Quantum Mechanical Methods Research Articles

CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods.

Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of QM/MM Interfacer has been achieved through integration with existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Solution Builder, and Membrane Builder. In addition, new functionalities have been developed to facilitate the one-stop preparation of QM/MM systems and enable interactive and intuitive ligand modifications and QM atom selections. QM/MM Interfacer offers support for a range of semiempirical QM methods, including AM1(+/d), PM3(+/PDDG), MNDO(+/d, +/PDDG), PM6, RM1, and SCC-DFTB, tailored for both AMBER and CHARMM. A nontrivial setup related to ligand modification, link-atom insertion, and charge distribution is automatized through intuitive user interfaces. To illustrate the robustness of QM/MM Interfacer, we conducted QM/MM simulations of three enzyme-substrate systems: dihydrofolate reductase, insulin receptor kinase, and oligosaccharyltransferase. In addition, we have created three tutorial videos about building these systems, which can be found at https://www.charmm-gui.org/demo/qmi. QM/MM Interfacer is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for hybrid QM/MM simulations.

ScaleLat: A chemical structure matching algorithm for mapping atomic structure of multi-phase system and high entropy alloys

ScaleLat (Scale Lattice) is a computer program written in C for performing the atomic structure analysis of multi-phase system or high entropy alloys (HEAs). The program implements an atomic cluster cell extraction algorithm to obtain all symmetry independent characteristic atomic cluster cells for the complex atomic configurations which are usually obtained from molecular dynamics or kinetic Monte-Carlo simulations at nanoscale or mesoscopic scale. ScaleLat implements an efficient and unique chemical structure matching algorithm to match all extracted atomic clusters from a large supercell (>104 atoms) to a representative small one (∼ 103 or less), providing the possibility to directly use the highly accurate quantum mechanical methods to study the electronic, magnetic, and mechanical properties of multi-component alloys for complex microstructures. We demonstrate the capability of ScaleLat code by conducting both the atomic structure matching analysis for Fe-12.8 at.% Cr binary alloy and equiatomic CrFeCoNiCu high entropy alloy, successfully obtaining the representative supercells containing 102∼103 atoms for two systems. The reliability of the proposed chemical structure matching scheme is tested and confirmed by calculating the electronic structures of both examples using trial supercells with various sizes. Overall, ScaleLat program provides a universal platform to efficiently map all essential chemical structures of large complex atomic structures to a relatively easy-handling small supercell for quantum mechanical calculations of various user interested properties. Program SummaryProgram Title: ScaleLatCPC Library link to program files: https://doi.org/10.17632/cv6wsxy938.1Developer's repository link: https://github.com/NanLi-xjtu/ScaleLat.gitLicensing provisions: MITProgramming language: CNature of Problem: Very large supercells containing more than 104 atoms must be used to describe the atomic structure of multi-phase materials or high entropy alloys, and their electronic and mechanical properties are almost not possible to be investigated using quantum mechanical calculations within conventional computational hardware. Decreasing the total number of atoms in a smaller representative supercell which preserves all essential chemical structures of the original large supercell is the key to tackling the problem.Solution to the Problem: An atomic cluster cell extraction algorithm is realized to thoroughly obtain all symmetry independent characteristic chemical structures of multi-phase system or high entropy alloys. Utilizing the direct atom swapping method, the efficient chemical structure matching procedure is developed to map all extracted characteristic atomic cluster cells of benchmark structure to the small supercell by minimizing their differences in both the types and relative fractions of atomic cluster cell sets.

MLatom Software Ecosystem for Surface Hopping Dynamics in Python with Quantum Mechanical and Machine Learning Methods.

We present an open-source MLatom@XACS software ecosystem for on-the-fly surface hopping nonadiabatic dynamics based on the Landau-Zener-Belyaev-Lebedev algorithm. The dynamics can be performed via Python API with a wide range of quantum mechanical (QM) and machine learning (ML) methods, including ab initio QM (CASSCF and ADC(2)), semiempirical QM methods (e.g., AM1, PM3, OMx, and ODMx), and many types of ML potentials (e.g., KREG, ANI, and MACE). Combinations of QM and ML methods can also be used. While the user can build their own combinations, we provide AIQM1, which is based on Δ-learning and can be used out-of-the-box. We showcase how AIQM1 reproduces the isomerization quantum yield of trans-azobenzene at a low cost. We provide example scripts that, in dozens of lines, enable the user to obtain the final population plots by simply providing the initial geometry of a molecule. Thus, those scripts perform geometry optimization, normal mode calculations, initial condition sampling, parallel trajectories propagation, population analysis, and final result plotting. Given the capabilities of MLatom to be used for training different ML models, this ecosystem can be seamlessly integrated into the protocols building ML models for nonadiabatic dynamics. In the future, a deeper and more efficient integration of MLatom with Newton-X will enable a vast range of functionalities for surface hopping dynamics, such as fewest-switches surface hopping, to facilitate similar workflows via the Python API.

Theoretical Study of Electron Capture, Excitation, and Ionization Processes in H+−H(2l) Collisions

The processes of single-electron charge exchange, excitation, and ionization during proton impact on H(2l) are investigated. We employ two different theoretical methods that are suitable for different collision energy regions: the full quantum-mechanical molecular orbital close-coupling method for energies from 0.001 to 1 keV u−1 and the two-center atomic orbital close-coupling (TC-AOCC) method for energies between 0.3 and 100 keV u−1. For charge exchange and excitation processes, the total and nl-resolved cross sections to the final reaction channels of H (nl, n = 1–4) have been obtained over a broad energy region. Moreover, the ionization cross sections in the TC-AOCC calculation are also reported for both H(2s) and H(2p) initial target states. The present results are all compared with those from other sources when available. It is found that the magnitude and energy behavior of nl-resolved excitation cross sections for H+–H(2p) collisions are significantly distinct from those of the H(2s) initial state in the entire energy range considered, particularly in the low-energy region. The energy behaviors of the nl-resolved charge exchange cross sections from the H(2p) initial state are similar to those from the H(2s) initial state, but their magnitudes are larger. The present accurate cross-section data are anticipated to provide insight into the research of astrophysics and controlled fusion plasmas.

Evaluation of the Xtb Semiempirical Method for the Prediction of Antioxidant Properties in Alzheimer’s Disease: Salen-Type Ligands

Alzheimer’s disease (AD) stands as the predominant form of dementia, accounting for up to 70% of all cases worldwide. AD is a complex disease with various contributing factors. Evidence suggests that the metalliccomplexes formed by the β-amyloid peptide (Aβ) and extraneuronal copper can catalyze the generation ofreactive oxygen species, consequently increasing oxidative stress and contributing to the decline of neurons. This interaction underscores the significance of bioavailable copper as a crucial redox-active target in exploring protocols for multifunctional agents in AD treatment. In the field of computational chemistry, density functional theory (DFT) is widely accepted as a standard method across different disciplines. Despite this, DFT presents computational challenges, particularly in screening extensive molecular sets during the initial phases of drug research. Recent advances in semiempirical quantum mechanical methods (SQM) offer a promising alternative, providing rapid molecular geometry optimization and approximate estimation of thermodynamical properties, being at least two orders of magnitude faster than traditional DFT calculations. In this work, we present an evaluation of the GFNn-xTB SQM methods in the rapid screening of antioxidant properties in AD, performed on a set of salen ligands by calculating the standard reduction potentials of their copper complexes as key property. Results show that the implementation of GFNn-xTB SQM calculations before DFT evaluations is

New Potential Energy Surface for the H + Cl2 Reaction and Quantum Dynamics Studies.

The reaction of H + Cl2 → HCl + Cl plays a crucial role in various fields. However, no previous study has investigated this reaction using accurate quantum mechanical methods. In this paper, we construct a global potential energy surface (PES) using the neural network method with more than 20,000 ab initio energies obtained by the MRCI-F12+Q method with the aug-cc-pV5Z basis and extrapolated to the complete basis set limit. The spin-orbit coupling of the Cl atom has been considered in the PES. With this new PES, product state-resolved quantum dynamics calculations for the H + Cl2 (v0 = 0, j0 = 0-2) → HCl + Cl reaction was carried out. Numerical results show that the initial rotational excitation of the Cl2 has negligible effects on the reactivity. Product state-resolved integral cross sections (ICS) and rate constants reveal that the HCl is most favorably produced in its v' = 2 vibrational state. The calculated product vibrational state-resolved and total reaction rate constants suggest that the new global PES is accurate enough, as compared with the available experimental measurements.

Effect of chalcogen atoms on the electronic band gaps of the quinoxaline containing donor-acceptor-donor type semiconducting polymers: a systematic DFT investigation.

Due to the widely known positive contributions of the quinoxaline group in organic semiconductors, we conducted a fully computational study using quantum mechanical methods to investigate the effect of quinoxaline in the electron acceptor unit with the combination of different chalcogen atoms on the band gap of a series of donor-acceptor-donor type conjugated polymers. Using density functional theory, we mainly calculated the electronic band gap values of the structures containing four different chalcogen atoms (O, S, Se, and Te) in the electron donor and acceptor units. While chalcogendiazoloquinoxaline groups were used as the electron acceptor units, furan, thiophene, selenophene, and tellurophene were used as the donor units. Our theoretical results showed that the use of heavy chalcogen atoms in both donor and acceptor units resulted in a low band gap. Besides this, the effect of heavy chalcogen atoms used in the electron donor units is much more pronounced compared to the ones used in the acceptor units. More importantly, our findings proved that the inclusion of the chalcogendiazoloquinoxaline group instead of benzochalcogenadiazole as the acceptor unit significantly decreases the electronic band gap of the conjugated polymer. The lowest band gap was found to be 0.10eV for the 4,9-di(tellurophen-2-yl)-[1,2,5]telluradiazolo[3,4-g]quinoxaline polymer. Conformational analysis of the monomers and their corresponding oligomers was performed at the B3LYP/LANL2DZ level of theory. Then, long-range corrected hybrid functional LC-BLYP in a combination with the LANL2DZ basis set was utilized for the calculation of electronic properties and HOMO and LUMO energy gaps of monomers and oligomers through the reoptimization of the lowest energy conformers obtained from the B3LYP/LANL2DZ calculations in the previous step. All energy minimum structures were confirmed through vibrational frequency analysis at both calculation levels. The Gaussian 09 rev. D.01 software was used for all calculations, and GaussView 5.0.9 for visualizations.

Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design.

With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.

Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.

Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality or even correcting the structure of biomacromolecules. However, vast computational costs and complex quantum mechanics/molecular mechanics (QM/MM) setups limit QR applications. Here we incorporate robust machine learning potentials (MLPs) in multiscale ONIOM(QM:MM) schemes to describe the core parts (e.g., drugs/inhibitors), replacing the expensive QM method. Additionally, two levels of MLPs are combined for the first time to overcome MLP limitations. Our unique MLPs+ONIOM-based QR methods achieve QM-level accuracy with significantly higher efficiency. Furthermore, our refinements provide computational evidence for the existence of bonded and nonbonded forms of the Food and Drug Administration (FDA)-approved drug nirmatrelvir in one SARS-CoV-2 main protease structure. This study highlights that powerful MLPs accelerate QRs for reliable protein-drug complexes, promote broader QR applications and provide more atomistic insights into drug development.

Essential oils from fennel plants as valuable chemical products: gas chromatography–mass spectrometry, FTIR, quantum mechanical investigation, and antifungal activity

AbstractIn the present study, the biomass produced by fennel plants (Foeniculum vulgare Mill.) was converted to yield bioactive chemicals, and the hydrodistillation method was used to extract the essential oils (EOs) from both the leaves and the umbels. The antifungal activity of the EOs was tested using bioassay against the development of Fusarium oxysporum MW854649 and Alternaria solani MT279570. Molecular spectroscopic detection techniques were used to evaluate the EO products using gas chromatography–mass spectrometer (GC–MS) and Fourier transform infrared spectroscopy (FTIR). GC–MS equipped with single quadruple analyzers have been used to measure the electron ionization (EI) mass spectra of the primary constituents of fennel EOs at 70 eV. The main chemical compounds in the EO from leaves were anethole, estragole, D-limonene, trans-β-ocimene, and fenchone, with percentages of 37.94, 35.56, 17.46, 1.53, and 1.49%, respectively. The abundant compounds in the EO from umbels were estragole, anethole, D-limonene, fenchone, and γ-terpinene, with percentages of 51.18, 25.08, 12.22, 6.57, and 2.86%, respectively. EI mass spectral fragmentation of the major compounds D-limonene, estragole, anethole, and fenchone has been investigated. Umbels and leaf EOs at 5000 mg/L displayed the strongest suppression of fungal growth against A. solani, with values of 87.78% and 79.63%, respectively, compared to the positive control (94.44%). The EOs from umbels and leaves at 5000 mg/L showed the highest inhibition of fungal growth against F. oxysprium as compared to the positive control (94.44%), with values of 77.77% and 72.96%, respectively. All of the important ions—including a few distinctive fragment ions—have comprehensive fragmentation pathways defined. Based on EI, the main routes of fragmentation for the primary compounds have been identified. The existence of alkenes, aliphatic alcohols, ethers, carboxylic acids, ester compounds, alkanes, hydrogen-bonded alcohols, and phenols was demonstrated by the FTIR analysis of fennel EOs. On the other hand, the reactive behavior of the studied molecules has been investigated using two quantum mechanics method: the modified neglect of diatomic overlap (MNDO), a semi-empirical method, and the density functional theory (DFT)/B3LYP hybrid density functional method with the 6-311G (d, p) basis set in the ground state for gas phase. The optimum geometries have been obtained through the execution of computations and electrostatic potential. The obtained analytical and calculated results were then used to understand the activity of the studied EOs in further medical applications.

Exploring the Light-Emitting Agents in Renilla Luciferases by an Effective QM/MM Approach.

Bioluminescence is a fascinating natural phenomenon, wherein organisms produce light through specific biochemical reactions. Among these organisms, Renilla luciferase (RLuc) derived from the sea pansy Renilla reniformis is notable for its blue light emission and has potential applications in bioluminescent tagging. Our study focuses on RLuc8, a variant of RLuc with eight amino acid substitutions. Recent studies have shown that the luminescent emitter coelenteramide can adopt multiple protonation states, which may be influenced by nearby residues at the enzyme's active site, demonstrating a complex interplay between protein structure and bioluminescence. Herein, using the quantum mechanical consistent force field method and the semimacroscopic protein dipole-Langevin dipole method with linear response approximation, we show that the phenolate state of coelenteramide in RLuc8 is the primary light-emitting species in agreement with experimental results. Our calculations also suggest that the proton transfer (PT) from neutral coelenteramide to Asp162 plays a crucial role in the bioluminescence process. Additionally, we reproduced the observed emission maximum for the amide anion in RLuc8-D120A and the pyrazine anion in the presence of a Na+ counterion in RLuc8-D162A, suggesting that these are the primary emitters. Furthermore, our calculations on the neutral emitter in the engineered AncFT-D160A enzyme, structurally akin to RLuc8-D162A but with a considerably blue-shifted emission peak, aligned with the observed data, possibly explaining the variance in emission peaks. Overall, this study demonstrates an effective approach to investigate chromophores' bimolecular states while incorporating the PT process in emission spectra calculations, contributing valuable insights for future studies of PT in photoproteins.

Electron impact broadening and atomic data for As IV-V, Mo V and In V spectral lines

Missing Stark broadening parameters for 33 spectral lines of several arsenic, molybdenum and indium ions (7 As IV, 4 As V, 12 Mo V and 10 In V lines) have been calculated using a quantum-mechanical method. All the considered spectral lines for As IV and As V have been detected for the first time in the atmospheres of cool DO white dwarfs HD 149499 B and p=HZ 21, these four As V lines that have been discovered in HD 149499 B are also present in the UV spectrum of hot white dwarf (WD) RE 0503−289. All the considered spectral lines for Mo V have been recently discovered for the first time in the ultraviolet (UV) spectrum of the DO-type white dwarf (WD) RE 0503−289. Also, the ten considered lines for In V have been detected in the ultraviolet (UV) spectrum of the DO-type white dwarf (WD) RE 0503−289, that five among those discovered — recently — for the first time. This recent discovery encourages us to calculate their Stark widths to fill the lack of the data base STARK-B and for use in investigations of observed spectra in such stars. Before the Stark widths evaluation, two calculation steps have been carried out : in the first step, we calculate the atomic structure and then the electron-ion collision as a second step using the sequence of the codes (superstructure, distorted wave, and jajom) of University College London. We provide our results for these lines at different temperature values and at density Ne=1017 cm−3.

Accurate Simulation for 2D Lubricating Materials in Realistic Environments: From Classical to Quantum Mechanical Methods.

2D materials such as graphene, MoS2, and hexagonal BN are the most advanced solid lubricating materials with superior friction and anti-wear performance. However, as a typical surface phenomenon, the lubricating properties of 2D materials are largely dependent on the surrounding environment, such as temperature, stress, humidity, oxygen, and other environmental substances. Given the technical challenges in experiment for real-time and in situ detection of microscopic environment-material interaction, recent years have witnessed the acceleration of computational research on the lubrication behavior of 2D materials in realistic environments. This study reviews the up-to-date computational studies for the effect of environmental factors on the lubrication performance of 2D materials, summarizes the theoretical methods in lubrication from classical to quantum-mechanics ones, and emphasizes the importance of quantum method in revealing the lubrication mechanism at atomic and electronic level. An effective simulation method based on ab initio molecular dynamics is also proposed to try to provide more ways to accurately reveal the friction mechanisms and reliably guide the lubricating material design. On the basis of current development, future prospects, and challenges for the simulation and modeling in lubrication with realistic environment areoutlined.

Confinement effects of mandrel degradation in ICF target fabrication.

Understanding and further regulating the degradation of mandrel materials is a key aspect of target fabrication in inertial confinement fusion (ICF). Here, a quasi-one-dimensional confinement model is developed using a series of single-walled carbon nanotubes with varying diameters (Dm), and the degradation of poly-α-methylstyrene (PAMS) as a typical mandrel material is investigated under such confined conditions by using the combined method of quantum mechanics and molecular mechanics. In comparison to the isolated system, the calculations show that confinement can decrease or increase the energy barriers of PAMS degradation, which directly depends on Dm. Following which a clear exponential relationship between the degradation rate of PAMS and its own density is derived, indicating that the density of PAMS can be used to regulate mandrel degradation. This work highlights the important effects of confinement on degradation and provides a valuable reference for further development of polymer degradation technologies in ICF target fabrication and other fields.

A model of ionization-induced reactions in CH4/N2 clusters in Titan's atmosphere: theoretical insights into mono- and divalent states

Abstract We propose a model for ionization-induced reactions between N2 and CH4, the main components of Titan's atmosphere, and examine their mechanism using quantum mechanical and molecular dynamics methods. Bimolecular CH4–N2 clusters form through collision, and their conformation depends on the encounter cross section due to weak intermolecular interaction. These clusters acquire a driving force through vertical ionization because the vertically ionized structure is not situated at the minimum of the potential energy surface in the ionized state. This leads to multiple reactions, overcoming energy barriers in the process. In the divalent state, a robust attractive interaction occurs between CH4 and N2 through charge transfer. Subsequently, the H4C–N2 covalent bond forms prior to reactions, resulting in the production of N2H+, CH3+, CH3N2+, and CH2N2+; otherwise only N2H+, CH3+, and CH2+ are generated. In contrast, when ionized to a monovalent state, although dissociation of N2H+ and isomerization to CH3NHN+ and CH3NNH+ occurs, a significant portion dissociates into CH4+ and N2 without undergoing further reactions. Additionally, the generation of N2H+ and CH3+ is limited in the monovalent state, primarily due to a lower driving force and the absence of Coulombic explosion. Our computational results highlight the pivotal role of divalent reactions within Titan's atmosphere, which are more efficient than monovalent reactions.

Design of Quantum Gates Using Quantum Scattering Theory

Given two Hamiltonians \(H_0,H_1=H_0+V\) corresponding respectively to a free particle Hamiltonian and the free particle Hamiltonian plus its interaction energy with a scattering centre, we can compute the S-matrix, i.e., the matrix that determines the quantum mechanical amplitude of the process involving a particle coming from a free particle state at an infinite distance from the scattering centre at time \(t=-\infty\), entering into an initial scattered state, interacting with the scattering centre, entering into a final scattered state, and then escaping away to infinity at time \(t\rightarrow\infty\) to a final free particle state. Such amplitudes were first studied by Lippmann and Schwinger (Steven Weinberg, The Quantum Theory of Fields, Vol. 1, W.O. Amrein, Hilbert Space Methods in Quantum Mechanics) and then analyzed in a mathematically precise way by [T. Kato], [W. Amrein], and [K.B. Sinha]. In this paper, we first derive the Lippmann-Schwinger equation for the input and output scattered states in terms of the input and output free particle states using intuitive arguments originally due to Lippmann and Schwinger, and then, using rigorous operator theoretic arguments revolving around the spectral theorem for unbounded self-adjoint operators in a Hilbert space, we obtain an elegant formula for the scattering matrix elements in terms of the interaction potential and the free particle Hamiltonian between two free particle states corresponding to the same measure. We then discuss a computationally more efficient method based on the Dyson series expansion (Steven Weinberg, The Quantum Theory of Fields, Vol. 1), which works even in the case when the interaction Hamiltonian is time varying, in contrast to the Lippmann-Schwinger method, for calculating the S-matrix. We assume that the scattering potential, which can be time varying, can be controlled by incorporating control parameters and explain how the resulting unitary S-matrix can be made to approximate a given unitary gate in infinite-dimensional Hilbert space by optimizing the Hilbert-Schmidt/Frobenius norm distance between the given gate and the S-matrix gate, in which the latter is approximated by a truncated Dyson series. Of course, the S-matrix given by the Dyson series is a Taylor series functional expansion in the interaction potential and hence is a highly nonlinear function of the control parameters, and hence we propose numerical methods for such optimization. We then observe that if the control parameters are taken as random variables with joint moments, then the TPCP map involving statistical averaging of the adjoint action of the S-matrix acting on an initial mixed state w.r.t. the probability distribution of the control parameters will result in a final mixed state that is linear in the statistical moments of the control parameters, and hence optimization w.r.t. these moments can be easily carried out. Our method of TPCP map design is to optimize the sum of Frobenius distance squares between a sequence of desired output mixed states and the S-matrix based formula for the TPCP map acting on the corresponding input mixed states w.r.t. the statistical moments of the control parameters. We then generalize this method to include the case of TPCP maps obtained from the Hudson-Parthasarathy quantum noisy Schrödinger equation. In summary, we simulate the S-matrix gate for independent realizations of the control parameters having a probability distribution defined by their joint moments obtained by the above optimization procedure and apply the adjoint action of these independent S-matrices on a given input state, and take their ensemble average to obtain a good approximation to the action of the desired TPCP map on any given input state. This suggests that TPCP maps of arbitrarily large size can be realized using scattering experiments in the laboratory.

THEORETICAL STUDY FOR COMPARISON OF pKa OF A NUMBER OF SCHIFF BASES BY EMPLOYING PARAMETERS DERIVED FROM DFT AND MP2 METHOD

The ionization constants of seven compounds derived from Schiff bases have been studied theoretically. In this study, the factors affecting the ionization constant pKa of Schiff bases were found, which are van der Waals forces, energy levels, hardness, chemical potential and spherical electrophile index by conducting a theoretical study of these compounds using two methods of quantum mechanics for the purpose comparison, which is the Ab-initio basic calculation methods. Two methods were chosen, which are the density function theory (DFT) method and the MP2 Mueller-Pleist perturbation theory method using Chem program. Office 2008 the extent to which these two methods correspond to the known chemical bases was determined by discussing the theoretical variables that were calculated using the two methods referred to above and finding the relationship between the calculated physical variables with each other and determining their nature. After conducting the multiple statistical analysis process, it was found that the best variables that affect the ionization constant in the DFT method are (Bond C1-C7, Bend, VDW) and the rest of the variables were theoretically excluded because the coefficients of those variables are very few or equal to zero and accordingly these variables were adopted to obtain A relationship with better results, as it is noted that the values of the correlation coefficient in this DFT method are (0.994). As for the MP2 method, the best variables that affect the ionization constant are (Ƞ, KE, Tors) and the rest of the variables were theoretically excluded because the coefficients of these variables are very few or equal Therefore, these variables were adopted to obtain a relationship with better results, as it is noted that the values of the correlation coefficient in this MP2 method are (0.989). By comparing the theoretical values with the practical values, it was found that the results of the DFT method were closer to the process than the results of the MP2 method.

An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes.

Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumental techniques that require a lot of time and money. Hence, the development of efficient and effective metal indicators is essential. Several synthetic metal detectors have been made, but due to their risk of harm, the use of natural pigments is considered a potential alternative. Experiments are needed for their development, but they are expensive and time-consuming. This review explores various computational methods and approaches that can be used to investigate metal-pigment interactions because choosing the right methods and approaches will affect the reliability of the results. The results show that quantum mechanical methods (ab initio, density functional theory, and semiempirical approaches) and molecular dynamics simulations have been used. Among the available methods, the density functional theory approach with the B3LYP functional and the LANL2DZ ECP and basis set is the most promising combination due to its good accuracy and cost-effectiveness. Various experimental studies were also in good agreement with the results of computational methods. However, deeper analysis still needs to be carried out to find the best combination of functions and basis sets.

Study of quantum electron diffraction for the LISA test-mass charging

The future Laser Interferometer Space Antenna (LISA) for gravitational wave detection in space and the precursor LISA Pathfinder missions rely on metal test masses (TMs) playing the role of free-falling geodesic-reference and interferometer end mirrors. Charge deposited on the TMs by high-energy particles of galactic and solar origin couples with stray electric fields thus perturbing the free-falling geodesic motion. In previous works it has been shown that sub-keV electrons play a relevant role for TM charging. In particular, electrons with energies below 100 eV show a wave-like behavior when impacting on the gold coatings of the TMs and electrode-housing (EH), the capacitive position sensor/actuator that surrounds the TMs. We aim at studying the effects of quantum diffraction of electrons on LISA Pathfinder and LISA TMs and EH gold lattice. We calculate the quantum diffraction probability of electrons with energies < 100 eV impinging on gold lattice from different directions by using the methods of quantum mechanics. The effects of electron quantum diffraction on LISA TM charging are reported here for the first time. This work is also of interest for the second-generation LISA-like space interferometers and for all space missions whose performance relies on free-falling metal test masses.

Perspective on Integrative Simulations of Bioenergetic Domains.

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.