Quantum-theoretical approaches to proteins and nucleic acids

2017 ◽  
Author(s):  
Mauro Boero ◽  
Masaru Tateno
Keyword(s):  
Nucleic Acids ◽  
Density Functional ◽  
A Priori ◽  
Alternative Methods ◽  
Parallel Tempering ◽  
Quantum Mechanical ◽  
Chemical Bonds ◽  
Functional Theory ◽  
Hartree Fock ◽  
Theoretical Approaches

This article describes quantum methods used to study proteins and nucleic acids: Hartree–Fock all-electron approaches, density-functional theory approaches, and hybrid quantum-mechanics/molecular-mechanics approaches. In addition to an analysis of the electronic structure, quantum-mechanical approaches for simulating proteins and nucleic acids can elucidate the cleavage and formation of chemical bonds in biochemical reactions. This presents a computational challenge, and a number of methods have been proposed to overcome this difficulty, including enhanced temperature methods such as high-temperature molecular dynamics, parallel tempering and replica exchange. Alternative methods not relying on the knowledge a priori of the final products make use of biasing potentials to push the initial system away from its local minimum and to enhance the sampling of the free-energy landscape. This article considers two of these biasing techniques, namely Blue Moon and metadynamics.

scholarly journals Electronegativity under Confinement

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6924
Author(s):  
Andrés Robles-Navarro ◽  
Carlos Cárdenas ◽  
Patricio Fuentealba
Keyword(s):  
High Pressure ◽  
Density Functional ◽  
Electronic Configuration ◽  
Chemical Bonds ◽  
Functional Theory ◽  
First Order ◽  
Hartree Fock ◽  
Confining Potential ◽  
Different Types ◽  
First Order Perturbation

The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms can change, and, thus, the bond patterns in molecules and solids are affected. In this work, we studied the effects of high pressure modeled by a confining potential on different definitions of electronegativity and, additionally, tested the accuracy of first-order perturbation theory in the context of density functional theory for confined atoms of the second row at the Hartree–Fock level. As expected, the electronegativity of atoms at high confinement is very different than that of their free counterparts since it depends on the electronic configuration of the atom, and, thus, its periodicity is modified at higher pressures.

Applications of Density Functional Theory to Biological Systems

1998 ◽  
Author(s):  
Tomasz Adam Wesolowski ◽  
Jacques Weber
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Biological Systems ◽  
Quantum Mechanical ◽  
Biological Processes ◽  
Biological Functions ◽  
Functional Theory ◽  
Hartree Fock ◽  
Functional Units

The term biological systems may be used in reference to a wide class of polyatomic systems. They can be defined as minimal functional units which perform specific biological functions: enzymatic reactions, transport across membranes, or photosynthesis. At present, such systems as a whole are not amenable to quantum-chemistry studies because of their large size. The smallest enzymes are built of few thousands of atoms (e.g., lysozyme consists of 129 amino-acid subunits), the smallest nucleic acids are of similar size (e.g., t-RNA molecules consist of about 80 nucleotide subunits), whereas biological membranes are even larger and include different biological macromolecules embedded in a phospholipide medium. On the other hand, a common-sense definition of the term biological systems refers to any chemical molecule or molecular complex which is involved in biological or biochemical processes. The latter definition, which will be used throughout this review, covers not only complete functional units performing biological functions but also fragments of such units. Theoretical studies have provided data on properties of such fragments and have helped understanding of the biological processes at the molecular level. Depending upon the size of such fragments, they can be studied by means of various quantum-chemical methods. Molecular systems of up to a few thousands of atoms can be studied using semi-empirical methods. For the Hartree-Fock or Kohn-Sham density functional theory (DFT) calculations, the current size limit is a few hundreds of atoms. (Throughout the text, Hartree-Fock refers to ab initio Self-Consistent Field calculations using the approximation of linear combination of atomic orbitals.) When the desired accuracy requires the calculation of electron correlation at the ab initio level, only systems containing no more than few tens of atoms can be treated. Therefore, a theoretician aiming at the elucidation of biological processes by quantum-mechanical calculations faces two crucial issues. The first one is the selection of a fragment for modeling at the quantum-mechanical level. The second one is the assessment of the effects associated with parts of the system which cannot be modeled at the quantum-mechanical level. In this review, the DFT studies of biological systems are divided into two groups corresponding to different ways of addressing the second aforementioned issue.

scholarly journals Unraveling the electrochemical and spectroscopic properties of neutral and negatively charged perylene tetraethylesters

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Wiebeler ◽  
Joachim Vollbrecht ◽  
Adam Neuba ◽  
Heinz-Siegfried Kitzerow ◽  
Stefan Schumacher
Keyword(s):  
Absorption Spectra ◽  
Density Functional ◽  
Energy Levels ◽  
Spectroscopic Properties ◽  
Absorption Bands ◽  
Functional Theory ◽  
Vertical Excitation ◽  
Hartree Fock ◽  
Tauc Plot ◽  
Electrochemical Approach

AbstractA detailed investigation of the energy levels of perylene-3,4,9,10-tetracarboxylic tetraethylester as a representative compound for the whole family of perylene esters was performed. It was revealed via electrochemical measurements that one oxidation and two reductions take place. The bandgaps determined via the electrochemical approach are in good agreement with the optical bandgap obtained from the absorption spectra via a Tauc plot. In addition, absorption spectra in dependence of the electrochemical potential were the basis for extensive quantum-chemical calculations of the neutral, monoanionic, and dianionic molecules. For this purpose, calculations based on density functional theory were compared with post-Hartree–Fock methods and the CAM-B3LYP functional proved to be the most reliable choice for the calculation of absorption spectra. Furthermore, spectral features found experimentally could be reproduced with vibronic calculations and allowed to understand their origins. In particular, the two lowest energy absorption bands of the anion are not caused by absorption of two distinct electronic states, which might have been expected from vertical excitation calculations, but both states exhibit a strong vibronic progression resulting in contributions to both bands.

Polaronic and Bipolaronic Enhancement of Second Hyperpolarizabilities in Dithienyl Polyenes from Ab Initio Quantum Methods

1999 ◽  
Vol 597 ◽  
Author(s):  
Steven Trohalaki ◽  
Robert J. Zellmer ◽  
Ruth Pachter
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Valence Bond ◽  
Closed Shell ◽  
Functional Theory ◽  
Molecular Conformations ◽  
Hartree Fock ◽  
Molecular Charge ◽  
Field Methodology ◽  
Moller Plesset

AbstractSpangler and He [1,2] have shown that dithienyl polyenes form extremely stable bipolaronic dications when oxidatively doped in solution. Previous theoretical studies applied empirical methods to predict bipolaronic enhancement of hyperpolarizabilities for simple polyenes [3,4]. Here, we employ density functional theory to optimize the gas-phase molecular conformations of neutral, cationic, and dicationic forms of a series of dithienyl polyenes, where the number of ethene units, N, is varied from 1–5. Ab initio Hartree-Fock, generalized valence bond, configuration interaction, and Møller-Plesset calculations demonstrate that the dications are farily well described with a closed shell and therefore have little biradicaloid character. Second hyperpolarizabilities, γ, are subsequently calculated using ab initio Hartree-Fock theory and a finite field methodology. As expected, γ increases with the number of ethene units for a given molecular charge. The cations also show the largest increase in γ with N. For a given value of N, the cations display the largest γ values. However, if we treat the dication as a triplet, which might be present in solution, then it displays the largest γ.

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