Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

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Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

10.26434/chemrxiv-2021-nccgc ◽

2021 ◽

Author(s):

Gal Buskila ◽

Arik Landau ◽

Idan Haritan ◽

Nimrod Moiseyev ◽

Debarati Bhattacharya

Keyword(s):

Ab Initio ◽

Decay Rates ◽

Biological Molecules ◽

Metastable States ◽

Basis Set ◽

Medium Size ◽

Molecular Systems ◽

Biologically Relevant ◽

Resonance Energies ◽

Experimental Findings

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

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Ab Initio SCF Procedure with Localized Molecular Orbitals of Fragments

Zeitschrift für Naturforschung A ◽

10.1515/zna-1975-1124 ◽

1975 ◽

Vol 30 (11) ◽

pp. 1499

Author(s):

J. Koller ◽

A. Ažman

Keyword(s):

Ab Initio ◽

Molecular Orbitals ◽

Basis Set ◽

Localized Orbitals ◽

Localized Molecular Orbitals ◽

Molecular Systems

An ab initio procedure is described with a basis set of localized orbitals of the fragments. The method was tested on three molecular systems. The results are in agreement with the results of LCAO calculations

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AB-INITIO CALCULATIONS OF ELECTRONIC PROPERTIES OF InP AND GaP

International Journal of Modern Physics B ◽

10.1142/s0217979213620130 ◽

2013 ◽

Vol 27 (15) ◽

pp. 1362013

Author(s):

Y. MALOZOVSKY ◽

L. FRANKLIN ◽

E. C. EKUMA ◽

G. L. ZHAO ◽

D. BAGAYOKO

Keyword(s):

Ab Initio ◽

Electronic Properties ◽

Gallium Phosphide ◽

Local Density ◽

Basis Set ◽

High Symmetry ◽

Optimal Basis ◽

Direct Band ◽

Experimental Values ◽

Experimental Findings

We present results from ab-initio, self-consistent local density approximation (LDA) calculations of electronic and related properties of zinc blende indium phosphide (InP) and gallium phosphide (GaP) . We employed a LDA potential and implemented the linear combination of atomic orbitals (LCAO) formalism. This implementation followed the Bagayoko, Zhao and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW–EF). This method searches for the optimal basis set that yields the minima of the occupied energies. This search entails increases of the size of the basis set and the related modifications of angular symmetry and of radial orbitals. Our calculated, direct band gap of 1.398 eV (1.40 eV), at the Γ point, is in excellent agreement with experimental values, for InP , and our preliminary result for the indirect gap of GaP is 2.135 eV, from the Γ to X high symmetry points. We have also calculated electron and hole effective masses for both InP and GaP . These calculated properties also agree with experimental findings. We conclude that the BZW–EF method could be employed in calculations of electronic properties of high-Tc superconducting materials to explain their complex properties.

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Complete basis set and gaussian ab initio exploration of singlet and triplet potential energy surface for molecular systems built from one hydrogen, oxygen and nitrogen atoms

Journal of Molecular Structure THEOCHEM ◽

10.1016/s0166-1280(99)00187-6 ◽

2000 ◽

Vol 496 (1-3) ◽

pp. 207-212 ◽

Cited By ~ 7

Author(s):

B.S. Jursic

Keyword(s):

Potential Energy ◽

Potential Energy Surface ◽

Ab Initio ◽

Energy Surface ◽

Basis Set ◽

Molecular Systems ◽

Complete Basis ◽

Complete Basis Set

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Vibrational spectra of medium size molecular systems from DFT and ab-initio quartic force field calculations

In the Frontiers of Computational Science ◽

10.1201/b12167-19 ◽

2005 ◽

pp. 168-179

Author(s):

C. Pouchan ◽

D. Bégué ◽

P. Carbonniére ◽

N. Gohaud

Keyword(s):

Force Field ◽

Ab Initio ◽

Vibrational Spectra ◽

Medium Size ◽

Force Field Calculations ◽

Molecular Systems

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A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

10.26434/chemrxiv.6160142 ◽

2018 ◽

Author(s):

Danilo Carmona ◽

David Contreras ◽

Oscar A. Douglas-Gallardo ◽

Stefan Vogt-Geisse ◽

Pablo Jaque ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Hydroxyl Radical ◽

Ab Initio ◽

Fenton Reaction ◽

Basis Set ◽

Basis Sets ◽

Dft Methods ◽

Elementary Steps ◽

Oxygen Oxygen ◽

Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

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An ab initio MO study of conformation structure of nicotinamide and its derivatives

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19831842 ◽

1983 ◽

Vol 48 (7) ◽

pp. 1842-1853 ◽

Cited By ~ 2

Author(s):

Stanislav Böhm ◽

Josef Kuthan

Keyword(s):

Ab Initio ◽

Wave Functions ◽

Semiempirical Calculations ◽

Rigid Rotor ◽

Qualitative Similarity ◽

Ab Initio Mo ◽

Experimental Findings

Conformation of nicotinamide (I), 3-carbamoylpyridinium (IIa), 1-methyl-3-carbamoylpyridinium (IIb), and 1-methyl-1,4-dihydronicotinamide (IIIa) has been studied in the rigid rotor approximation on the basis of non-empirical STO-3G wave functions. The rotation barriers decrease in the order: IIIa > I ~ IIb > IIa. When confronted with semiempirical calculations, the conformation curves of molecular energy show a better qualitative similarity to the EHT than to NDDO and particularly to CNDO/2 curves. Relation of the calculated characteristics to experimental findings is discussed.

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Rotational de-excitations of C3H+ (1Σ+) by collision with He: new ab initio potential energy surface and scattering calculations

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/staa1086 ◽

2020 ◽

Vol 494 (4) ◽

pp. 5675-5681 ◽

Cited By ~ 1

Author(s):

Sanchit Chhabra ◽

T J Dhilip Kumar

Keyword(s):

Potential Energy ◽

Potential Energy Surface ◽

Ab Initio ◽

Cross Sections ◽

Energy Surface ◽

Molecular Ions ◽

Basis Set ◽

Rate Coefficients ◽

Close Coupling ◽

Collisional Rate Coefficients

ABSTRACT Molecular ions play an important role in the astrochemistry of interstellar and circumstellar media. C3H+ has been identified in the interstellar medium recently. A new potential energy surface of the C3H+–He van der Waals complex is computed using the ab initio explicitly correlated coupled cluster with the single, double and perturbative triple excitation [CCSD(T)-F12] method and the augmented correlation consistent polarized valence triple zeta (aug-cc-pVTZ) basis set. The potential presents a well of 174.6 cm−1 in linear geometry towards the H end. Calculations of pure rotational excitation cross-sections of C3H+ by He are carried out using the exact quantum mechanical close-coupling approach. Cross-sections for transitions among the rotational levels of C3H+ are computed for energies up to 600 cm−1. The cross-sections are used to obtain the collisional rate coefficients for temperatures T ≤ 100 K. Along with laboratory experiments, the results obtained in this work may be very useful for astrophysical applications to understand hydrocarbon chemistry.

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