Application Of Quantum Chemical Calculations Research Articles

Revisiting the Use of Quantum Chemical Calculations in LogPoctanol-water Prediction.

The partition coefficients of drug and drug-like molecules between an aqueous and organic phase are an important property for developing new therapeutics. The predictive power of computational methods is used extensively to predict partition coefficients of molecules. The application of quantum chemical calculations is used to develop methods to develop structure-activity relationship models for such prediction, either based on molecular fragment methods, or via direct calculation of solvation free energy in solvent continuum. The applicability, merits, and shortcomings of these developments are revisited here.

Infrared Spectroscopy-Mid-infrared, Near-infrared, and Far-infrared/Terahertz Spectroscopy.

This article aims to overview infrared (IR) spectroscopy. Simultaneously, it outlines mid-infrared (MIR), near-infrared (NIR), and far-infrared (FIR) or terahertz (THz) spectroscopy separately, and compares them in terms of principles, characteristics, advantages, and applications. MIR spectroscopy is the central spectroscopic technique in the IR region, and is mainly concerned with the fundamentals of molecular vibrations. NIR spectroscopy incorporates both electronic and vibrational spectroscopy; however, in this review, I have chiefly discussed vibrational NIR spectroscopy, where bands due to overtones and combination modes appear. FIR or THz spectroscopy contains both vibrational and rotational spectroscopy. However, only vibrational FIR or THz spectroscopy has been discussed in this review. These three spectroscopy cover wide areas in their applications, making it rather difficult to describe these various topics simultaneously. Hence, I have selected three key topics: hydrogen bond studies, applications of quantum chemical calculations, and imaging. The perspective of the three spectroscopy has been discussed in the last section.

Quantum chemical calculations of 77 Se and 125 Te nuclear magnetic resonance spectral parameters and their structural applications.

An accurate quantum chemical (QC) modeling of 77 Se and 125 Te nuclear magnetic resonance (NMR) spectra is deeply involved in the NMR structural assignment for selenium and tellurium compounds that are of utmost importance both in organic and inorganic chemistry nowadays due to their huge application potential in many fields, like biology, medicine, and metallurgy. The main interest of this review is focused on the progress in QC computations of 77 Se and 125 Te NMR chemical shifts and indirect spin-spin coupling constants involving these nuclei. Different computational methodologies that have been used to simulate the NMR spectra of selenium and tellurium compounds since the middle of the 1990s are discussed with a strong emphasis on their accuracy. A special accent is placed on the calculations resorting to the relativistic methodologies, because taking into account the relativistic effects appreciably influences the precision of NMR calculations of selenium and, especially, tellurium compounds. Stereochemical applications of quantum chemical calculations of 77 Se and 125 Te NMR parameters are discussed so as to exemplify the importance of integrated approach of experimental and computational NMR techniques.

Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

AbstractAerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy‐metal transport in the troposphere. The chemical and physical complexity of atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.

Using calculations of the electronically excited states for investigation of fluorescent sensors: A review

AbstractIn this review, the calculations of the electronically excited states were introduced as the recent outstanding applications of quantum chemical calculations for developing the fluorescent sensors. The applications of the ground state and excited state optimized geometry‐based calculations for the absorption and fluorescence properties have been introduced along with their advantages and limitations.

Quantum chemical calculations and molecular modeling for methylene blue removal from water by a lignin-chitosan blend

A comprehensive analysis of the molecular dynamics and quantum chemical calculation methods for methylene blue removal by adsorption were carried out. The experimentally measured adsorption data of methylene blue from water effluent on a novel lignin and chitosan blend were used to validate the modeling results. The method and required steps for application of quantum chemical calculations and molecular modeling techniques as the state of the art approach for predictive modeling and investigation of adsorption were provided, and the model findings were validated by comparing with the experimental data; close agreement between the results was observed. The conductor-like screening model (COSMO) approach was used for calculation of equilibrium concentration of solute at the adsorbent-solute interface. The results revealed that the approach is highly recommended as it provides an alternative assessment for feasibility analysis before any experiments to be undertaken, resulting in time and cost saving.

Reactivity, stability, and thermodynamic feasibility of H2O2/H2O at graphite cathode: Application of quantum chemical calculations in MFCs

A microbial fuel cell (MFC) is a sustainable technology which commonly uses graphite as cathode for the production of hydrogen peroxide. Besides, water formation through four‐electron oxygen reduction mechanism is a commonly observed product. Determining the selectivity of H2O2/H2O reaction through experimental means is time consuming because of the slow kinetics of oxygen reduction reaction. Therefore, quantum chemical approaches are essential to comprehend the molecular nature of this process. Thus, density functional theory (DFT) was employed and quantum chemical calculations were performed to predict the chemical reactivity, stability, and thermodynamic properties of molecules participating in oxygen reduction reaction at graphite cathode. The calculations showed that graphene with higher value of “highest occupied molecular orbital” (HOMO), i.e., −4.544 eV has a higher tendency to donate electron for oxygen reduction reaction Furthermore, with an aim of predicting the most favorable conditions for H2O2 production, two different points, i.e., at the edge and middle of graphene plane were investigated. Calculated values showed that oxygen adsorption with the lowest energy requirement of 43.638 kcal/mol is energetically favorable at the edge of graphene plane. Nevertheless, oxygen complexes (O2*, HOO*, and HO*) characterized by high HOMO values −4.96, −4.37, and −4.34 eV are highly polarizable in the middle of the graphene plane. Furthermore, thermodynamic feasibility analysis showed that oxygen reduction required for hydrogen peroxide production had lower ΔG values of −90.94 (edge) and −98.44 (middle) kcal/mole than that of water synthesis (i.e., ΔG = −48.37(edge), −48.97 (middle) kcal/mole) at two‐electron reduction step. Therefore, it was concluded that H2O2 which followed the lowest energy pathway would be more thermodynamically feasible compared to water synthesis. © 2017 American Institute of Chemical Engineers Environ Prog, 37: 1291–1304, 2018

Weak but strong: role of weak C–H···X (X=O, N) hydrogen bonds in organization of crystals of (1S,2S,3S,4R,5R,8S)-diethyl 2,4-dicyano-3-(furan-2-yl)-8-morpholino-6-oxobicyclo[3.2.1]octane-2,4-dicarboxylate

An X-ray diffraction study of (1S,2S,3S,4R,5R,8S)-diethyl 2,4-dicyano-3-(furan-2-yl)-8-morpholino-6-oxobicyclo[3.2.1]octane-2,4-dicarboxylate reveals the absence of strong specific intermolecular interactions in the crystal. Application of quantum-chemical calculations allows estimating the interaction energy between basic molecule located in the asymmetric part of the unit cell and molecules belonging to its first coordination sphere. This analysis clearly indicates the layered structure of crystals where the total interaction energy between the basic molecule and neighboring molecules belonging to the layer is significantly higher as compared to the energy of the interactions with molecules of neighboring layers.

ChemInform Abstract: The Many Roles of Quantum Chemical Predictions in Synthetic Organic Chemistry

AbstractReview: [26 refs.

The Many Roles of Quantum Chemical Predictions in Synthetic Organic Chemistry

This account discusses representative case studies for various applications of quantum chemical calculations in synthetic organic chemistry. These include confirmation of target structures, methodology development, and catalyst design. These examples demonstrate how predictions from quantum chemical calculations can be utilized to streamline synthetic efforts.

Walking in the woods with quantum chemistry – applications of quantum chemical calculations in natural products research

This Highlight describes applications of quantum chemical calculations to problems in natural products chemistry, including the elucidation of natural product structures (distinguishing between constitutional isomers, distinguishing between diastereomers, and assigning absolute configuration) and determination of reasonable mechanisms for their formation.

Hydrogen bonded networks in formamide [HCONH2]n (n = 1 − 10) clusters: A computational exploration of preferred aggregation patterns#

Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide clusters, a prototype model for motifs found in protein secondary structure. DFT calculations have been performed on four arrangements of formamide clusters [HCONH2]n, (n = 1 − 10) linear, circular, helical and stacked forms. These studies reveal the maximum cooperativity in the stacked arrangement followed by the circular, helical and linear arrangements and is based on interaction energy per monomer. In all these arrangements as we increase cluster size, an increasing trend in cooperativity of hydrogen bonding is observed. Atoms-in-molecule analysis establishes the nature of bonding between the formamide monomers on the basis of electron density values obtained at the bond critical point (BCP).

Introduction

The earliest applications of quantum chemical calculations were devoted to very small systems, which in large part served as tests of their accuracy and usefulness. Given the computational limitations of the day, the drive toward approximate methods, which could extend the reach of quantum chemistry to larger systems by a number of simplifying assumptions, was inevitable. As an early instance, our understanding of aromatic systems took a leap forward with the development of Hückel molecular orbital theory, the equations of which could be solved on the back of an envelope. As computers developed further, these simplifying approximations could be dispensed with, one by one, as ab-initio calculations were able to extend their reach into ever-enlarging systems. The later establishment of density functional theory (DFT) approaches renewed and reinvigorated the drive toward ever larger systems. In a parallel sense, the earliest ab-initio studies of chemical systems focused primarily on closed-shell systems, in part because solution of the associated equations was simplified by the spin-pairing of all electrons. However, the very reactive nature of free radicals imbues them with great importance in chemistry and biology. As quantum chemical methods have been developed which can handle such systems with high accuracy, the topic of radicals and their associated reactions has undergone an accelerated level of study in recent years. The present issue of this journal is devoted to the task of presenting to the reader a sampling of some of the most current work that is taking place, dealing with radicals and their reactions. The first two papers examine some of the different specific methods that can be applied to these sorts of problems, and the level of accuracy that might be expected of each, using particular reactions as a test bed. Both works evaluate the accuracy of certain DFT methods. The succeeding three papers consider a variety of different radicals, generally small ones such as CH3SO. The next three papers are devoted to the very important role that radicals play in atmospheric chemistry, again considering small systems such as HOO. The size of the radicals is enlarged a bit in the next three papers, which focus on the aromatics as a class. And finally, as a number of biological processes are intimately connected with radicals, it is their role in biology that serves as the theme of the last four papers in this issue. These papers cover such diverse matters as enzyme activity and inhibition, nucleic acids, and selenopeptides. In summary, the purpose of this issue is not thorough and comprehensive coverage of the entire range of topics that fall under the rubric of quantum calculations of radicals. Such a goal could not be accomplished in a single issue. The aim is more limited in scope, providing a window into just a small sampling of the topics in radical chemistry that are currently being studied by modern quantum chemical approaches.

ChemInform Abstract: Biosynthesis via Carbocations: Theoretical Studies on Terpene Formation

AbstractReview: ca. 100 refs.

Biosynthesis via carbocations: Theoretical studies on terpene formation

This review describes applications of quantum chemical calculations in the field of terpene biosynthesis, with a focus on insights into the mechanisms of terpene-forming carbocation rearrangements arising from theoretical studies.

Application of quantum chemical calculations to two non-trivial cases in the field of molecular spectroscopy

In this paper, we illustrate the contribution of the quantum chemical calculations to the simulation of two types of spectra. In a first part, the calculations of theoretical resonance Raman spectra of transient species are presented. The comparison of the theoretical and experimental spectra allows validating the methodology. From calculation results, the molecular structure and the spectra assignment of radicals have been deduced. In a second part, the TD-DFT methodology is applied to the determination of the preferential chelating site involved in the metal fixation by a ligand possessing several complexing functions in competition. We show that the use of UV-visible spectroscopy combined with quantum chemical calculations is well adapted to resolve the molecular structure of a complex. The reaction pathway calculations allow a better understanding of the regioselectivity of the complexation mechanism.

Combined Quantum Mechanism and Molecular Mechanism Method

Till now, theoretical research has focused on some chemical behaviors, structural properties of bio-macromolecules in solutions. When the molecular force field was used to treat solution systems, not considering the movement of electrons, in many force fields the chemical bonds between atoms must be confirmed to make sure that they can’t be destroyed or formed in modeling procedure. Using quantum chemical calculation based on B-O approximation to treat solution systems, because it can consume much more resources, this method can’t treat large systems, which restricts the application of quantum chemical calculations. Moreover the hybrid QM/MM method has been widely used in research of chemical reaction in condense phase and biologic macromolecules especially the mechanisms of enzyme catalysis reactions, which has developed rapidly and takes advantage of the accuracy of QM method and high efficiency of MM method. This article will describe a brief introduction of the principle and development history of QM/MM method and give some application introductions.

Application of quantum chemical calculations of 13C NMR chemical shifts to quinoxaline structure determination

Comparison of experimental and theoretical (GIAO DFT) 13C NMR chemical shifts allows the reliable assignment of isomeric structures of heteroaromatic compounds. This methodology was applied to establish the structures of isomeric quinoxalines. A modern 1D NOE technique permitted independent proof of the proposed structures.

Challenges for the application of quantum chemical calculations to problems in catalysis

A long-standing goal of researchers in the field of catalysis is to develop first-principles methods for determining catalyst activity and selectivity. Advances in quantum chemical methods and codes, together with impressive improvements in computer speed, have contributed significantly towards the achievement of this objective. A review of current quantum chemical theories and models of catalytically active sites is presented with the aim of defining what is possible today and what needs to be done. Particular attention is given to identifying the trade-offs between achieving accurate energies of adsorbed and transition states and computational cost. Methods available for finding reaction pathways and calculating rate coefficients are also reviewed and discussed.

Application of Quantum Chemical Calculations to the Identification of Positional Isomers of Polysubstituted Alkylbenzenes

The problem of assignment of positional isomers of alkylbenzenes to chromatographic peaks is addressed. Probable structures are attributed based on the correlation of stabilities of the isomers, which are expressed as the total molecular energies calculated by the MINDO/3 semiempirical quantum chemical method, and the proportions of the isomers in the reaction mixture. Multicomponent alkylbenzene mixtures were prepared and separated by capillary gas chromatography, and the identity of the isomers was confirmed by the gas chromatography-mass spectrometry combination.