On the origins of intersecting potential energy surfaces

Techniques developed for investigating nonadiabatic processes in molecular systems are adapted to study the structure and properties of holomorphic and meromorphic functions of a complex variable, \(f(z)=\mathfrak {R}(f)+i\,\mathfrak {I}(f)\). The connection is that \(\mathfrak {R}(f)\) and \(\mathfrak {I}(f)\) are correlated two-dimensional scalar functions, interrelated by the Cauchy–Riemann equations. Exploiting this fact, it is demonstrated that \(\mathfrak {R}(f)\) and \(\mathfrak {I}(f)\) of f can be envisaged in Euclidean \({\mathbb {R}}^{3}\) space as a two-state set of constrained, intersecting two-dimensional potential energy surfaces (PESs), called the graph of f. Importantly, the analytic and algebraic properties of f dictate the geometric structure evinced in the graph of f. This parallels multi-state sets of higher-dimensional, constrained, intersecting PESs linked with correlated electronic eigenstates of the parameterized molecular Hamiltonian operator. In view of this association, the language and mathematical infrastructure devised by chemists for discussing and analyzing intersections in higher-dimensional PESs are suitably modified for f. Notably, an algorithm capable of optimizing roots and poles of f through analysis of the real, two-dimensional \(\mathfrak {R}(f)\) and \(\mathfrak {I}(f)\) functions is derived, which is based on intersection-adapted coordinate and constrained Lagrangian methodologies. As constrained, intersecting PESs are indispensible for conceptualizing and characterizing the physics governing nonadiabatic phenomena, f represents a foundational bridge to these more abstract constructions.     

Synthesis and properties of <Emphasis Type="Italic">N</Emphasis>-(alkenylidene)trifluoromethanesulfonamides

N-Alkenylidenetrifluoromethanesulfonamides TfN=CH–CR=C(Me)R′ (R, R′ = H, Me) have been synthesized by reaction of N-sulfinyltrifluoromethanesulfonamide TfNSO with (E)-but-2-enal, (E)-2-methylbut- 2-enal, and 3-methylbut-2-enal. Despite greater stability of N-alkenylidenetrifluoromethanesulfonamides relative to their propargyl isomers TfNHCH₂C≡CR, no rearrangement of the latter into the former occurs due to the presence of an acidic NH proton, which hampers formation of carbon-centered anion.     

Dual Stereochemical Control in Reaction of Di- and Trialkyl Phosphites with Aldimines

Stereochemistry of addition of di- and trialkyl phosphites to C=N compounds was investigated. Reactions of achiral dialkyl phosphites with chiral aldimines as well as that of chiral di-(1R,2S,5R)-menthyl phosphite with achiral aldimines result in low diastereomeric enrichment of the addition compound. Reaction stereoselectivity increased when supplementary chiral inductor was introduced to the reaction system. Reaction of di-(1R,2S, 5R)-menthyl phosphite with (S)-α-methylbenzylbenzaldimine proceeds as concerted asymmetric induction to form practically one diastereomer of N-substituted aminophosphonic acid. However, reaction of di-(1R,2S, 5R)-menthyl phosphite with (R)-α-methylbenzylbenzaldimine proceeded as not concerted asymmetric induction, and diastereomeric enrichment of the product was low. By chemical extrapolation, absolute configuration of compounds formed was established. Tri-(1R,2S,5R)-menthyl phosphite reacts with C=N compounds in the presence of boron trifluoride etherate to form aminophosphonic acid derivatives with the absolute configuration opposite to that appearing in the reaction of di-(1R,2S,5R)-menthyl phosphite with the same C=N compounds.     

Quantum chemical studies of azoles 3. Thermodynamic stabilities of neutral molecules and intermediates formed in electrophilic substitution of azoles containing three or four heteroatoms

Density functional theory quantum chemical calculations of thermodynamic stabilities in the gas phase and in water were carried out for 1,3,4-oxadiazole and 1,3,4-thiadiazole, 1,2,4-1H-triazole and 1,2,4-4H-triazole, 1,2,3,4-1H-tetrazole and 1,2,3,4-2H-tetrazole molecules, and for cationic and bipolar (carbenoid) intermediates formed by these molecules in electrophilic substitution reactions (with proton as model electrophile) and the results obtained are compared. Differences in the chemical behavior of pairs of isomeric 1H- and 4H-1,2,4-triazoles and 1H- and 2H-tetrazoles are analyzed.     

RBaCuCoO<Subscript>5 + δ</Subscript> (R = Nd,Sm, Gd) layered cuprocobaltites: Synthesis,structure, and properties

Cuprocobaltites RBaCuCoO_{5 + gd}(R = Nd, Sm, Gd) were prepared. Their unit cell parameters were determined, and thermal expansion, electrical conductivity (σ), and Seebeck coefficient (S) were studied in air in the range 300–1100 K. The compounds have tetragonal structures (space group P4/mmm, Z = 1). Their unit cell parameters are a = 0.3906(2) nm, c= 0.7648(7) nm for NdBaCuCoO_5.21; a = 0.3904(2) nm, c = 0.7609(6) nm for SmBaCuCoO_5.06; and a = 0.3891(2), c = 0.7592(6) nm for GdBaCuCoO_5.02. The RBaCuCoO_{5 + δ} cuprocobaltites at room temperature are p-type semiconductors, whose electrical conductivity and linear thermal expansion coefficient (LTEC) increase with increasing R³⁺ ionic radius, whereas the Seebeck coefficient decreases. The LTECs of RBaCuCoO_{5 + δ} phases in the range 500–575 K increase by a factor of 1.2–1.5 because of the elimination of weakly bound oxygen. S = f(T) curves for RBaCuCoO_{5 + δ} (R = Nd, Sm, Gd) feature maxima at 510 K for R = Sm and 365 K for R = Gd, probably, due to the change in the spin state of cobalt cations in these phases.     

Stereochemical nonrigidity of homophenalenyl cations

A strong temperature dependence was observed of chemical shifts in the ¹³C NMR spectra of 3b,4-exo-4a,5-tetramethyl-3b,4,4a,5-tetrahydro-4H-cyclopropa[a]phenalen-5-yl cation and its endo-epimer revealing their stereochemical nonrigidity.     

Interaction of 9-substituted anthracenes with oxidation systems <Emphasis Type="Italic">tert</Emphasis>-butylhydroperoxide-metal <Emphasis Type="Italic">tert</Emphasis>-butoxide

9-R-Anthracenes (R = Me, Ph) are effective acceptors of peroxyl and metalalkoxyl radicals in the systems tert-butylhydroperoxide-metal tert-butoxide (M = Al, V, Cr; C₆H₆, 20°C). Isolation of 9-R-9,10-dihydro-9,10-di-tert-butylperoxyanthracenes, 10-R-10-tert-butylperoxy-9-anthrones as major products reliably confirms the formation of tert-butylperoxy radicals and can be used for quantitative assessment of their content.     

Thermal Rearrangements of 3<Emphasis Type="Italic">H</Emphasis>- and 4<Emphasis Type="Italic">H</Emphasis>-Pyrazoles Prepared by Reactions of 9-Diazofluoren with Methyl Tetrolate and Methyl 3-Phenylpropiolate

9-Diazofluoren adds in Et₂O at 20°C to methyltetrolate in keeping with Auwers rule and nonregioselectively adds to methyl-3-phenylpropiolate with the formation of spirocyclic 3H-pyrazoles. The methyltetrolate adduct at boiling in toluene converts into methyl 3a-methyl-3aH-dibenzo[e,g]indazole-3-carboxylate, at 190°C in benzene, into methyl 3-methyl-2H-dibenzo[e,g]indazole-2-carboxylate, and at 160°C in methanol, into 3-methyl-2H-dibenzo[e,g]indazole. Auwers adduct of methyl 3-phenylpropiolate at boiling in benzene gives cyclopropene derivative and at boiling in methanol isomerizes into methyl 3a-phenyl-3aHdibenzo[e,g]indazole-3-carboxylate. Anti-Auwers adduct at boiling in benzene isomerizes into methyl 2-phenylpyrazolo[1,5-f]phenanthridine-3-carboxylate.     

Description of the even-odd alternation of the clearing temperatures over homologous series of mesogens by second-order differential equations

It is shown for liquid crystals of various chemical classes that the nematic-isotropic transition temperatures in homologous series of compounds undergoing enantiotropic transitions are described by secondorder inhomogeneous recurrent equations with constant coefficients: T(n + 2) = aT(n + 1) + bT(n) + c (n is the number of alkyl carbon atoms). Solutions of the corresponding differential equations as T(n) functions allow reproduction of the even-odd alternation of the clearing temperatures.     

<Emphasis Type="Italic">CrMAPK3</Emphasis> regulates the expression of iron-deficiency-responsive genes in <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis>

Background

Under iron-deficient conditions, Chlamydomonas exhibits high affinity for iron absorption. Nevertheless, the response, transmission, and regulation of downstream gene expression in algae cells have not to be investigated. Considering that the MAPK pathway is essential for abiotic stress responses, we determined whether this pathway is involved in iron deficiency signal transduction in Chlamydomonas.

Results

Arabidopsis MAPK gene sequences were used as entry data to search for homologous genes in Chlamydomonas reinhardtii genome database to investigate the functions of mitogen-activated protein kinase (MAPK) gene family in C. reinhardtii under iron-free conditions. Results revealed 16 C. reinhardtii MAPK genes labeled CrMAPK2–CrMAPK17 with TXY conserved domains and low homology to MAPK in yeast, Arabidopsis, and humans. The expression levels of these genes were then analyzed through qRT-PCR and exposure to high salt (150 mM NaCl), low nitrogen, or iron-free conditions. The expression levels of these genes were also subjected to adverse stress conditions. The mRNA levels of CrMAPK2, CrMAPK3, CrMAPK4, CrMAPK5, CrMAPK6, CrMAPK8, CrMAPK9, and CrMAPK11 were remarkably upregulated under iron-deficient stress. The increase in CrMAPK3 expression was 43-fold greater than that in the control. An RNA interference vector was constructed and transformed into C. reinhardtii 2A38, an algal strain with an exogenous FOX1:ARS chimeric gene, to silence CrMAPK3. After this gene was silenced, the mRNA levels and ARS activities of FOX1:ARS chimeric gene and endogenous CrFOX1 were decreased. The mRNA levels of iron-responsive genes, such as CrNRAMP2, CrATX1, CrFTR1, and CrFEA1, were also remarkably reduced.

Conclusion

CrMAPK3 regulates the expression of iron-deficiency-responsive genes in C. reinhardtii.

     

Oxidative Addition of <Emphasis Type="Italic">N</Emphasis>-Aminophthalimide to Alkenyl-4,5-dihydropyrazoles and Alkenylpyrazoles. Synthesis of Aziridinylpyrazoles

Oxidation of N-aminophthalimide with lead tetraacetate in the presence of 1,5-diaryl-3-[(E)-2-arylethenyl]-1H-pyrazoles, as well as of 1,3-diphenyl-5-[(E)-2-phenylethenyl]-1H-pyrazole, gives adducts at the exocyclic C=C bond, the corresponding phthalimidoaziridinylpyrazoles. From 1,5-diphenyl-3-[(1E,3E)-4-phenyl-1,3-butadienyl]-1H-pyrazole, only product of addition at both exocyclic C=C bonds was obtained. In the reaction with 1-phenyl-3-[(1E, 3E)-4-phenyl-1,3-butadienyl]-5-[(E)-2-phenylethenyl]-1H-pyrazole, the adduct at the styryl C=C bond was isolated. Analogous 4,5-dihydropyrazoles, 1,5-diphenyl-3-[(1E, 3E)-4-phenyl-1,3-butadienyl]-4,5-dihydro-1H-pyrazole and 1-phenyl-3-[(1E, 3E)-4-phenyl-1,3-butadienyl]-5-[(E)-2-phenylethenyl]-4,5-dihydro-1H-pyrazole, turned out to be inert in oxidative addition of N-aminophthalimide.     

Estimation of boiling points of organic compounds at various pressures using recurrent relations

A new approach is proposed for the estimation of boiling points (T _b) of organic compounds at reduced pressure from their values at atmospheric pressure based on the application of a recurrent relation: T _b (log P + Δlog P) = aT _b (log P) + b. Estimation of coefficients in this relation for the compounds different by their chemical nature gives the following average values: a = 1.126, b = ?41.7. Successive application of this relation with Δlog P = 1 (that corresponds to 10-fold decrease in pressure) allows estimation of the T _b values at the pressure values of 100, 10 and 1 torr from the value of T _b (760 torr) by simple arithmetic calculation with an average accuracy about 8°C.     

Structure and Reactivity of Bicyclo[2.2.1]hept-2-ene-<Emphasis Type="Italic">endo</Emphasis>-5,<Emphasis Type="Italic">endo</Emphasis>-6-dicarboxylic (endic) Acid Hydrazide

Establishing of the structure of hydrazinolysis product obtained from bicyclo[2.2.1]hept-2-ene-endo-5, endo-6-dicarboxylic (endic) acid was performed by preparation of the compound under alternative conditions followed by comparison of the characteristics and spectral parameters of the resulting substances, and also by quantum-chemical calculations by the density functional method of the chemical shifts in ¹H and ¹³C NMR spectra of different reaction products. The X-ray diffraction analysis of the hydrazide was also carried out. The compound obtained was assigned a structure of N-aminobicyclo[2.2.1] hept-2-ene-endo-5,endo-6-dicarboximide. The products were prepared by its reactions with arylsulfonyl chlorides, benzoyl chlorides, m-tolyl and p-toluene-sulfonyl isocyanates, phenyl isothiocyanate, with o-nitrobenzaldehyde, and oxiranes (1,2-epoxycyclohexane and 2,3-epoxypropylcarbazole). The aromatic sulfonamides, carboxamides, and ureas were epoxidized by performic acid obtained in situ from the formic acid and hydrogen peroxide. Products of [3+2]-cycloaddition of aryl azides to the strained double bond in the N-aminobicyclo[2.2.1] hept-2-ene-endo-5,endo-6-dicarboximide and its derivatives. The structures of compounds obtained were confirmed by their IR, 1H and 13C NMR spectra.     

Synthesis and structure of silicon-containing <Emphasis Type="Italic">N</Emphasis>-methyland <Emphasis Type="Italic">N</Emphasis>-benzoylamides of diisopropylphosphoric acid

Diisopropyl N-benzoyl-N-(trimethylsilyl)phosphoramidate reacts with ClCH₂SiMe₂Cl under mild conditions to form diisopropyl N-benzoyl-N-[(chlorodimethylsilyl)methyl]phosphoramidate (III). Diisopropyl N-methyl-N-(trimethylsilyl)phosphoramidate with ClCH₂SiMe₂Cl affords an N-transsilylation product which does not rearrange into diisopropyl N-[(chlorodimethylsilyl)methyl]-N-methylphosphoramidate (XV) even under severe conditions (4 h, 130°C). Compound XV was prepared by the reaction of diisopropyl phosphorochloridate with N-[(methoxydimethylsilyl)methyl]-N-methylamine followed by treatment of diisopropyl N-[(methoxydimethylsilyl)methyl]-N-methylphosphoramidate with boron trichloride. Analysis of experimental and calculated ²⁹Si chemical shifts points to a five-coordinate silicon atom in compound III and a fourcoordinate silicon atom in compound XV. According to B3LYP calculations with due regard to solvent effects, compound III is an isomer with a C=O→Si bond. By variation of substituents at silicon, phosphorus, and carbonyl carbon atoms, chelate structures with either C=O→Si or P=O→Si dative bonds can be obtained.     

Crystal structures of 1,1,1-trifluoro-4-hydroxy-4-phenyl-but-3-en-2-one, 2,2,6,6-tetramethyl-3-hydroxy-hept-3-en-5-one, 2,2,6,6-tetramethyl-3-methylamino-hept-3-en-5-one and a study of the ability of these ligands to complex formation with metals

Crystal structures are determined (Bruker Nonius X8 Apex, 4K CCD-detector, λMoK _α, graphite monochromator, T 150 K and 293 K) for two β-diketones F₃CC(O)CH₂C(O)Ph (1) (space group P2₁/c, a = 7.0713(3)Å, b = 11.5190(6)Å, c = 11.3602(6) Å, β = 99.405(2)°, V = 912.90(8) ų, Z = 4), (CH₃)₃CC(O)CH₂C(O)C(CH₃)₃ (2) (space group Pbca, a = 11.5536(8) Å, b = 11.5796(10) Å, c = 17.2523(13) Å, V = 2308.1(3) ų, Z = 8) and a ketoimine (CH₃)₃CC(NCH₃)CH₂C(O)C(CH₃)₃ (3) (space group I4₁/a, a = 18.7687(6) Å, b = 18.7687(6) Å, c = 14.5182(6) Å, V = 5114.2(3) ų, Z = 16). All structures are molecular and comprise isolated molecules joined by van der Walls interactions. The substitution energy of a Na atom for a hydrogen atom in free ligands is calculated by the hybrid B3LYP quantum chemical method. A successful preparation of Na(I) chelates with ligands 1, 2 and failed attempts to prepare a complex with ligand 3 are in accordance with the calculations. Geometrical simulation of a copper(II) complex with ligand 3 reveals the overlap of CH₃ groups which hinders the complexation.     

Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic <Emphasis Type="Italic">Corynebacterium urealyticum</Emphasis> DSM 7109

Background

Corynebacterium urealyticum, a pathogenic, multidrug resistant member of the mycolata, is known as causative agent of urinary tract infections although it is a bacterium of the skin flora. This pathogenic bacterium shares with the mycolata the property of having an unusual cell envelope composition and architecture, typical for the genus Corynebacterium. The cell wall of members of the mycolata contains channel-forming proteins for the uptake of solutes.

Results

In this study, we provide novel information on the identification and characterization of a pore-forming protein in the cell wall of C. urealyticum DSM 7109. Detergent extracts of whole C. urealyticum cultures formed in lipid bilayer membranes slightly cation-selective pores with a single-channel conductance of 1.75 nS in 1 M KCl. Experiments with different salts and non-electrolytes suggested that the cell wall pore of C. urealyticum is wide and water-filled and has a diameter of about 1.8 nm. Molecular modelling and dynamics has been performed to obtain a model of the pore. For the search of the gene coding for the cell wall pore of C. urealyticum we looked in the known genome of C. urealyticum for a similar chromosomal localization of the porin gene to known porH and porA genes of other Corynebacterium strains. Three genes are located between the genes coding for GroEL2 and polyphosphate kinase (PKK2). Two of the genes (cur_1714 and cur_1715) were expressed in different constructs in C. glutamicum ΔporAΔporH and in porin-deficient BL21 DE3 Omp8 E. coli strains. The results suggested that the gene cur_1714 codes alone for the cell wall channel. The cell wall porin of C. urealyticum termed PorACur was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 4 kDa on tricine-containing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).

Conclusions

Biophysical characterization of the purified protein (PorACur) suggested indeed that cur_1714 is the gene coding for the pore-forming protein in C. urealyticum because the protein formed in lipid bilayer experiments the same pores as the detergent extract of whole cells. The study is the first report of a cell wall channel in the pathogenic C. urealyticum.

     

Comparative Study on Different Expression Hosts for Alkaline Phytase Engineered in <Emphasis Type="Italic">Escherichia coli</Emphasis>

The application of alkaline phytase as a feed additive is restricted by the poor specific activity. Escherichia coli is a frequently used host for directed evolution of proteins including alkaline phytase towards improved activity. However, it is not suitable for production of food-grade products due to potential pathogenicity. To combine the advantages of different expression systems, mutants of the alkaline phytase originated from Bacillus subtilis 168 (phy168) were first generated via directed evolution in E. coli and then transformed to food-grade hosts B. subtilis and Pichia pastoris for secretory expression. In order to investigate the suitability of different expression systems, the phy168 mutants expressed in different hosts were characterized and compared in terms of specific activity, pH profile, pH stability, temperature profile, and thermostability. The specific activity of B. subtilis-expressed D24G/K70R/K111E/N121S mutant at pH 7.0 and 60 °C was 30.4 U/mg, obviously higher than those in P. pastoris (22.7 U/mg) and E. coli (19.7 U/mg). Moreover, after 10 min incubation at 80 °C, the B. subtilis-expressed D24G/K70R/K111E/N121S retained about 70 % of the activity at pH 7.0 and 37 °C, whereas the values were only about 25 and 50 % when expressed in P. pastoris and E. coli, respectively. These results suggested B. subtilis as an appropriate host for expression of phy168 mutants and that the strategy of creating mutants in one host and expressing them in another might be a new solution to industrial production of proteins with desired properties.     

Thermal deformation thermodynamics of a smectite mineral

A method has been purposed to calculate some of the thermodynamic quantities for the thermal deformation of a smectite without using any basic thermodynamic data. The Hanç?l? (Keskin, Ankara, Turkey) bentonite containing a smectite of 88% by volume was taken as material. Thermogravimetric (TG) and differential thermal analysis (DTA) curves of the sample were obtained. Bentonite samples were heated at various temperatures between 25–900°C for the sufficient time (2 h) until to establish the thermal deformation equilibrium.Cation-exchange capacity (CEC) of heated samples was determined by using the methylene blue standard method. The CEC was used as a variable of the equilibrium. An arbitrary equilibrium constant (K _a) was defined similar to chemical equilibrium constant and calculated for each temperature by using the corresponding CEC-value. The arbitrary changes in Gibbs energy (ΔG _a ⁰ ) were calculated from K _a-values. The real change in enthalpy (ΔH ⁰) and entropy (ΔS ⁰) was calculated from the slopes of the lnK vs. 1/T and ΔG vs. T plots, respectively. The real changes in Gibbs energy (ΔG ⁰) and real equilibrium constant (K) were calculated by using the ΔH ⁰ and ΔS ⁰ values. The results at the two different temperature intervals are summarized as below: ΔG ₁ ⁰ =ΔH ₁ ⁰ ?ΔS ₁ ⁰ T=?RTlnK ₁=47000?53t, (200–450°C), and ΔG ₂ ⁰ =ΔH ₂ ⁰ -ΔS ₂ ⁰ T=?RTlnK ₂=132000?164T, (500–800°C).     

Gas electron diffraction and quantum chemical studies of the molecular structure of 2-nitrobenzenesulfonic acid

A combined gas electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pVTZ) study of the molecular structure of 2-nitrobenzenesulfonic acid (2-NBSA) is performed. Quantum chemical calculations show that the 2-NBSA molecule has five conformers, and the Gibbs energy of one of them is lower by more than 4.5 kcal/mol than the energy of the other conformers. It is found experimentally that the saturated vapor of 2-NBSA at T = 394(5) K contains only the low-energy conformer that has an intramolecular hydrogen bond between the H atom of the hydroxyl group and one of the O atoms of the NO₂ group. The C-C-S-O(H) torsion angle determining the position of the S-O(H) bond is ?72(7)°, while the NO₂ group is substantially turned relative to the benzene ring plane (C1-C2-N-O = 40(5)°). The following experimental values of the internuclear distances are obtained for this conformer (Å): r _h1(C-H)_av = 1.07(2), r _h1(C-C)_av = 1.401(4), r _h1(C-S) = 1.767(6), r _h1(S=O)_av = 1.412(4), r _h1(S-O) = 1.560(6), r _h1(N-O)_av = 1.217(5), r _h1(C-N) = 1.461(8), r _h1(O-H) = 0.99(3).