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A) Dissociation free energy profiles of cisoid and transoid dimer (C(Ag + )C) 2 (for standard deviation indicated by the error bars see SI) and b) schematic illustration of process. Detailed illustration of selected points on dissociation profile of c) cisoid (C(Ag + )C) 2 , d) transoid (C(Ag + )C) 2 with depicted character of bonding and NCI descriptors. For clarity solvent is omitted.
Source publication
We report a biased QM/MM molecular dynamics study of the dissociation process of cytosine-cytosine complexes mediated by Ag⁺ or H⁺ ions in monomeric and dimeric forms. We performed calculations under explicit solvent conditions and obtained the free energy profiles by thermodynamic integration technique to give deep insights on the dissociation pro...
Context in source publication
Context 1
... a result the distances N3-N3 of the global minima lie in a close proximity and agree well with the equilibrium distances obtained earlier by pure QM [28,30] or QM/MM [9] geometry optimization methods and crystal structures, and no local minima was observed. The π-π stacking interactions support the smooth dissociation along the plane as illustrated by NCI at Figure 3. QM/MM-MD calculations vary Ag-Ag distances for cisoid in the range of 2.94-4.27 ...
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Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD simulations are computationally expensive compared to fully classical simulations as all valence electrons are treat...
Citations
... Other QM/MM studies include the dissociation of the cytosine-Ag cations bonds [81] through free energy estimation via thermodynamic integration. The Free Energy landscape shows that the tetramer (C-Ag þ -C) 2 has as global minimum: the transoid configuration with two stabilizing interplanar hydrogen bonds (H-bonds), in agreement with experiments and Espinosa et al.'s simulations. ...
A QM/MM method is an atomistic simulation algorithm that allows researchers to describe different regions of a system with different physical laws. Here, we review this hybrid method’s applications to the study of copper, silver, and gold atoms and clusters interacting with biological and organic molecules. In particular, we highlight efforts to characterize the relaxation process in a copper(I) phenanthroline complex; details of Cu’s secretory path; the atomic structure of Ag-homopolymers of cytosine and guanine; DNA-stabilized silver clusters; effects related to temperature and solvent on thiolate-protected gold clusters’ optical properties; and the effect of a medium-like noble gas on a cluster’s optical spectrum. The results of these efforts demonstrate how QM/MM methods are applied successfully to a wide range of processes that include the study of excited state evolution, charge transport, light absorption, and emission, and determining an atomic structure in the absence of crystal-determined structure. We expect QM/MM methods will continue supporting the exploration of novel hybrid organo-metallic materials and their safe use in the environment, while also providing guidance on mechanisms to deal with diseases associated with a failure in cells’ proper behavior.
Rationale
Cytosine and its conjugates are prone to form protonated, triply‐bonded dimers. Therefore, the nucleic‐acid cytosine‐rich sequence forms the four‐stranded noncanonical secondary structure known as the intercalated motif (i‐motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations.
Methods
To obtain the precursor ion fragmentation curve, the plot of SY against E comδ , the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q‐TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6‐31G(d,p).
Results
The precursor ion fragmentation curve allowed the rating of the gas‐phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas‐phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine–deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine–cytosine nucleoside dimers but not in the formation of cytosine dimers.
Conclusions
The results obtained for nucleoside dimers indicated that the SY method may reflect the i‐motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine–cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i‐motif stabilities. Cytosine tautomer containing C2‐OH … N(2H)‐C4 moiety may be involved in the formation of protonated cytosine–cytosine nucleoside dimers.
Partially reduced silver clusters growing in a polycytosine matrix could simultaneously possess stabilizing ability and remarkable optical features. The mechanisms of this phenomenon are not fully understood so far. We examined the thermodynamic stability of a cytosine–silver associate comprising four cytosines and three silver atoms that can be considered the smallest known luminescent silver marker stabilized on DNA. Quantum and molecular mechanical representations thermodynamic integration toward the dissociation pathway of the cytosine tetramer, time‐dependent density functional theory calculations of the lowest energy excited states and quantum theory of atoms in molecules analysis of bonding showed that the reduction of two ions within the silver trimer mediating cytosine tetramer leads to the appearance of the green‐emitting silver cluster with low stabilization ability of cytosines relative to a tetramer stabilized by two silver ions.
Metal mediated DNA are mismatches where a metal ion bridges the base pairs and are of interest for biosensors. Here, we study T-Hg2+-T, which is known to be stabilized by base pair metal mediated bonds, and C-Ag+-C whose stabilization mechanism is less well understood. We use a mesoscopic model and published melting temperatures of sequences containing CC or TT mismatches in the presence of the metal ions. For T-Hg2+-T we obtain a strong base pair bond potential and moderate one for C-Ag+-C, only one stacking potential for each configuration is stronger than usual.
Ag+-mediated base pairing is valuable for synthesising DNA-based silver nanoparticles (AgNPs) and nanoclusters (AgNCs). Recently, we reported the formation of a [Ag(cytidine)2]+ complex in dimethyl sulfoxide (DMSO), which facilitated the evaluation of the effect of cytosine-Ag+-cytosine (C-Ag+-C) base pairing on the degree of AgNP aggregation in solution. As an aprotic solvent, DMSO was expected to dissolve the [Ag(cytidine)2]+ complex, and powerful reducing agents, such as organic electron donors. In this study, the chemical reduction of a cytidine/Ag+ system using a powerful reducing agent tetrakis(dimethylamino)ethylene (TDAE) was investigated. 1H/13C/15N NMR spectroscopic evidence was obtained to identify the iminium dication (TDAE2+), which is an oxidised form of TDAE. The results were compared with those obtained using another organic electron donor, tetrathiafulvalene (TTF), which exhibits a relatively lower reduction activity than TDAE. AgNPs prepared via redox reaction between [Ag(cytidine)2]+ and organic electron donors (TDAE and TTF) were characterised using UV-Vis spectroscopy and nanoparticle tracking analysis. It was found that the formation of C-Ag+-C base pairing inhibited the aggregation of AgNPs in solution. In addition, in the presence of cytidine, the total concentration of the AgNP solution was affected by the reduction activity of the reducing agent.
The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.
