scholarly journals Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 10 ◽  
Author(s):  
Albert Rimola ◽  
Mariona Sodupe ◽  
Piero Ugliengo
Keyword(s):  
Chemical Evolution ◽  
In Silico ◽  
Density Functional ◽  
Quantum Mechanical ◽  
Mineral Surfaces ◽  
Chemical Complexity ◽  
Organic Mineral ◽  
Mechanical Methods ◽  
Prebiotic Chemical

There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic–mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic–mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic–mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.

Adsorption of HCN onto sodium montmorillonite dependent on the pH as a component to chemical evolution

2014 ◽  
Vol 13 (4) ◽  
pp. 310-318 ◽  
Author(s):  
M. Colin-Garcia ◽  
A. Heredia ◽  
A. Negron-Mendoza ◽  
F. Ortega ◽  
T. Pi ◽  
...  
Keyword(s):  
Chemical Evolution ◽  
Molecular Model ◽  
Three Dimensional ◽  
Channel Structure ◽  
Mineral Surfaces ◽  
Sodium Montmorillonite ◽  
Complex Molecules ◽  
Prebiotic Chemical ◽  
Physical And Chemical

AbstractThe aim of this work is to study the behaviour of hydrogen cyanide (HCN) adsorbed onto mineral surfaces (sodium montmorillonite, a clay mineral) in different pH environments as a possible prebiotic process for complexation of organics. Our experimental results show that specific sites on the surface of the clay increased the concentration of HCN molecules dependent on the pH values. Moreover, this adsorption can occur through physical and chemical interactions enhanced by the channel structure of the sodium montmorillonite. The three-dimensional channelling structure of the clay accumulates the organics, hindering the releasing (desorption) of the organic molecules. A molecular model developed here also confirms the role of the pH as a regulating factor in the adsorption of HCN onto the inorganic surfaces and the possibility for further reactions forming more complex molecules, as an abiotic mechanism important in prebiotic chemical evolution processes.

Histidine Self-assembly and Stability on Mineral Surfaces as a Model of Prebiotic Chemical Evolution: An Experimental and Computational Approach

2021 ◽  
Author(s):  
D. Madrigal-Trejo ◽  
P.S. Villanueva-Barragán ◽  
R. Zamudio-Ramírez ◽  
K. E. Cervantes-de la Cruz ◽  
I. Mejía-Luna ◽  
...  
Keyword(s):  
Chemical Evolution ◽  
Self Assembly ◽  
Computational Approach ◽  
Mineral Surfaces ◽  
Prebiotic Chemical

scholarly journals Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

2021 ◽  
Author(s):  
Aashish Bhatt ◽  
Md. Ehesan Ali
Keyword(s):  
Hydrogen Bonding ◽  
In Silico ◽  
Density Functional ◽  
Experimental Studies ◽  
Salt Bridge ◽  
Md Simulations ◽  
Enzymatic Activities ◽  
Wild Type ◽  
Long Distance

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated <i>In Silico</i> dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

DFT calculation of crystallographic properties of dioctahedral 2:1 phyllosilicates

Clay Minerals ◽  
2008 ◽  
Vol 43 (3) ◽  
pp. 351-361 ◽  
Author(s):  
J. Ortega-Castro ◽  
N. Hernández-Haro ◽  
A. Hernández-Laguna ◽  
C. I. Sainz-Díaz
Keyword(s):  
Density Functional ◽  
Basis Sets ◽  
Quantum Mechanical ◽  
Functional Theory ◽  
Oh Groups ◽  
Low Degree ◽  
Mechanical Methods ◽  
Weak Interlayer ◽  
Low Charge ◽  
Cation Substitutions

AbstractThe low-charge dioctahedral 2:1 phyllosilicates are an important group of clay minerals that have a low degree of cation substitution and very weak interlayer interatomic interactions which are difficult to reproduce with quantum mechanical calculations. In order to study the crystallographic properties of these compounds with density functional theory (DFT) quantum-mechanical methods, an optimization of norm-conserving pseudopotentials of Al, Si, O, H and Na atoms has been carried out, and an optimization of the cutoff radii of the basis sets has been accomplished. Crystallographic properties and vibrational stretching frequencies of the OH groups, ν(OH), have been calculated, being consistent with previous computational and experimental results. All frequencies can be related to the different molecular environment of the OH groups. The effect of octahedral Fe3+ substitution on the ν(OH) frequency is reproduced. Several configurations of cation substitutions and interlayer cation (IC) positions are studied in low-charge dioctahedral 2:1 phyllosilicates, such as Al4(Si7–xAlx)O20(OH)4Nax, with x = 0.25, 0.50 and 0.75, indicating that the IVAl3+ is highly dispersed and the IC tends to be in the substituted ditrigonal hole. For the Al4(Si7Al)O20(OH)4Na composition, the trans-vacant form is more stable than the cis-vacant one.

scholarly journals Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling

2021 ◽  
Author(s):  
Marco Zaccaria ◽  
Luigi Genovese ◽  
Michael Farzan ◽  
William Dawson ◽  
Takahito Nakajima ◽  
...  
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
First Generation ◽  
Weak Link ◽  
Host Cells ◽  
Spike Protein ◽  
Quantum Mechanical ◽  
Protein Receptor ◽  
Protein Mutants

Evolved SARS-CoV-2 variants are currently challenging the efficacy of first-generation vaccines, largely through the emergence of spike protein mutants. Among these variants, Delta is presently the most concerning. We employ an ab initio quantum mechanical model based on Density Functional Theory to characterize the spike protein Receptor Binding Domain (RBD) interaction with host cells and gain mechanistic insight into SARS-CoV-2 evolution. The approach is illustrated via a detailed investigation of the role of the E484K RBD mutation, a signature mutation of the Beta and Gamma variants. The simulation is employed to: predict the depleting effect of the E484K mutation on binding the RBD with select antibodies; identify residue E484 as a weak link in the original interaction with the human receptor hACE2; and describe SARS-CoV-2 Wuhan strand binding to the bat Rhinolophus macrotis ACE2 as more optimized than the human counterpart. Finally, we predict the hACE2 binding efficacy of a hypothetical E484K mutation added to the Delta variant RBD, identifying a potential future variant of concern. Results can be generalized to other mutations, and provide useful information to complement existing experimental datasets of the interaction between randomly generated libraries of hACE2 and viral spike mutants. We argue that ab initio modeling is at the point of being aptly employed to inform and predict events pertinent to viral and general evolution.

scholarly journals Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes

2020 ◽  
Vol 2 ◽  
pp. e8 ◽  
Author(s):  
Jitnapa Sirirak ◽  
Narin Lawan ◽  
Marc W. Van der Kamp ◽  
Jeremy N. Harvey ◽  
Adrian J. Mulholland
Keyword(s):  
Density Functional ◽  
Good Choice ◽  
Basis Set ◽  
Basis Sets ◽  
Quantum Mechanical ◽  
Spin Component ◽  
Energy Calculation ◽  
Mp2 Calculations ◽  
Mechanical Methods ◽  
Reaction Energies

To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.

scholarly journals Transient Absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study

2021 ◽  
Author(s):  
Daniil A. Fedotov ◽  
Alexander C. Paul ◽  
Henrik Koch ◽  
Fabrizio Santoro ◽  
Sonia Coriani ◽  
...  
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Transient Absorption ◽  
Chloroform Solution ◽  
Excited State Absorption ◽  
Polarizable Continuum Model ◽  
Photon Absorption ◽  
Dna Bases ◽  
Quantum Mechanical ◽  
Mechanical Methods

We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, i.e. equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for Thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are also consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the pp  states (one for pyrimidine, two for purines) associated with the lowest energy absorption band, and for the close-lying np  state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effect by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the np  state. Finally, ESA spectra have been computed from the minima of the lowest energy pp  state, and are consistent with the available experimental transient absorption spectra of the nucleosides in solution, providing a final validation of our computational approach.

scholarly journals Ab Initio Quantum–Mechanical Predictions of Semiconducting Photocathode Materials

Micromachines ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1002
Author(s):  
Caterina Cocchi ◽  
Holger-Dietrich Saßnick
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Particle Accelerator ◽  
Quantum Mechanical ◽  
Many Body ◽  
Computational Accuracy ◽  
Electron Sources ◽  
Mechanical Methods ◽  
The Status ◽  
Many Body Perturbation Theory

Ab initio quantum–mechanical methods are well-established tools for material characterization and discovery in many technological areas. Recently, state-of-the-art approaches based on density-functional theory and many-body perturbation theory were successfully applied to semiconducting alkali antimonides and tellurides, which are currently employed as photocathodes in particle accelerator facilities. The results of these studies have unveiled the potential of ab initio methods to complement experimental and technical efforts for the development of new, more efficient materials for vacuum electron sources. Concomitantly, these findings have revealed the need for theory to go beyond the status quo in order to face the challenges of modeling such complex systems and their properties in operando conditions. In this review, we summarize recent progress in the application of ab initio many-body methods to investigate photocathode materials, analyzing the merits and the limitations of the standard approaches with respect to the confronted scientific questions. In particular, we emphasize the necessary trade-off between computational accuracy and feasibility that is intrinsic to these studies, and propose possible routes to optimize it. We finally discuss novel schemes for computationally-aided material discovery that are suitable for the development of ultra-bright electron sources toward the incoming era of artificial intelligence.

Sign in / Sign up

Export Citation Format

Share Document