Application Of Quantum Chemical Methods Research Articles

Models nanocomplexes based on C60 fullerene for creation of biologically active agents for medicine

Complex drugs based on C[Formula: see text] fullerence and pyrrole derivatives are promising for the development of antitumor and anti-inflammatory agents for use in targeted therapy, but have little efficiency in the synthesis of such complexes and have virtually no stable synthesis products with fullerene. The stability of the nanocomplex based on [60] PCBA and the intermediate compound based on “[Formula: see text]-pyrrole-2,5-dione” effective for the synthesis of targeted therapeutic agents was investigated by means of numerical calculations. The application of quantum-chemical methods in the Gaussian package establishes the stability of the nanocomplex at human body temperatures, the possibility of using such complexes for further study of the therapeutic properties of the individual components of the decomposition products of the nanocomplex.

Protective Effects of [6]-Gingerol Against Chemical Carcinogens: Mechanistic Insights.

[6]-Gingerol from ginger has received considerable attention as a potential cancer therapeutic agent because of its chemopreventive and chemotherapeutic effects, as well as its safety. In the current study, we examined [6]-gingerol as a natural scavenger of nine ultimate chemical carcinogens to which we are frequently exposed: glycidamide, styrene oxide, aflatoxin B1 exo-8,9-epoxide, β-propiolactone, ethylene oxide, propylene oxide, 2-cyanoethylene oxide, chloroethylene oxide, and vinyl carbamate epoxide. To evaluate [6]-gingerol efficacy, we expanded our research with the examination of glutathione—the strongest natural scavenger in human cells. The corresponding activation free energies were calculated using Hartree-Fock method with three flexible basis sets and two implicit solvation models. According to our results, [6]-gingerol proves to be an extremely effective scavenger of chemical carcinogens of the epoxy type. On the other hand, with the exception of aflatoxin B1 exo-8,9-epoxide, glutathione represents a relatively poor scavenger, whose efficacy could be augmented by [6]-gingerol. Moreover, our quantum mechanical study of the alkylation reactions of chemical carcinogens with [6]-gingerol and glutathione provide valuable insights in the reaction mechanisms and the geometries of the corresponding transition states. Therefore, we strongly believe that our research forms a solid basis for further computational, experimental and clinical studies of anticarcinogenic properties of [6]-gingerol as well as for the development of novel chemoprophylactic dietary supplements. Finally, the obtained results also point to the applicability of quantum chemical methods to studies of alkylation reactions related to chemical carcinogenesis.

Nucleic Bases Alkylation with Acrylonitrile and Cyanoethylene Oxide: A Computational Study.

Acrylonitrile (AN) is widely used in the manufacture of resins, plastics, and polymers, where workers are exposed to it during its production, transportation, and application. After intake a portion of AN is converted to cyanoethylene oxide (CEO) by cytochrome P450 2E1. Both AN and CEO represent possible chemical carcinogens leading to DNA damage mainly in the form of the major 7-(2-oxoethyl)deoxyguanosine adduct. A kinetic model for its formation was devised and a corresponding second-order rate constant obtained from the experimental data on the reaction with CEO. A series of ab initio, density functional theory, and semiempirical calculations of activation free energies was then performed on the alkylation of nucleic bases with both CEO and AN. The combination of Hartree-Fock level of theory with the flexible 6-311++G(d,p) basis set and Langevin dipoles implicit solvation model gave the best agreement with the experimental activation barrier. It also predicted relative reactivities of all four nucleobases that are in agreement with the experimentally reported adduct yields. Moreover, this combination predicted higher reactivity of CEO than AN with all four nucleobases corroborating the experimental hypothesis that SN2 substitution of CEO rather than direct Michael addition of AN is responsible for the genotoxic properties of AN. In a broader context this paper points to the applicability of quantum chemical methods to the studies of carcinogenesis.

Quantum Chemical Modeling of Homogeneous Water Oxidation Catalysis.

The design of efficient and robust water oxidation catalysts has proven challenging in the development of artificial photosynthetic systems for solar energy harnessing and storage. Tremendous progress has been made in the development of homogeneous transition-metal complexes capable of mediating water oxidation. To improve the efficiency of the catalyst and to design new catalysts, a detailed mechanistic understanding is necessary. Quantum chemical modeling calculations have been successfully used to complement the experimental techniques to suggest a catalytic mechanism and identify all stationary points, including transition states for both O-O bond formation and O2 release. In this review, recent progress in the applications of quantum chemical methods for the modeling of homogeneous water oxidation catalysis, covering various transition metals, including manganese, iron, cobalt, nickel, copper, ruthenium, and iridium, is discussed.

Molecular modeling of bioorganometallic compounds: thermodynamic properties of molybdocene-glutathione complexes and mechanism of Peptide hydrolysis.

The computational study of bioinorganic complexes between transition metals and flexible ligands is still challenging, given that, besides requiring extensive conformational searches, the treatment of metal-ligand bonds demands the application of quantum chemical methods. Herein, the adducts formed between molybdocene, which exhibits antitumor activity and reacts with thiol groups to give stable water-soluble complexes, and the tripeptide glutathione, which is a major source of biological thiols, are studied. Conformational searches are performed using the semiempirical PM6 method followed by geometry optimizations and single-point calculations using density functional theory methods. In addition, molecular dynamics simulations of the molybdocene-glutathione complex involved in the regioselective hydrolysis of the Cys-Gly linkage are performed in explicit solvent. The reactive process is also studied theoretically on cluster models of both the molybdocene-bound and the free peptide.

An experimental and density functional study on conformational and spectroscopic analysis of 5-methoxyindole-2-carboxylic acid

In this article, a brief conformational and spectroscopic characterization of 5-methoxyindole-2-carboxylic acid (5-MeOICA) via experimental techniques and applications of quantum chemical methods is presented. The conformational analysis of the studied molecule was determined theoretically using density functional computations for ground state, and compared with previously reported experimental findings. The vibrational transitions were examined by measured FT-IR and FT-Raman spectroscopic data, and also results obtained from B3LYP and CAM-B3LYP functionals in combination with 6-311++G(d,p) basis set. The recorded proton and carbon NMR spectra in DMSO solution were analyzed to obtain the exact conformation. Due to intermolecular hydrogen bondings, NMR calculations were performed for the dimeric form of 5-MeOICA and so chemical shifts of those protons were predicted more accurately. Finally, electronic properties of steady compound were identified by a comparative study of UV absorption spectra in ethanol and water solution and TD-DFT calculations.

A Mössbauer study on iron(II) complex of 2-acetyl-1,3-indandione ⎼ spin-crossover or structural changes

An air stable Fe(II) complex of a cyclic β-triketone, 2-acetyl-1,3-indandione (2AID) was obtained in two different ways and studied by Mossbauer spectroscopy. The Mossbauer data at room temperature point to six-coordinated, high spin Fe(II) complex. The temperature-dependent measurements indicate a phase transition in going from 293 to 77 K. Further lowering the temperature, however, do not cause the expected changes for spin-crossover transition. This data provoked application of quantum chemical methods to determine the origin of the observed appearance of spectral component attributable to low spin Fe(II) complex at 77 K. Based on the results from the theoretical calculations of the Mossbauer parameters of several different geometries and spin states of the Fe complexes of 2AID it was possible to conclude that the obtained Fe(II) complex has a pseudo-octahedral geometry. The experimentally observed temperature-dependence of the Mossbauer spectra is attributed to changes of the axial Fe-O bonds, rather than to spin transition. Discussion is given on the role of the type of the axial ligands for conditioning a spin-crossover process, as suggestion for experimental modelling of novel target materials with desired magnetic properties.

Application of Hartree-Fock Method for Modeling of Bioactive Molecules Using SAR and QSPR

The central importance of quantum chemistry is to obtain solutions of the Schrodinger equation for the accurate determination of the properties of atomic and molecular systems that occurred from the calculation of wave functions accurate for many diatomic and polyatomic molecules, us- ing Self Consistent Field method (SCF). The application of quantum chemical methods in the study and planning of bioactive compounds has become a common practice nowadays. From the point of view of planning it is important to note, when it comes to the use of molecular modeling, a collec- tive term that refers to methods and theoretical modeling and computational techniques to mimic the behavior of molecules, not intend to reach a bioactive molecule simply through the use of computer programs. The choice of method for energy minimization depends on factors related to the size of the molecule, parameters of availability, stored data and computational resources. Mo- lecular models generated by the computer are the result of mathematical equations that estimate the positions and properties of the electrons and nuclei, the calculations exploit experimentally, the characteristics of a structure, providing a new perspective on the molecule. In this work we show that studies of Highest Occupied Molecular Orbital Energy (HOMO), Low Unoccupied Mole- cular Orbital Energy (LUMO) and Map of molecular electrostatic potential (MEP) using Hatree- Fock method with different basis sets (HF/3-21G*, HF/3-21G**, HF/6-31G, HF/6-31G*, HF/ * Corresponding author.

Theory‐Guided Experiments on the Mechanistic Elucidation of the Reduction of Dinuclear Zinc, Manganese, and Cadmium Complexes

Since the recognition of the first Zn Zn bond in the dinuclear sandwich decamethyldizincocene [(h-C5Me5)Zn Zn(h-C5Me5)], [1] the chemistry of Zn Zn-bonded species has grown so rapidly that many complexes of the type LZn ZnL have been characterized and studied. Regardless of the denticity of the supporting ligands L, they all coordinate to Zn in a terminally chelating mode. However, formation of these dinuclear compounds has not been mechanistically examined. We recently described the characterization of dinuclear Zn Zn-bonded species [{k-Me2Si(NDipp)2}Zn Zn{k-Me2Si(NDipp)2}] 2 (2) (Dipp= 2,6-iPr2C6H3) from KC8 reduction of dinuclear zinc complex [Zn2(m-k -Me2Si(NDipp)2)2] (1), whereby the coordination mode of the diamido ligands dramatically changes from bridging to chelating. We thus became interested in the structural preference and the formation mechanism of Zn Zn-bonded complexes. Elaborate calculations were performed to understand the reduction of 1, and a plausible mechanism was then proposed (Scheme 1). On two-electron reduction of 1, two intermediates, Ia and Ib, are generated, and the energy difference between them is only 0.3 kcalmol . The Zn Zn-bonded mixed-valent intermediate Ia is produced by one-electron reduction of 1, and subsequently undergoes a dramatic structural rearrangement to give Ib, in which one threecoordinate and one one-coordinate Zn atoms are proposed. The exact valence of the Zn atoms in Ib is still not clear. Although the application of quantum chemical methods (ab initio molecular orbital and density functional theory) to elucidate reaction mechanisms has been very successful, most of the time it is difficult to prove the theoretically developed reaction mechanisms by experiments. This is indeed the case for the transformation from 1 to 2. Attempts to probe both intermediates Ia and Ib failed. To this end, we turned our attention from zinc to manganese and cadmium, because they not only show structural similarity in the reported M M-bonded dinuclear complexes [(k-Nacnac)M M(k-Nacnac)] (M=Zn, Mn; Nacnac= HC[C(Me)NDipp]2) and [Ar’M MAr’] (M=Zn, Cd; Ar’= 2,6-(2,6-iPr2C6H3)2C6H3), but also feature an identical M M s-bonding scheme. Herein we report structural transformations on reduction of dinuclear manganese and cadmium complexes [Mn2{k -Me2Si(NDipp)2}2] (3) and [Cd2{mk-Me2Si(NDipp)2}2] (4). Characterization of the products supports the computed mechanism shown in Scheme 1. As shown in Scheme 2, reactions of the dilithiated diamido ligand and 1 equiv of anhydrous MnCl2 and CdCl2 in diethyl ether and THF, respectively, yielded the corresponding dimeric compounds 3 and 4 in good yields. The dinuclear nature of 3 and 4 was deciphered by single-crystal X-ray crystallography, and their molecular structures are provided in Figures S1 and S2 of the Supporting Information. Complex 3 is essentially composed of two MnN2Si fourmembered rings, which are brought together by two Mn N bonds, and consequently exhibit a boat conformation with two manganese atoms at the stern and two Si atoms at the bow. Each Mn atom is embraced by three nitrogen atoms and adopts a distorted T-shaped geometry. The central Mn2N2 Scheme 1. Calculated mechanism of transformation of 1 into 2.

Role of quantum chemical calculations in molecular biophysics with a historical perspective

We discuss how the basic principles of quantum chemistry and quantum mechanics can be and have been applied to a variety of problems in molecular biophysics. First, the historical development of quantum concepts in biophysics is discussed. Next, we describe a series of interesting applications of quantum chemical methods for studying biologically active molecules, molecular structures, and some of the important processes which play a role in living organisms. We discuss the application of quantum chemistry to such processes as energy storage and transformation, and the transmission of genetic information. Quantum chemical approaches are essential to comprehend and understand the molecular nature of these processes. To conclude our work, we present a short discussion of the perspectives of quantum chemical methods in modern biophysics, the field of experimental and theoretical chiral vibrational and electronic spectroscopy.

Use of quantum-chemical methods in selecting catalysts for the removal of carbon and nitrogen oxides from exhaust gases

Carbon and nitrogen oxides contained in automobile exhaust gases are among the most hazardous air pollutants. Therefore, the search for new methods of the neutralization of noxious substances in exhaust gases is an urgent problem. Catalytic purification is among the most promising methods. The aim of this work is to show the applicability of quantum-chemical methods to the study of the mechanisms of NO x reduction and CO oxidation on the Rh-catalyst surface. A faujasite zeolite was used as the carrier. Calculations showed that the support enhances the electrophilic properties of rhodium and, thus, improves its catalytic activity.

Special issue “Advances in Chiroptical Methods”

Special issue “Advances in Chiroptical Methods”

New applications and challenges for computational ROA spectroscopy

In this article, applications of quantum chemical methods in calculations of the vibrational Raman optical activity (ROA) spectra are reviewed and new developments are discussed. Modeling of ROA spectra of amino acids and peptides and applications for establishing absolute configuration are briefly outlined. Particular attention is paid to the modeling of solvent effects on ROA spectra, anharmonicity in ROA, resonance and pre-resonance ROA spectra, and ROA spectra of molecules adsorbed on metal surfaces or metal nanoparticles (surface-enhanced Raman optical activity, SEROA). Remaining challenges in computational ROA spectroscopy are also pointed out.

Carcinogenicity of Acrylamide: A Computational Study

This paper reports a series of ab initio, density functional theory (DFT), and semiempirical molecular orbital (MO) calculations concerning the reaction between the ultimate carcinogen of acrylamide and guanine. Acrylamide--a product of the Maillard reaction--is present in a variety of fried and oven-cooked food. After intake, it is epoxidized by cytochrome P450 2E1 to yield the ultimate carcinogen--glycidamide. Effects of solvation were considered using the Langevin dipoles (LD) model of Florian and Warshel and the solvent reaction field (SCRF) model of Tomasi and co-workers. In silico activation free energies are in very good agreement with the experimental value of 22.8 kcal/mol. This agreement presents strong evidence in favor of the validity of the proposed S N2 reaction mechanism and points to the applicability of quantum chemical methods to studies of reactions associated with carcinogenesis. In addition, insignificant stereoselectivity of the studied reaction was predicted. Finally, the competing reaction of glycidamide with adenine was simulated, and the experimentally observed regioselectivity was successfully reproduced.

Ab INITIO COMPUTATIONAL MODELS IN MATERIALS SCIENCE: A COMMON PLAYGROUND FOR SURFACE CHEMISTRY AND SOLID-STATE PHYSICS

This article describes the usefulness of embedded cluster and periodic models to solve a number of problems in computational materials science. To this end, two different well-defined problems are selected and discussed. The first problem concerns magnetic coupling in high Tc superconductor parent compounds. It is taken to exemplify the application of quantum chemical methods to derive excited-state properties of extended systems. The second problem concerns the selectivity of a partial oxidation reaction catalyzed by a metal surface. This second example serves to illustrate the efficacy of solid-state band theory methods in the study of chemical reactions taking place at surfaces. Possible extensions of ab initio computational materials science are further discussed.

Guanine Alkylation by the Potent Carcinogen Aflatoxin B1: Quantum Chemical Calculations

We report a series of ab initio and density functional theory simulations of guanine alkylation by aflatoxin B 1 exo-8,9-epoxide. This reaction represents an initial step of carcinogenesis associated with aflatoxin B 1, a potent genotoxic fungal metabolite. Effects of hydration were considered in the framework of the Langevin dipoles solvation model and the solvent reaction field method of Tomasi and co-workers. In silico-calculated activation free energies are in good agreement with the experimental value of 15.1 kcal/mol. This agreement presents strong evidence in favor of the validity of the proposed S(N)2 reaction mechanism and points to the applicability of quantum chemical methods in studies of reactions associated with carcinogenesis. In addition, we predict that the preference of aflatoxin B 1 exo-8,9-epoxide over the endo stereoisomer for the reaction with guanine exists in the aqueous solution and is only further amplified in the DNA duplex. Finally, through comparison with an analogous reaction between 3a,6a-dihydrofuro[2,3- b]furan exo-4,5-epoxide and guanine, we show that the large planar body of aflatoxin B 1 does not enhance its reactivity and related carcinogenicity. This explains why the planar region of related mycotoxins sterigmatocystin and aflatoxin G 1 could have been evolutionarily optimized in a different way.

Use of Quantum Chemical Methods to Study Cyclodextrin Chemistry

AbstractFor Abstract see ChemInform Abstract in Full Text.

Use of Quantum Chemical Methods to Study Cyclodextrin Chemistry

Studies of cyclodextrin chemistry by quantum chemical methods are briefly surveyed. Emphases are put on what types of quantum chemical methods can be used for cyclodextrin chemistry, how to use quantum chemical methods to find the global minimum, to study the structures, binding energies, driving forces for cyclodextrin complexes, as well as chemical reactions occurring inside cyclodextrin cavities. Problems associated with the application of quantum chemical methods in cyclodextrin chemistry are also discussed.

Accuracy and Applicability of Quantum Chemical Methods in Computational Medicinal Chemistry

AbstractFor Abstract see ChemInform Abstract in Full Text.

Recent trends in carbohydrate modeling.

The exploding activities in modeling of carbohydrates during the past few years is reviewed with emphasis on advances in improving force fields, coupling of NMR measurements with molecular dynamics simulations, direct calculation of thermodynamic properties, application of quantum chemical methods on a large scale, and web-access to modeling.