Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell

Fogarasi, Géza; Szalay, Péter G.

doi:10.1039/c5cp04563k

Cited by 11 publications

(15 citation statements)

References 31 publications

(73 reference statements)

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“…A more thorough list of isomers and their structures is given in the Supporting Information. For Cy microhydrates, both G4MP2 and ωB97XD results are qualitatively consistent with previous theoretical studies regarding the stability order among various Cy·(H 2 O) n isomers. ,− The G4MP2 energies agree very well with the more accurate CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ results (see Table ), providing a good justification to use this efficient method for larger Cy clusters. Boltzmann populations of some important Cy monohydrates and dihydrates listed in Table were calculated with the Δ G s obtained from the G4MP2 results of all isomers listed in Figures S1 and S2, respectively.…”

Section: Methodssupporting

confidence: 88%

“…For the hexahydrate (n = 6), the most stable isomer is the AABBCC-type that forms a three-dimensional cage-like structure along the Watson−Crick edge. A recent MP2(fc)/aug-cc-pVDZ study 38 predicted that the most stable isomers of both n = 5 and 6 microhydrates involve such cagelike structures. However, we found that, at the G4MP2 level, the pentahydrate isomer containing such a cage-like structure is much higher in energy than the most stable AABBC-type isomer (see Figure S5).…”

Section: Methodsmentioning

confidence: 99%

“…In addition, single-point calculations at the CCSD(T)/aug-cc-pVTZ level of theory were also carried out at a few important Cy monohydrates structures optimized at the ωB97X-D/aug-cc-pVTZ for accuracy assessments. In this work, H-bonding sites of Cy are denoted as A, B, C, and D (see Figure ) following the notation used by previous authors. − Isomers of Cy microsolvated clusters are labeled (letters after the underscore) by the binding sites where solvent molecules bound, e.g., keto-Cy·(H 2 O) 3 _AAB denotes a complex of keto-form Cy with two H 2 O molecules bound at site A and another one at site B.…”

Section: Methodsmentioning

confidence: 99%

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Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Wei

Yen

et al. 2018

J. Phys. Chem. A

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Microsolvation effects on the ultrafast excitedstate deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump−probe ionization spectroscopy. Two protic solvents, water (H 2 O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy•(H 2 O) 1−6 , Cy•(MeOH) 1−3 , and Cy•THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the lowenergy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy•(H 2 O) n are 0.5 ps for n = 1 and ∼0.2−0.25 ps for n = 2−6. For Cy•(MeOH) n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy•THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy•THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.

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Section: Methodssupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Wei

Yen

et al. 2018

J. Phys. Chem. A

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“…We also considered the influence of the cytosine binding process with graphene on the interaction of this cytosine with water molecules (the role of the solvation effects) limiting this consideration only the first hydration shell (ex., including only the strong bounded water molecules). There have been numerous quantum chemical calculation on the interaction between cytosine and water (see, for example,ref ). The number of water molecules may be up to seven water molecules that can bind directly to cytosine .…”

Section: Results and Discussionmentioning

confidence: 99%

“…The number of water molecules may be up to seven water molecules that can bind directly to cytosine. 60 We determined the number of H-bonds formed by cytosine5 with water molecules at each step and showed their variation with time (Figure S6). This number of H-bonds was varied from 2 until 15 with time and the mean value was about 6−7 bonds (depending on the stacked cytosine number).…”

Section: Computer Simulation Of Cytosine Oligomer Adsorption Onmentioning

confidence: 99%

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

et al. 2017

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Hybridization of nucleic acids with graphene nanomaterials is of great interest due to its potential application in genosensing and nanomedicine. In this work we study the interaction between polyribocytidylic acid (poly(rC)) and graphene oxide (GO). The study involves comparing the UV absorption spectra of the free polymer and the polymer bonded to graphene oxide and analyzing the vibrational structure of the systems and their components using FTIR spectroscopy. Spectral shifts of the electronic and vibrational bands of the poly(rC) and changes of their thermostability due to the adsorption on GO are observed. Molecular dynamics simulation of the adsorption process of the r(C)10 and r(C)30 oligomers on graphene demonstrates their disordering due to the π–π stacking of cytosines on graphene and shows that the longer oligomer adsorbs slower. The binding energies of a single cytosine stacked with graphene in water and in vacuum were determined. The calculated IR lines of the stacked cytosine with graphene are red-shifted by up to 20 cm–1 compared to free cytosine. A strong decrease of the intensities of the cytosine vibrations in the 1800–1400 cm–1 range resulting from the interaction with graphene is revealed in the spectra. When cytosine is adsorbed to graphene oxide, their complex is additionally stabilized by H-bonding. It leads to an increase of the red shifting of the cytosine lines.

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A theoretical investigation of water–solute interactions: from facial parallel to guest–host structures

2017

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Encapsulation of small (bio-)organic molecules within water cages is governed by a subtle equilibrium between water-water and water-solute interactions. The competition between the formation of exohedral and endohedral complexes is investigated. The first step prior to a theoretical characterization of interactions involved in such complexes lies in the judicious choice of a level of theory. The β-propiolactone (BPL), a solute for which the micro-hydration was recently characterized by means of high resolution microwave spectroscopy (Angew. Chem. 2015, 127, 993), was selected for the present study, and a calibration step is carried out. It is shown that the dispersion-corrected density functional theory (DFT-D) suitably reproduce the geometric, energetic and spectroscopic features of the BPL:(H 2 O) 1-5 complexes. The experimentally-deduced structures of the BPL:(H 2 O) 4,5 species are fully understood in terms of the maximization of interactions between complementary sites in the MESPs. DFT-D calculations followed by the topological analysis within the Quantum Theory of Atoms in Molecules framework have shown that the solute could efficiently interact with (H 2 O) 6,10 clusters in a similar manner that the (H 2 O) 4,5 clusters do. The interaction of the solute with two larger water clusters is further investigated. The exohedral and endohedral BPL:(H 2 O) 20 isomers are close in energy with each other, whereas the formation of an inclusion complex is energetically more favored than the facial interaction in the case of the BPL:(H 2 O) 24 cluster. The topological analysis suggests that the substantial energetic stability is due to interactions between the solute and almost all oxygen atoms of the water cage.

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Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell

Cited by 11 publications

References 31 publications

Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Binding of Polycitydylic Acid to Graphene Oxide: Spectroscopic Study and Computer Modeling

A theoretical investigation of water–solute interactions: from facial parallel to guest–host structures

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