Basis Of Quantum Mechanical Calculations Research Articles

Rational Design of Persistent Phosphorus-Centered Singlet Tetraradicals and Their Use in Small-Molecule Activation.

Biradicals are important intermediates in the process of bond formation and breaking. While main-group-element-centered biradicals have been thoroughly studied, much less is known about tetraradicals, as their very low stability has hampered their isolation and use in small-molecule activation. Herein, we describe the search for persistent phosphorus-centered tetraradicals. Starting from an s-hydrindacenyl skeleton, we investigated the introduction of four phosphorus-based radical sites linked by an N-R unit and bridged by a benzene moiety. By varying the size of the substituent R, we finally succeeded in isolating a persistent P-centered singlet tetraradical, 2,6-diaza-1,3,5,7-tetraphospha-s-hydrindacene-1,3,5,7-tetrayl (1), in good yields. Furthermore, it was demonstrated that tetraradical 1 can be utilized for the activation of small molecules such as molecular hydrogen or alkynes. In addition to the synthesis of P-centered tetraradicals, the comparison with other known tetraradicals as well as biradicals is described on the basis of quantum mechanical calculations with respect to its multireference character, coupling of radical electrons, and aromaticity. The strong coupling of radical electrons enables selective discrimination between the first and the second activations of small molecules, which is shown by the example of H2 addition. The mechanism of hydrogen addition is investigated with parahydrogen-induced hyperpolarization NMR studies and DFT calculations.

How to evict HP1 from H3: Using a complex salt bridge

In an effort to unravel the unknown “binary switch” mechanisms underlying the “histone code” hypothesis of gene silencing and activation, we study the dynamics of Heterochromatin Protein 1 (HP1). We find in the literature that when HP1 is bound to tri-methylated Lysine9 (K9me3) of histone-H3 through an aromatic cage consisting of two tyrosines and one tryptophan, it is evicted upon phosphorylation of Serine10 (S10phos) during mitosis. In this work, the kick-off intermolecular interaction of the eviction process is proposed and described in detail on the basis of quantum mechanical calculations: specifically, an electrostatic interaction competes with the cation-π interaction and draws away K9me3 from the aromatic cage. An arginine, abundant in the histonic environment, can form an intermolecular “complex salt bridge” with S10phos and dislodge HP1. The study attempts to reveal the role of phosphorylation of Ser10 on the H3 tail in atomic detail.

Production of cold-resistant metals by nanomodification in 3D printing by electric arc welding using quantum mechanical and neural network modeling

A methodology is developed for nanomodification of carbon steels during 3D printing by electric arc welding to improve their mechanical properties and cold resistance. The alloying chemical element is selected on the basis of quantum mechanical calculations and optimization of the content of nanoparticles introduced into the melt using neural network modeling. Keywords: 3D printing, cold resistance, mechanical and fatigue properties, 09Г2С steel. uru.40@mail.ru

Magnesium radicals MgC5N and MgC6H in IRC +10216

After the previous discovery of MgC3N and MgC4H in IRC +10216, a deeper Q-band (31.0–50.3 GHz) integration on this source had revealed two additional series of harmonically related doublets that we assigned on the basis of quantum mechanical calculations to the larger radicals MgC5N and MgC6H. The results presented here extend and confirm previous results on magnesium-bearing molecules in IRC +10216. We derived column densities of (4.7 ± 1.3) × 1012 for MgC5N and (2.0 ± 0.9) × 1013 for MgC6H, which imply that MgC5N/MgC3N = 0.5 and MgC6H/MgC4H = 0.9. Therefore, MgC5N and MgC6H are present with column densities not so different from those of the immediately shorter analogs. The synthesis of these large magnesium cyanides and acetylides in IRC +10216 can be explained for their shorter counterparts by a two-step process initiated by the radiative association of Mg+ with large cyanopolyynes and polyynes, which are still quite abundant in this source, followed by the dissociative recombination of the ionic complexes.

Mechanistic Insights into the ortho-Defluorination-Hydroxylation of 2-Halophenolates Promoted by a Bis(μ-oxo)dicopper(III) Complex.

C-F bonds are one of the most inert functionalities. Nevertheless, some [Cu2O2]2+ species are able to defluorinate-hydroxylate ortho-fluorophenolates in a chemoselective manner over other ortho-halophenolates. Albeit it is known that such reactivity is promoted by an electrophilic attack of a [Cu2O2]2+ core over the arene ring, the crucial details of the mechanism that explain the chemo- and regioselectivity of the reaction remain unknown, and it has not being determined either if CuII2(η2:η2-O2) or CuIII2(μ-O)2 species are responsible for the initial attack on the arene. Herein, we present a combined theoretical and experimental mechanistic study to unravel the origin of the chemoselectivity of the ortho-defluorination-hydroxylation of 2-halophenolates by the [Cu2(O)2(DBED)2]2+ complex (DBED = N,N'-di-tert-butylethylenediamine). Our results show that the equilibria between (side-on)peroxo (P) and bis(μ-oxo) (O) isomers plays a key role in the mechanism, with the latter being the reactive species. Furthermore, on the basis of quantum-mechanical calculations, we were able to rationalize the chemoselective preference of the [Cu2(O)2(DBED)2]2+ catalyst for the C-F activation over C-Cl and C-H activations.

Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces

Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm−1 for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms. The relative energetic stabilities of the enol/keto and the amino/imino tautomeric forms of Cyt and 5MC have been estimated using DFT calculations, before and after binding six atom gold clusters. Among the six tautomeric forms, the 7H keto amino and the 4H imino trans forms are expected to be predominant in binding gold atoms, whereas the enol trans/cis conformers would coexist in the free gas phase. Our approach may provide useful theoretical guidelines for identifying 5MC from Cyt by analyzing Raman spectra on gold surfaces on the basis of quantum-mechanical calculations.

Rate coefficients of the elementary stages of heterogeneous catalytic recombination of dissociated air on thermal-protective coatings

On the basis of quantum-mechanical calculations within the framework of the cluster models and the literature data the rate coefficients of the elementary stages of the complete system of heterogenous catalytic recombination of dissociated air on the surfaces of thermal-protective β-cristobalite and α-Al2O3 ceramic coatings are determined. The processes of impact and associative recombination of adsorbed oxygen and nitrogen atoms are taken into account.

ChemInform Abstract: Toward Bis C,C‐Glycosyl Compounds and Anomeric γ‐Glycoamino Acids Through Michael Addition Reaction of Nitromethane on Z/E Push‐Pull Sugar Olefins.

The nucleophilic addition of a nitronate anion on push-pull anomeric sugar olefins has been studied and the results reveal that this reaction opens a new and efficient access to anomeric γ-nitro esters when applied to furanoglycosylidenes. The 1,4-addition reaction occurs mainly from the less-crowded face, i.e. the opposite side to the 4,5-isopropylidene protecting group. Very different reactivities for E and Z isomers were observed and this experimental finding was rationalized on the basis of quantum mechanical calculations. Chemical manipulation of the nitro function of these bis C,C-glycosyl compounds led to a series of new γ-glycoamino acids, which are chiral building blocks that may be useful for the synthesis of glycopeptides oligomers or scaffolds for the construction of bioactive compounds. Under the same reaction conditions, pyranoglycosylidenes were more prone to migration of the double bond than to the expected 1,4 addition reaction.

Toward Bis C,C‐Glycosyl Compounds and Anomeric γ‐Glycoamino Acids through Michael Addition Reaction of Nitromethane on Z/E Push‐Pull Sugar Olefins

AbstractThe nucleophilic addition of a nitronate anion on push‐pull anomeric sugar olefins has been studied and the results reveal that this reaction opens a new and efficient access to anomeric γ‐nitro esters when applied to furanoglycosylidenes. The 1,4‐addition reaction occurs mainly from the less‐crowded face, i.e. the opposite side to the 4,5‐isopropylidene protecting group. Very different reactivities for E and Z isomers were observed and this experimental finding was rationalized on the basis of quantum mechanical calculations. Chemical manipulation of the nitro function of these bis C,C‐glycosyl compounds led to a series of new γ‐glycoamino acids, which are chiral building blocks that may be useful for the synthesis of glycopeptides oligomers or scaffolds for the construction of bioactive compounds. Under the same reaction conditions, pyranoglycosylidenes were more prone to migration of the double bond than to the expected 1,4 addition reaction.

On the molecular origin of secondary relaxations in amorphous protic ionic conductor chlorpromazine hydrochloride — High pressure dielectric studies

In this paper, we report the study of sub-Tg dynamics of chlorpromazine hydrochloride. The substance is another pharmaceutical and glass-forming protic ionic conductor investigated by our group. We describe both ionic and dipolar behaviors and show the way in how to tell them apart. Mainly, we focus on the dynamics of the slower of the two secondary relaxation processes found. By means of the dielectric spectroscopy we study its behavior as a function of temperature and pressure. Moreover, on the basis of quantum-mechanical calculations, we designate the mechanism for faster secondary relaxation as the conformational change of the dimethylamine group. Finally, we compare the findings with data of lidocaine hydrochloride, procaine hydrochloride and procainamide hydrochloride to answer the question of which features are typical for the protic ionic glasses and which are associated with specific chemical structure.

Structure and the catalysis mechanism of oxidative chlorination in nanostructural layers of a surface of alumina.

On the basis of X-ray diffraction and mass spectrometric analysis of carrier γ-Al2O3 and catalysts CuCl2/CuCl on its surface, the chemical structure of the active centers of two types oxidative chlorination catalysts applied and permeated type of industrial brands “Harshow” and “MEDС-B” was investigated. On the basis of quantum-mechanical theory of the crystal, field complexes were detected by the presence of CuCl2 cation stoichiometry and structure of the proposed model crystal quasichemical industrial catalyst permeated type MEDС-B for oxidative chlorination of ethylene. On the basis of quantum-mechanical calculations, we propose a new mechanism of catalysis crystal quasichemical oxidative chlorination of ethylene reaction for the catalysts of this type (MEDС-B) and confirmed the possibility of such a mechanism after the analysis of mass spectrometric studies of the active phase (H2 [CuCl4]) catalyst oxidative chlorination of ethylene. The possibility of the formation of atomic and molecular chlorine on the oxidative chlorination of ethylene catalyst surface during Deacon reaction was displaying, which may react with ethylene to produce 1,2-dichloroethane. For the active phase (H [CuCl2]), catalyst offered another model of the metal complex catalyst oxidative chlorination of ethylene deposited type (firm ‘Harshow,’ USA) and the mechanism of catalysis of oxidative chlorination of ethylene with this catalyst.

Structure Determination of Pentacyclic Pyridoacridine Alkaloids from the Australian Marine Organisms Ancorina geodides and Cnemidocarpa stolonifera

AbstractChemical investigation of two marine samples A. geodides and C. stolonifera led to the isolation of six pentacyclic pyridoacridine alkaloids, in which two compounds, ancorine A and cnemidine A, are new pyridoacridines. Their structures were determined by NMR spectroscopic analysis supported by quantum mechanical calculations of 13C NMR chemical shifts. This is the first study demonstrating that the pyridoacridine structure class can be assigned on the basis of quantum mechanical calculations. The isolated pyridoacridine alkaloids showed selective cytotoxicity against human prostate cancer cells (PC3) compared with human neonatal foreskin fibroblast noncancer cells (NFF).

Subfemtosecond steering of hydrocarbon deprotonation through superposition of vibrational modes.

Subfemtosecond control of the breaking and making of chemical bonds in polyatomic molecules is poised to open new pathways for the laser-driven synthesis of chemical products. The break-up of the C-H bond in hydrocarbons is an ubiquitous process during laser-induced dissociation. While the yield of the deprotonation of hydrocarbons has been successfully manipulated in recent studies, full control of the reaction would also require a directional control (that is, which C-H bond is broken). Here, we demonstrate steering of deprotonation from symmetric acetylene molecules on subfemtosecond timescales before the break-up of the molecular dication. On the basis of quantum mechanical calculations, the experimental results are interpreted in terms of a novel subfemtosecond control mechanism involving non-resonant excitation and superposition of vibrational degrees of freedom. This mechanism permits control over the directionality of chemical reactions via vibrational excitation on timescales defined by the subcycle evolution of the laser waveform.

Spectroscopic (FT-IR, FT-Raman and 1H and 13C NMR) and theoretical in MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels study of benzenesulfonic acid and alkali metal benzenesulfonates

The FT-IR, FT-Raman and NMR (1H and 13C) spectra of benzenesulfonic acid as well as lithium, sodium, potassium, rubidium and caesium benzenesulfonates were registered, assigned and compared. The molecular structures of ligand and alkali metal salts were discussed. On the basis of quantum mechanical calculations in MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels the geometric parameters, infrared spectra, NMR spectra, the magnetic and geometric aromaticity indices for acid and alkali metal benzenesulfonates and benzoates were obtained. The effect of alkali metal ions on the electronic charge distribution of benzenesulfonic acid was studied and compared with the alkali metal benzoates and benzoic acid.

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.

All-atom force fields are important for predicting thermodynamic, structural, and dynamic properties of RNA. In this paper, results are reported for thermodynamic integration calculations of free energy differences of duplex formation when CG pairs in the RNA duplexes r(CCGG)2, r(GGCC)2, r(GCGC)2, and r(CGCG)2 are replaced by isocytidine–isoguanosine (iCiG) pairs. Agreement with experiment was improved when ε/ζ, α/γ, β, and χ torsional parameters in the AMBER99 force field were revised on the basis of quantum mechanical calculations. The revised force field, AMBER99TOR, brings free energy difference predictions to within 1.3, 1.4, 2.3, and 2.6 kcal/mol at 300 K, respectively, compared to experimental results for the thermodynamic cycles of CCGG → iCiCiGiG, GGCC → iGiGiCiC, GCGC → iGiCiGiC, and CGCG → iCiGiCiG. In contrast, unmodified AMBER99 predictions for GGCC → iGiGiCiC and GCGC → iGiCiGiC differ from experiment by 11.7 and 12.6 kcal/mol, respectively. In order to test the dynamic stability of the above duplexes with AMBER99TOR, four individual 50 ns molecular dynamics (MD) simulations in explicit solvent were run. All except r(CCGG)2 retained A-form conformation for ≥82% of the time. This is consistent with NMR spectra of r(iGiGiCiC)2, which reveal an A-form conformation. In MD simulations, r(CCGG)2 retained A-form conformation 52% of the time, suggesting that its terminal base pairs may fray. The results indicate that revised backbone parameters improve predictions of RNA properties and that comparisons to measured sequence dependent thermodynamics provide useful benchmarks for testing force fields and computational methods.

Carbon–Carbon Bond-Forming Reactions of α-Thioaryl Carbonyl Compounds for the Synthesis of Complex Heterocyclic Molecules

Strategies for the formation of carbon-carbon bonds from the α-thioaryl carbonyl products of substituted lactams are described. Although direct functionalization is possible, a two step process of oxidation and magnesium-sulfoxide exchange has proven optimal. The oxidation step results in the formation of two diastereomers that exhibit markedly different levels of stability toward elimination, which is rationalized on the basis of quantum mechanical calculations and X-ray crystallography. Treatment of the sulfoxide with i-PrMgCl results in the formation of a magnesium enolate that will undergo an intramolecular Michael addition reaction to form two new stereogenic centers. The relationship between the substitution patterns of the sulfoxide substrate and the efficiency of the magnesium exchange reaction are also described.

Iron(III) complexes with 2-aminobenzothiazole: compounds governed by non-covalent interactions

Two new iron(III) coordination compounds with 2-aminobenzothiazole have been prepared and identified as (C6H4NHC(NH2)S)2[FeCl4]Cl(H2O) (1) and (C6H4NHC(NH2)S)3[Fe(C2O4)3](H2O)2 (2). The compounds were characterized by thermogravimetric analysis in conjunction with evolved gases in air and spectroscopic studies. On the basis of quantum-mechanical calculations the interplay between two non-covalent interactions in 1, anion ··· π and ion-pair interactions, was analyzed.

Aggregation of Perfluoroctanoate Salts Studied by 19F NMR and DFT Calculations: Counterion Complexation, Poly(ethylene glycol) Addition, and Conformational Effects

The aggregation of perfluoroctanoate salts in H(2)O is studied by (19)F NMR on solutions of LiPFO, NaPFO, and CsPFO, without and with the addition of two poly(ethylene glycol) (PEG) oligomers of molecular weight 1500 and 3400 Da, respectively, and with the addition of suitable crown ethers. The (19)F chemical shift (cs) trends are monitored, at 25 °C, in a concentration range including the critical micellar concentration (cmc) or, in the presence of PEG, the critical aggregation concentration (cac). The cac values in the samples with PEG are lower than the cmc values of the corresponding samples without PEG; moreover, the (19)F cs trends above the cac and above the polymer saturation concentration reveal and help to explain some peculiarities of the aggregation process of PEG on PFO micelles, which, in the first step, seems to occur while the surfactant concentration in water is still increasing. Also in LiPFO/H(2)O or NaPFO/H(2)O solutions containing 12-crown-4 or 15-crown-5 ethers, suitable to complex Li(+) or Na(+) ions, respectively, the cmc decreases. On the other hand, the micellization process in the presence of crown ethers does not show other peculiarities. The prevailing conformations of the PFO chain are discussed on the basis of quantum-mechanical calculations. The theoretical chemical shifts were computed at the DFT level of theory, taking into account the effects of the environment by means of the IEF-PCM method. The helical structure is the most stable one, but anti conformations are easily accessible, in both the aqueous and fluorinated environment. The comparison between computed and experimental chemical shifts indicates that anti conformations are more important in the micelles than in water and in CsPFO micelles than in LiPFO or NaPFO ones.

Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

Despite exhaustive chemical and crystal structure studies, the mechanistic details of how F(o)F(1)-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent high-resolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO(3)(-) ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the gamma-subunit rotation, may effectively block the back reaction in beta(TP) and, thus, promote ATP.

Comparison of Flavonoids and Isoflavonoids as Antioxidants

The isoflavonoid genistein was found to be a better antioxidant than the isomeric flavonoid apigenin in phosphatidyl liposomes at pH 7.4. The higher antioxidation activity of genistein compared with apigenin is in agreement with its lower oxidation potential (0.73 vs 0.86 V as determined by cyclic voltammetry in aqueous solution of pH= 7.4), lower dissociation enthalpy (87.03 vs 87.88 kcal mol(-1) as calculated for the more reducing 4'-hydroxyl group), and higher radical scavenging capacity in the TEAC assay. On the basis of quantum mechanical calculations for genistein and apigenin in comparison with the flavonoid naringenin and the isoflavonoids puerarin, daidzein, and equol, a lower dipole moment and a larger deviation for the A-to-B dihedral angle from coplanarity (39.3 degrees for genistein, 18.5 degrees for apigenin) are suggested to be important for the increased antioxidant efficiency at water/lipid interfaces among (iso) flavonoids with an equal number of phenolic groups.