scholarly journals Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5191
Author(s):  
Danillo Valverde ◽  
Adalberto de Araújo ◽  
Antonio Borin
Keyword(s):  
Linear Interpolation ◽  
Relaxation Mechanism ◽  
Basis Sets ◽  
Triplet States ◽  
Complete Active Space ◽  
Pyrimidine Analogue ◽  
Characteristic Points ◽  
Energy Hypersurface ◽  
Crossing Point ◽  
Potential Energy Hypersurface

The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning’s cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.

scholarly journals Computational Study of the C-H∙∙∙H-C Contacts in Valine-Methane Complexes.

2021 ◽  
Author(s):  
Neetha Mohan ◽  
Adrián Varela-Álvarez ◽  
Chintalapalle V. Ramana ◽  
suman sirimulla
Keyword(s):  
Computational Study ◽  
Single Point ◽  
Topological Analysis ◽  
Basis Sets ◽  
Interaction Energies ◽  
Energy Decomposition ◽  
Protein Protein Interaction ◽  
Energy Hypersurface ◽  
Different Levels ◽  
Potential Energy Hypersurface

<div> <p>A series of complexes between neutral Valine and methane that feature potential homopolar C-H∙∙∙H-C contacts were located on the MP2/aug-cc-pVTZ potential energy hypersurface. In order to better estimate the strength of this contacts, the interaction energies were improve by single-point calculations at different levels of theory (MP2, CCSD(T), SAPT2, SAPT2+3) together with Dunning’s basis sets (aug-cc-pVXZ; X=T,Q,5). Topological analysis of the electron density within the QTAIM framework, NCI plots and energy decomposition within the SAPT framework were used to discuss the nature of this interactions. The complexes whose monomers only interact though C-H∙∙∙H-C contacts indicate that these interactions are entirely due to dispersion forces, are not directional and are much stronger than expected (the interaction energies of the complexes range from -0.7 to -1.0 kcal/mol). This large value is remarkable considering the small size of the interacting groups herein considered (methane, and one or two Valine’s methyl groups), and indicates that in biological systems, where those interactions can be very numerous in the presence of multiple aliphatic amino acids, if those interactions are not properly model, magnitudes as ligand-receptor affinities, protein-protein interaction energies and protein stabilities might be grossly misestimated. Finally, since some of the computed complexes also include stronger interactions than homopolar C-H∙∙∙H-C contacts, we analyzed if the potential C-H∙∙∙H-C contacts in these complexes are really contributing to stabilize the complexes or are just a geometrical artifact arising from the maximization of stronger interactions.</p> </div>

scholarly journals Computational Study of the C-H∙∙∙H-C Contacts in Valine-Methane Complexes.

2021 ◽  
Author(s):  
Neetha Mohan ◽  
Adrián Varela-Álvarez ◽  
Chintalapalle V. Ramana ◽  
suman sirimulla
Keyword(s):  
Computational Study ◽  
Single Point ◽  
Topological Analysis ◽  
Basis Sets ◽  
Interaction Energies ◽  
Energy Decomposition ◽  
Protein Protein Interaction ◽  
Energy Hypersurface ◽  
Different Levels ◽  
Potential Energy Hypersurface

<div> <p>A series of complexes between neutral Valine and methane that feature potential homopolar C-H∙∙∙H-C contacts were located on the MP2/aug-cc-pVTZ potential energy hypersurface. In order to better estimate the strength of this contacts, the interaction energies were improve by single-point calculations at different levels of theory (MP2, CCSD(T), SAPT2, SAPT2+3) together with Dunning’s basis sets (aug-cc-pVXZ; X=T,Q,5). Topological analysis of the electron density within the QTAIM framework, NCI plots and energy decomposition within the SAPT framework were used to discuss the nature of this interactions. The complexes whose monomers only interact though C-H∙∙∙H-C contacts indicate that these interactions are entirely due to dispersion forces, are not directional and are much stronger than expected (the interaction energies of the complexes range from -0.7 to -1.0 kcal/mol). This large value is remarkable considering the small size of the interacting groups herein considered (methane, and one or two Valine’s methyl groups), and indicates that in biological systems, where those interactions can be very numerous in the presence of multiple aliphatic amino acids, if those interactions are not properly model, magnitudes as ligand-receptor affinities, protein-protein interaction energies and protein stabilities might be grossly misestimated. Finally, since some of the computed complexes also include stronger interactions than homopolar C-H∙∙∙H-C contacts, we analyzed if the potential C-H∙∙∙H-C contacts in these complexes are really contributing to stabilize the complexes or are just a geometrical artifact arising from the maximization of stronger interactions.</p> </div>

Quantum-Chemical Ab Initio Calculations on Inda- and Thallabenzene (C5H5In and C5H5Tl) and their Structural Isomers η5-C5H5In and η5-C5H5Tl

2018 ◽  
Vol 71 (3) ◽  
pp. 102
Author(s):  
Emma Persoon ◽  
Yuekui Wang ◽  
Gerhard Raabe
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Density Functional ◽  
Single Point ◽  
Normal Modes ◽  
Dft Method ◽  
Basis Sets ◽  
Triplet States ◽  
Structural Isomers ◽  
Td Dft

Quantum-chemical ab initio, time-independent, as well as time-dependent density functional theory (TD-DFT) calculations were performed on the so far elusive heterocycles inda- and thallabenzene (C5H5In and C5H5Tl), employing several different methods (MP2, CISD, CCSD, CCSD(T), BD, BD(T), QCISD, QCISD(T), CASSCF, DFT/B3LYP), effective core potentials, and different basis sets. While calculations on the MP2 level predict the ground states of the title compounds to be singlets with the first triplet states between 13 and 15 kcal mol−1 higher in energy, single point calculations with the QCISD(T), CCSD(T), and BD(T) methods at CCSD-optimized structures result in energy differences between the singlet and the triplet states in the range between 0.3 and 2.1 kcal mol−1 in favour of the triplet states. According to a CASSCF(8,8) calculation the triplets are also more stable by about 2.5–2.9 kcal mol−1. Calculations were also performed for the C5v-symmetric η5 structural isomers (cyclopentadienylindium, CpIn, and cyclopentadienylthallium, CpTl, Cp = C5H5) of the title compounds. At the highest level of theory employed in this study, C5H5In is between 79 and 88 kcal mol−1 higher in energy than CpIn, while this energy difference is even larger for thallabenzene where C5H5Tl is energetically between 94 and 102 kcal mol−1 above CpTl. In addition we report on the UV/vis spectra calculated with a TD-DFT method as well as on the spectra of the normal modes of C5H5In and C5H5Tl. Both types of spectra might facilitate identification of the title compounds eventually formed in photolysis or pyrolysis experiments.

scholarly journals Gas-phase reaction between calcium monocation and fluoromethane: Analysis of the potential energy hypersurface and kinetics calculations

2009 ◽  
Vol 131 (14) ◽  
pp. 144309 ◽  
Author(s):  
Adrián Varela-Álvarez ◽  
V. M. Rayón ◽  
P. Redondo ◽  
C. Barrientos ◽  
José A. Sordo
Keyword(s):  
Potential Energy ◽  
Gas Phase ◽  
Phase Reaction ◽  
Gas Phase Reaction ◽  
Energy Hypersurface ◽  
Potential Energy Hypersurface

The Method of Probabilistic Nodes Combination in Decision Making and Risk Analysis

2016 ◽  
pp. 32-60
Author(s):  
Dariusz Jacek Jakóbczak
Keyword(s):  
Decision Making ◽  
Distribution Function ◽  
Probability Distribution ◽  
Risk Analysis ◽  
Probability Distribution Function ◽  
Linear Interpolation ◽  
Distribution Functions ◽  
Probability Distribution Functions ◽  
Characteristic Points ◽  
Basic Probability

Proposed method, called Probabilistic Nodes Combination (PNC), is the method of 2D curve interpolation and extrapolation using the set of key points (knots or nodes). Nodes can be treated as characteristic points of data for modeling and analyzing. The model of data can be built by choice of probability distribution function and nodes combination. PNC modeling via nodes combination and parameter ? as probability distribution function enables value anticipation in risk analysis and decision making. Two-dimensional curve is extrapolated and interpolated via nodes combination and different functions as discrete or continuous probability distribution functions: polynomial, sine, cosine, tangent, cotangent, logarithm, exponent, arc sin, arc cos, arc tan, arc cot or power function. Novelty of the paper consists of two generalizations: generalization of previous MHR method with various nodes combinations and generalization of linear interpolation with different (no basic) probability distribution functions and nodes combinations.

A theoretical approach to the acid-catalyzed hydration of the carbonyl group: the case of formaldehyde

1991 ◽  
Vol 69 (9) ◽  
pp. 1376-1387 ◽  
Author(s):  
Daniel Peeters ◽  
Georges Leroy
Keyword(s):  
Reaction Mechanism ◽  
Potential Energy ◽  
Water Molecules ◽  
Hydration Reaction ◽  
Second Derivatives ◽  
Hydrated Proton ◽  
Energy Reaction ◽  
Derivatives Of ◽  
Energy Hypersurface ◽  
Potential Energy Hypersurface

The analysis of the hydration of formaldehyde in the presence of a hydrated proton was performed. Molecular quantum chemistry methods were used to explore the potential energy hypersurface. Calculations were performed at RHF-4-31G level. The structures were obtained through the use of first and second derivatives of the potential energy hypersurface thereby guaranteeing the nature of the extremum. The incidence of one or two water molecules on the reaction is discussed. It has been found that a low energy reaction path exists when the hydration process is catalyzed by a proton and two water molecules. The reaction mechanism rests on successive addition/elimination processes and reveals the respective roles of the oxygen lone pairs and of the C=O double bond upon the mechanism. Key words: ab initio calculations, carbonyl reactivity, acid catalysis, hydration, reaction mechanism.

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