s):  
Charge Density ◽  
Electrostatic Interactions ◽  
Crystal Packing ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Lone Pair ◽  
Valence Shell ◽  
Resonance Theory ◽  
Density Analysis ◽  
Charge Concentration

The experimental charge density analysis of the anti-hyperglycemic agent metformin chloride with high-resolution X-ray diffraction data at low temperature (100 K) has been performed and these experimental results were compared with that derived from the corresponding periodic theoretical calculations at the B3LYP/6-31G** level of theory. The experimental and theoretical multipolar charge-density analyses of metformin chloride have been accomplished in order to understand its structural and electronic properties. The C and N atoms of the molecular backbone adopt a near trigonal geometry due to the occurrence of extensive delocalization/resonance of C—N bonds, as confirmed by topological analysis and also found by Natural Resonance Theory calculations performed in the isolated metformin cation. The molecule contains six C—N bonds and the topological bond order analysis shows that four bonds have bond orders close to 4/3 and two bonds can be considered as single. The analysis of numerical parameters of the valence shell charge concentration reports that the N3 atom, which forms two bonds with C atoms, possesses one non-bonding valence-shell charge concentration (VSCC) in the direction of the electron lone pair. Among the intermolecular interactions of the chloride atom with the H—C and H—N atoms, eight have been found to be shorter than the sum of van der Waals radii. The analysis of contacts on the Hirshfeld surface reveals that the H—N...Cl hydrogen bonds are enriched (over-represented) and act as the driving force in the crystal packing formation. The metformin cations form favorable electrostatic interactions with the chloride anions which have globally a stronger energy than the unfavorable cation/cation interactions.

Does the Affinity of Cisplatin to B-Vitamins Impair the Therapeutic Effect in the Case of Patients with Lung Cancer-consuming Carrot or Beet Juice?

2019 ◽  
Vol 19 (14) ◽  
pp. 1775-1783 ◽  
Author(s):  
Beata Szefler ◽  
Przemysław Czeleń ◽  
Adam Szczepanik ◽  
Piotr Cysewski
Keyword(s):  
Computational Study ◽  
Lone Pair ◽  
B Vitamins ◽  
Basis Set ◽  
Free Energies ◽  
Aromatic Rings ◽  
Reaction Field ◽  
Vitamin B Group ◽  
Solvation Free Energies ◽  
Derivatives Of

Background: Cisplatin (CisPt) has a well-recognized anticancer activity by interacting with DNA and inducing programmed cell death. However, theoretical studies performed on the molecular level suggest that such nonspecific interactions can also take place with many competitive compounds, such as vitamins containing aromatic rings with lone-pair orbitals. Objective: This work is a theoretical study on the initial Pt-N7(N1) bond formation with vitamins from B group and their comparison with values characterizing native purines. Methods: Geometries of studied structures were optimized with an aid of Gaussian 09 using the B3LYP functional with the 6-31G** basis set. Atomic orbitals of platinum were represented by the lanl2dz basis. Solvation free energies were evaluated by a self-consistent reaction field (SCRF) approach. A dielectric constant of 78 for water was used in the PCM continuum model computations along with radii Bondii. Results: The affinities of mono-aqua cis~[Pt(NH3)2Cl(H2O)]+ and di-aqua cis~ [Pt(NH3)2(H2O)2]2+ derivatives of Cisplatinum toward compounds belonging to the group of eight B vitamins were studied and compared to interactions with canonical purines. All the values of ΔGr unambiguously indicate that reactions with cisPt-diaqua are more preferable, but the comparison of ΔGr values obtained for compounds from vitamin B group and the ones characterizing complexes created by Guanine molecules indicates higher affinity of cisPt monomers toward purines. Conclusion: Based on the observations, the regular intake of vitamin-rich beetroot or carrot juices is strongly discouraged during anticancer therapy using CisPt drug. To confirm the results of the performed computational study, detailed clinical trials should be performed.

Utilizing proton transfer to produce molecular salts in bromanilic acid substituted-pyridine molecular complexes – predictable synthons?

2013 ◽  
Vol 69 (11) ◽  
pp. 1279-1288 ◽  
Author(s):  
Lynne H. Thomas ◽  
Martin S. Adam ◽  
Andrew O'Neill ◽  
Chick C. Wilson
Keyword(s):  
Proton Transfer ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Molecular Complexes ◽  
Design Tool ◽  
Acid Molecule ◽  
Protonation State ◽  
Molecular Salts ◽  
Potential Strategy ◽  
A Charge

Controlled introduction of proton transfer into the design of a series of molecular complexes is described, delivering the systematic production of ionic molecular complexes (molecular salts). The controlled production of molecular salts has relevance as a potential strategy in the design of pharmaceutical materials. In nine molecular complexes consisting of bromanilic acid with the N-heterocyclic compounds 2-, 3- and 4-picoline [bis(2/3/4-methylpyridinium) 2,5-dibromo-3,6-dioxocyclohexa-1,4-diene-1,4-diolate, 2C6H8N+·C6Br2O42−], 2,3-, 2,4-, 2,5- and 3,5-lutidine [2,3/2,4/2,5/3,5-dimethylpyridinium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate, C7H10N+·C6HBr2O4−], and 3-bromo-4-methylpyridine [3-bromo-4-methylpyridinium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate, C6H7BrN+·C6HBr2O4−] and 2-bromo-3-methylpyridine [2-bromo-3-methylpyridine–2,5-dibromo-3,6-dihydroxycyclohexa-2,5-diene-1,4-dione (1/1), C6H6BrN·C6H2Br2O4], proton transfer occurs readily between the bromanilic acid molecule and the N heteroatom of the pyridine ring, in all cases producing a charge-assisted bifurcated N—H...O hydrogen bond. This reinforces the value of this motif as a design tool in the crystal engineering of such complexes. The protonation state (and stoichiometry) significantly affect the supramolecular synthons obtained, but 1:2 stoichiometries reliably give rise to PBP synthons and 1:1 stoichiometries to PBBP synthons (where P indicates a methylpyridine co-molecule and B a bromanilic acid molecule). The influence of halogen interactions on the wider crystal packing is also discussed, with C—H...Br and Br...O interactions the most prevalent; only one Br...Br interaction is found.

An NBO-TS predictive approach for torquoselectivity of ring opening in 3-substituted cyclobutenes

2017 ◽  
Author(s):  
Arpita Yadav ◽  
Dasari L V K Prasad ◽  
Veejendra Yadav
Keyword(s):  
Transition State ◽  
Ring Opening ◽  
Natural Bond Orbital ◽  
Theoretical Calculations ◽  
Lone Pair ◽  
Product Distribution ◽  
Acceptor Substituent ◽  
Important Contributor ◽  
Predictive Approach ◽  
Donor Substituent

<p>The torquoselectivity, the inward or outward ring opening of 3-substituted cyclobutenes, is conventionally guided by the donor and/or acceptor ability of the substituent (S). It is typically predicted by estimating the respective ring opening transition state (TS) barriers. While there is no known dissent in regard to the outward rotation of electron-rich substituents from the approaches of TS calculations, the inward rotation was predicted for some electron-accepting substituents and outward for others. To address this divergence in predicting the torquoselectivity, we have used reliable orbital descriptors through natural bond orbital theoretical calculations and demonstrated that (a) interactions <i>n</i><i><sub>S</sub></i>→s*<sub>C3C4</sub> for a lone pair containing substituent, s<sub>S</sub>→s*<sub>C3C4</sub> for a s-donor substituent, s<sub>C3C4</sub>→p*<sub>S</sub> for a resonance-accepting substituent and s<sub>C3C4</sub>→s*<sub>S</sub> for a s-acceptor substituent constitute the true electronic controls of torquoselectivity, and (b) reversibility of the ring opening event is an additional important contributor to the observed product distribution.</p>

scholarly journals Crystal Structure and Computational Study on Methyl-3-Aminothiophene-2-Carboxylate

Crystals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 19 ◽  
Author(s):  
Yaping Tao ◽  
Ligang Han ◽  
Andong Sun ◽  
Kexi Sun ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Computational Study ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Dispersion Energy ◽  
Monoclinic Crystal ◽  
Hydrogen Bond Interactions ◽  
Calculation Results ◽  
Reduced Density Gradient ◽  
Reduced Density

Methyl-3-aminothiophene-2-carboxylate (matc) is a key intermediate in organic synthesis, medicine, dyes, and pesticides. Single crystal X-ray diffraction analysis reveals that matc crystallizes in the monoclinic crystal system P21/c space group. Three matc molecules in the symmetric unit are crystallographically different and further linked through the N–H⋯O and N–H⋯N hydrogen bond interactions along with weak C–H⋯S and C–H⋯Cg interactions, which is verified by the three-dimensional Hirshfeld surface, two-dimensional fingerprint plot, and reduced density gradient (RDG) analysis. The interaction energies within crystal packing are visualized through dispersion, electrostatic, and total energies using three-dimensional energy-framework analyses. The dispersion energy dominates in crystal packing. To better understand the properties of matc, electrostatic potential (ESP) and frontier molecular orbitals (FMO) were also calculated and discussed. Experimental and calculation results suggested that amino and carboxyl groups can participate in various inter- and intra-interactions.

The Through-Bond Interaction of a Sulfur Lone Pair with Oxygenated Substituents in the Thiacyclohexane Framework

2005 ◽  
Vol 58 (7) ◽  
pp. 531
Author(s):  
Laura Andrau ◽  
Jonathan M. White
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Bond Distance ◽  
Lone Pair ◽  
X Ray ◽  
Ester Derivative ◽  
Bond Interaction ◽  
Derivatives Of ◽  
Electron Demand

Low-temperature X-ray crystal structures were determined on a range of derivatives of 4-thiacyclohexanol 5a of varying electron demand with a view to finding evidence for a through-bond interaction between the sulfur lone pair and the oxygenated substituent. In contrast to earlier suggestions, plots of C–OR bond distance versus pKa (ROH) showed that any interaction between the sulfur and the OR group is unlikely to be of a through-bond origin. Furthermore, unimolecular solvolysis rate measurements on the nosylate ester derivative 5g showed that the sulfur actually retards the reaction slightly in comparison with the corresponding sulfur-free analogue 6.

Synthesis, structural characterization and cytotoxicity of a new proton transfer compound based on 2,4-diamino-1,3,5-triazine: an experimental and computational study

2021 ◽  
Author(s):  
Khodayar Gholivand ◽  
Leila Sarmadi ◽  
Nasrin Fallah ◽  
Mohammad Feraghi ◽  
Michal Dušek ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Structural Characterization ◽  
Computational Study ◽  
Water Soluble ◽  
Cytotoxic Compound ◽  
Proton Transfer Compound

In the present study, a new water-soluble proton transfer cytotoxic compound (dpp)(dapt).H2O (Dx) (where dpp = diphenylphosphinate and dapt = 2,6-diamino-4-phenyl-1,3,5-triazin-1-ium ) was synthesized and characterized by IR and NMR...

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