Evolution of electron density towards the conical intersection of a nucleic acid purine

Gutiérrez‐Arzaluz, Luis; Ramírez-Palma, David; Buitrón-Cabrera, Frida; Rocha‐Rinza, Tomás; Cortés‐Guzmán, Fernando; Peón, Jörge

doi:10.1016/j.cplett.2017.03.021

Cited by 7 publications

(3 citation statements)

References 29 publications

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“…Recent advances in genome-wide association studies (GWAS) in genetics have enabled us to identify thousands of genetic variants that are associated with phenotype variations. It is well known that SNPs are closely linked with various phenotypes or traits (Kimchi-sarfaty et al, 2007; Helyar et al, 2011; Gutierrez-arzaluz et al, 2017), such as obesity and age-related macular degeneration(Sangiovanni et al, 2017; Dong et al, 2018). Herein, several assumptions were made to explore the relationships between SNPs and phenotype variations.…”

Section: Resultsmentioning

confidence: 99%

Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs

Yuan

Wang

et al. 2019

Front. Chem.

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Single nucleotide polymorphisms (SNPs) affect base pair stacking, which is the primary factor for maintaining the stability of DNA. However, the mechanism of how SNPs lead to phenotype variations is still unclear. In this work, we connected SNPs and base pair stacking by a 3-mer base pair stacking free energy matrix. The SNPs with large base pair stacking free energy differences led to phenotype variations. A molecular dynamics (MD) simulation was then applied. Our results showed that base pair stacking played an important role in the transcription factor (TF)-DNA interaction. Changes in DNA structure mainly originate from TF-DNA interactions, and with the increased base pair stacking free energy, the structure of DNA approaches its free type, although its binding affinity was increased by the SNP. In addition, quantitative models using base pair stacking features revealed that base pair stacking can be used to predict TF binding specificity. As such, our work combined knowledge from bioinformatics and structural biology and provided a new understanding of the relationship between SNPs and phenotype variations. The 3-mer base pair stacking free energy matrix is useful in high-throughput screening of SNPs and predicting TF-DNA binding affinity.

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Section: Resultsmentioning

confidence: 99%

Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs

Yuan

Wang

et al. 2019

Front. Chem.

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“…19 No matter which of the aforementioned interpretations is used, the role that QCT descriptors, such as the ELF, have played in the study of chemical bonding and the electronic structure of molecules and solids is undeniable. However, most of the work done in the context of QCT has been devoted to the characterization of ground-state systems, and only moderate attention has emerged in recent years on extending these efforts to the photochemistry realm, with the aim of shining light on the changes undergone by chemical bonds upon electronic excitation [20][21][22][23][24][25][26][27][28][29][30][31][32][33][34] . The importance of this extension is further motivated by the overwhelming abundance of new phenomena taking place in excited states such as in the photodissociation 35 and photoisomerization 36 of a large number of molecules.…”

Section: Introductionmentioning

confidence: 99%

Calculation of the ELF in the excited state with single determinant methods

Echeverri

Gallegos

Gómez

et al. 2023

Preprint

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Since its first definition, back in 1990, the Electron Localization Function (ELF) has settled as one of the most commonly employed techniques to characterize the nature of the chemical bond in real space. Although most of the work using the ELF has been focused on the study of ground-state chemical reactivity, a growing interest has blossomed to apply these techniques to the nearly unexplored realm of excited states and photochemistry. Since accurate excited electronic states usually require to account appropriately for electron correlation, the standard single-determinant ELF formulation cannot be blindly applied to them, and it is necessary to turn to correlated ELF descriptions based on the two-particle density matrix (2-PDM). The latter require costly wavefunction approaches, unaffordable for most of the systems of current photochemical interest. Here, we compare exact, 2-PDM-based ELF results with those of approximate 2-PDM reconstructions taken from Reduced Density Matrix Functional Theory (RDMFT). Our approach is put to the test in a wide variety of representative scenarios, such as those provided by the lowest-lying excited electronic states of simple diatomic and polyatomic molecules. Altogether, our results suggest that even approximate 2-PDMs are able to accurately reproduce, on a general basis, the topological and statistical features of the ELF scalar field, paving the way toward the application of cost-effective methodologies, such as TD-HF or TD-DFT, in the accurate description of the chemical bonding in excited states of photochemical relevance.

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“…The topological analysis of electron density allows for direct comparisons between the ground and excited states and permits the isolation of specific effects that determine the energetic landscape. Several groups have reported the results of quantum chemical topology studies of the photophysical and ‐chemical processes of organic systems, describing the electron density redistribution during excitation as a driving force for excited‐state dynamics …”

Section: Introductionmentioning

confidence: 99%

Origin of the Photoinduced Geometrical Change of Copper(I) Complexes from the Quantum Chemical Topology View

Gutiérrez‐Arzaluz

Ramírez-Palma

Ramírez‐Palma

et al. 2018

Chemistry A European J

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Copper(I) complexes (CICs) are of great interest due to their applications as redox mediators and molecular switches. CICs present drastic geometrical change in their excited states, which interferes with their luminescence properties. The photophysical process has been extensively studied by several time‐resolved methods to gain an understanding of the dynamics and mechanism of the torsion, which has been explained in terms of a Jahn–Teller effect. Here, we propose an alternative explanation for the photoinduced structural change of CICs, based on electron density redistribution. After photoexcitation of a CIC (S0→S1), a metal‐to‐ligand charge transfer stabilizes the ligand and destabilizes the metal. A subsequent electron transfer, through an intersystem crossing process, followed by an internal conversion (S1→T2→T1), intensifies the energetic differences between the metal and ligand within the complex. The energy profile of each state is the result of the balance between metal and ligand energy changes. The loss of electrons originates an increase in the attractive potential energy within the copper basin, which is not compensated by the associated reduction of the repulsive atomic potential. To counterbalance the atomic destabilization, the valence shell of the copper center is polarized (defined by ∇2ρ(r) and ∇2Vne(r)) during the deactivation path. This polarization increases the magnitude of the intra‐atomic nuclear–electron interactions within the copper atom and provokes the flattening of the structure to obtain the geometry with the maximum interaction between the charge depletions of the metal and the charge concentrations of the ligand.

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Evolution of electron density towards the conical intersection of a nucleic acid purine

Cited by 7 publications

References 29 publications

Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs

Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs

Calculation of the ELF in the excited state with single determinant methods

Origin of the Photoinduced Geometrical Change of Copper(I) Complexes from the Quantum Chemical Topology View

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