Aromaticity and Chemical Bonding of Chalcogen-Bonded Capsules Featuring Enhanced Magnetic Anisotropy

We present a theoretical study of chalcogen bonded container capsules ( A_X+A_X ) where X=O, S, Se, and Te, and their encapsulation complexes with n-C₉H₂₀ (n-C₉H₂₀@ A_X+A_X ). Both Se and Te encapsulation complexes have significant experimental and computed binding energies, analogous to the hydrogen bonded counterparts, while the S and O capsules and their encapsulation complexes show only weak binding energies, which are attributed to different types of bonding: chalcogen S⋅⋅⋅N bonds for S-capsules and π–π stacking and weak hydrogen bonds for the O case. All A_X+A_X and C₉H₂₀@ A_X+A_X present unusually high magnetic anisotropies in their interiors. The ¹H NMR spectra of the encapsulation complexes display the proton signals of the encapsulated n-nonane highly upfield shifted, in agreement with the available experimental data for the Se capsule. We found that different factors contribute to the observed magnetic anisotropy of the capsule's interior: for the Te capsule the most important factor is Te's large polarizability; for the O analogue the inductive effects produced by the electronegative nature of the O and N heteroatoms; and for the S and Se capsules, the polarizability of the heteroatoms combines with electric field effects.     

An NMR Method To Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins

Targeting protein surfaces involved in protein–protein interactions by using supramolecular chemistry is a rapidly growing field. NMR spectroscopy is the method of choice to map ligand‐binding sites with single‐residue resolution by amide chemical shift perturbation and line broadening. However, large aromatic ligands affect NMR signals over a greater distance, and the binding site cannot be determined unambiguously by relying on backbone signals only. We herein employed Lys‐ and Arg‐specific H2(C)N NMR experiments to directly observe the side‐chain atoms in close contact with the ligand, for which the largest changes in the NMR signals are expected. The binding of Lys‐ and Arg‐specific supramolecular tweezers and a calixarene to two model proteins was studied. The H2(C)N spectra track the terminal CH₂ groups of all Lys and Arg residues, revealing significant differences in their binding kinetics and chemical shift perturbation, and can be used to clearly pinpoint the order of ligand binding.     

Mass Spectrometric Strategies to Improve the Identification of Pt(II)-Modification Sites on Peptides and Proteins

To further explore the binding chemistry of cisplatin (cis-Pt(NH₃)₂Cl₂) to peptides and also establish mass spectrometry (MS) strategies to quickly assign the platinum-binding sites, a series of peptides with potential cisplatin binding sites (Met(S), His(N), Cys(S), disulfide, carboxyl groups of Asp and Glu, and amine groups of Arg and Lys, were reacted with cisplatin, then analyzed by electron capture dissociation (ECD) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Radical-mediated side-chain losses from the charge-reduced Pt-binding species (such as CH₃S^? or CH₃SH from Met, SH^? from Cys, CO₂ from Glu or Asp, and NH₂ ^? from amine groups) were found to be characteristic indicators for rapid and unambiguous localization of the Pt-binding sites to certain amino acid residues. The method was then successfully applied to interpret the top-down ECD spectrum of an inter-chain Pt-crosslinked insulin dimer, insulin?+?Pt(NH₃)₂?+?insulin (>10 kDa). In addition, ion mobility MS shows that Pt binds to multiple sites in Substance P, generating multiple conformers, which can be partially localized by collisionally activated dissociation (CAD). Platinum(II) (Pt(II)) was found to coordinate to amine groups of Arg and Lys, but not to disulfide bonds under the conditions used. The coordination of Pt to Arg or Lys appears to arise from the migration of Pt(II) from Met(S) as shown by monitoring the reaction products at different pH values by ECD. No direct binding of cisplatin to amine groups was observed at pH 3?~?10 unless Met residues were present in the sequence, but noncovalent interactions between cisplatin hydrolysis and amination [Pt(NH₃)₄]²⁺ products and these peptides were found regardless of pH.

Acylation Reactions of Dibenzo-7-phosphanorbornadiene: DFT Mechanistic Insights

Extensive DFT calculations provide deep mechanistic insights into the acylation reactions of tert-butyl dibenzo-7-phosphanobornadiene with PhCOX (X=Cl, Br, I, OTf) in CH₂Cl₂ solution. Such reactions are initialized by the nucleophilic P⋅⋅⋅C attack to the carbonyl group to form the acylphosphonium intermediate A⁺ together with X⁻ anion, followed either by nucleophilic X⁻⋅⋅⋅P attack (X=Cl, Br, and I) toward A⁺ to eliminate anthracene or by slow rearrangement or decomposition of A⁺ (X=OTf). In contrast to the first case (X=Cl) that is rate-limited by the initial P⋅⋅⋅C attack, other reactions are rate-limited by the second X⁻⋅⋅⋅P attack for X=Br and I and even thermodynamically prevented for X=OTf, leading to isolable phosphonium salts. The rearrangement of phosphonium A⁺ is initiated by a P-C bond cleavage, followed either by sequential proton-shifts to form anthracenyl acylphosphonium or by deprotonation with additional base Et₃N to form neutral anthracenyl acylphosphine. Our DFT results strongly support the separated acylphosphonium A⁺ as the key reaction intermediate that may be useful for the transfer of acylphosphenium in general.     

Ab initio study of low-lying electronic states of the PF2 radical

The equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X²B₁, ²A₁, ²B₂, and ²A₂ of the PF₂ radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X²B₁ state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the ²A₁ → X²B₁ and ²A₂ → X²B₁ transitions, and radiative lifetimes for the ²A₁ and ²A₂ states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.     

Investigation on the pH-dependent binding of benzocaine and lysozyme by fluorescence and absorbance

The interaction mechanism between benzocaine (BZC) and lysozyme (Lys) has been investigated by fluorescence, synchronous fluorescence, ultraviolet–vis (UV) absorption spectra, and three-dimensional fluorescence (3-D) in various pH medium. The observations of fluorescence spectra were mainly rationalized in terms of a static quenching process at lower concentration of BZC (C_BZC/C_Lys < 9) and a combined quenching process at higher concentration of BZC (C_BZC/C_Lys > 9) at pH 7.4 and 8.4. However, the fluorescence quenching was mainly arisen from static quenching by complex formation in all studied drug concentrations at pH 3.5. The structural characteristics of BZC and Lys were probed, and their binding affinities were determined under different pH conditions (pH 3.5, 7.4, and 8.4). The results indicated that the binding abilities of BZC to Lys decreased at the pH below and above the simulative physiological condition (pH 7.4) due to the alterations of the protein secondary and tertiary structures or the structural change of BZC. The effect of BZC on the conformation of Lys was analyzed using UV, synchronous fluorescence and three-dimensional fluorescence under different pH conditions. These results indicate that the binding of BZC to Lys causes apparent change in the secondary and tertiary structures of Lys. The effect of Zn²⁺ on the binding constant of BZC with Lys under various pH conditions (pH 3.5, 7.4, and 8.4) was also studied.     

Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

A series of theoretical approaches, including conventional FF03 and FF03-based polarization model, as well as the generalized energy-based fragmentation (GEBF) quantum chemistry method, have been applied to investigate the interactions between acetate ion (CH₃COO⁻) and the α-subunit of human adult hemoglobin (designated as Hb-α) at four binding sites (Lys16, Lys90, Arg92, and Lys127), respectively. The FF03-based polarizable force fields show that the interaction energies between the CH₃COO⁻ group and Hb-α follow the trend of Arg92 > Lys127 > Lys90 > Lys16. The complexation of CH₃COO⁻ with Hb-α is governed by the long-range electrostatic interactions and steric effect.     

A Crossed Molecular Beam Study on the Reaction of Boron Atoms with Methylacetylene and Partially Deuterated Methylacetylene

The reactions of ground‐state boron atoms, B(²P_j), with methylacetylene, CH₃CCH(X¹A₁), and its [D3]‐substituted isotopomer, CD₃CCH(X¹A₁), are studied under single collision conditions using the crossed molecular beam technique at collision energies of 21.6 and 21.9 kJ mol^?1, respectively. Utilizing the CD₃CCH reactant, detailed information on the dynamics is obtained. The reaction followed indirect scattering dynamics and proceeded through at least two reaction channels via atomic deuterium and hydrogen atom elimination pathways leading eventually to two isotopomers, that is, the C_2v symmetric D₂CCCBH(X¹A₁) and D₂CCCBD(X¹A₁) structures via statistical and non‐statistical reaction pathways, respectively.     

Structural Elucidation of the Bispecificity of A Domains as a Basis for Activating Non‐natural Amino Acids

Many biologically active peptide secondary metabolites of bacteria are produced by modular enzyme complexes, the non‐ribosomal peptide synthetases. Substrate selection occurs through an adenylation (A) domain, which activates the cognate amino acid with high fidelity. The recently discovered A domain of an Anabaenopeptin synthetase from Planktothrix agardhii (ApnA A₁) is capable of activating two chemically distinct amino acids (Arg and Tyr). Crystal structures of the A domain reveal how both substrates fit into to binding pocket of the enzyme. Analysis of the binding pocket led to the identification of three residues that are critical for substrate recognition. Systematic mutagenesis of these residues created A domains that were monospecific, or changed the substrate specificity to tryptophan. The non‐natural amino acid 4‐azidophenylalanine is also efficiently activated by a mutant A domain, thus enabling the production of diversified non‐ribosomal peptides for bioorthogonal labeling.     

The MRSDCI studies of four low-lying electronic states of the BF2 radical

The equilibrium geometries, excitation energies, force constants, and vibrational frequencies for four low-lying electronic states X ²A₁, ²B₁, ²B₂, and ²A₂ of the BF₂ radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated excitation energy for X²A₁ → ²B₁ is in agreement with available experimental data. The electronic transition dipole moments, oscillator strengths for the ²B₁ → X²A₁ and ²B₂ → X²A₁ transitions, radiative lifetimes for the ²B₁ and ²B₂ states, and the spin properties for the X²A₁ state are calculated based on the MRSDCI wave functions, predicting results in reasonable agreement with available experimental data. © 1993 John Wiley & Sons, Inc.     

Comparison of three GPCR structural templates for modeling of the P2Y<Subscript>12</Subscript> nucleotide receptor

The P2Y₁₂ receptor (P2Y₁₂R) is an ADP-activated G protein-coupled receptor (GPCR) that is an important target for antithrombotic drugs. Three homology models of P2Y₁₂R were compared, based on different GPCR structural templates: bovine rhodopsin (bRHO), human A_2A adenosine receptor (A_2AAR), and human C-X-C chemokine receptor type 4 (CXCR4). By criteria of sequence analysis (25.6% identity in transmembrane region), deviation from helicity in the second transmembrane helix (TM2), docked poses of ligands highlighting the role of key residues, accessibility of a conserved disulfide bridge that is reactive toward irreversibly-binding antagonists, and the presence of a shared disulfide bridge between the third extracellular loop (EL3) and the N-terminus, the CXCR4-based model appeared to be the most consistent with known characteristics of P2Y₁₂R. The docked poses of agonist 2MeSADP and charged anthraquinone antagonist PSB-0739 in the binding pocket of P2Y₁₂R-CXC agree with previously published site-directed mutagenesis studies of Arg256 and Lys280. A sulfonate at position 2 of the anthraquinone core created a strong interaction with the Lys174(EL2) side chain. The docking poses of the irreversibly-binding, active metabolite (existing as two diastereoisomers in vivo) of the clinically utilized antagonist Clopidogrel were compared. The free thiol group of the 4S diastereoisomer, but not the 4R isomer, was found in close proximity (~4.7 Å) to the sulfur atom of a disulfide bridge involving Cys175, suggesting greater activity in covalent binding. Therefore, ligand docking to the CXCR4-based model of the P2Y₁₂R predicted poses of both reversibly and irreversibly-binding small molecules, consistent with observed pharmacology and mutagenesis studies.     

Does in-source decay occur independent of the ionization process in matrix-assisted laser desorption?

The influence of the acidic and basic characters of constituent amino acid residues on the peptide fragment ions produced by in-source decay under matrix assisted laser desorption/ionization (MALDI) conditions has been studied using positive- and negative-ion experiments. Whereas the in-source decay spectra of peptides containing basic Arg and/or Lys residues near the N-terminus showed so-called c_n- and a_n-series ions in positive-ion mode, a peptide that has an acidic amino acid cluster near the N-terminus and a basic residue near the C-terminus characteristically formed y_n- and z_n-series ions in the positive-ion in-source decay spectrum. These results indicated that fragment ion series produced by in-source decay depend strongly upon the acidic and basic characters of the constituent amino acid residues and the near N- and C-termini. It was suggested that in-source decay processes occur intrinsically at NH–C^α and CO–NH bonds independent of the formation of molecular-related ions, and that the cleavages at the NH–C^α and CO–NH bonds occurred independently and were dependent on the matrix used.     

The Effect of Temperature on the Equivalent Conductivities and Ion-Association Constants of Some Tris-(ethylenediamine)chromium(III) Complexes in N,N-dimethylformamide and N,N-dimethylacetamide

The equivalent conductivities of tris-(ethylenediamine)chromium complexes, [Cr(en)₃]X₃ (where X⁻= Cl⁻, Br⁻, I⁻; en = ethylenediamine) were measured as functions of temperature (278.15 to 328.15 K) and concentration [(1.948 ×10⁻⁴ to 10.728 ×10⁻⁴ mol⋅dm⁻³) and (2.282 ×10⁻⁴ to 11.246 ×10⁻⁴ mol⋅dm⁻³)] in N,N-dimethylformamide (DMF) and N,N-dimethylacetamide (DMAC), respectively. Equivalent conductivity values for [Cr(en)₃]X₃ in DMF were found to be higher than those in DMAC. The conductivity data were analyzed with the Robinson-Stokes equations. For [Cr(en)₃]X₃, the limiting equivalent ionic conductivities of [Cr(en)₃]³⁺ and the ion-association constants (K _A) of the ion-pair between [Cr(en)₃]³⁺ and the monovalent halide anions were determined in DMF and DMAC. The values of K _A for three complex salts in DMF were higher than those in DMAC. This can be ascribed to an increase of the ion-association constants with a decrease of the relative permittivity of the solvents. The values of K _A at 298.15 K decreased in the order Cl⁻> Br⁻> I⁻ in DMF and Cl⁻> I⁻> Br⁻ in DMAC. The K _A values for [Cr(en)₃]Cl₃ increased with increasing temperature in both DMF and DMAC. For [Cr(en)₃]X₃(X⁻= Br⁻, I⁻) in both solvents, this indicates increasing disorder occurs with increasing temperature. Thermodynamic parameters (standard Gibbs energy, enthalpy and entropy changes) were determined from the temperature dependence of K _A in DMF and DMAC. These parameters were inter-compared in their dependences on temperature and solvent.     

The coordination chemistry ofN,N′-ethylenebis(2-acetylpyridine imine) andN,N′-ethylenebis(2-benzoylpyridine imine); two potentially tetradentate ligands containing four nitrogen atoms

Summary New complexes of the general formulae [ML_A(H₂O)₂]-Cl₂ (M=Ni or Cu), [ML_AX₂] (M=Co or Cu; X=Cl or Br), [NiL_ABr₂]·H₂O, [ML_A] [MCl₄] (M=Pd or Pt), [NiL_B(H₂O)₂]Cl₂·2H₂O, [ML_BCl₂] (M=Co, Ni, Cu, Pd or Pt; X=Cl or Br) and [ML_B] [MCl₄] (M=Pd or Pt), where L_A=N,N-ethylenebis(2-acetylpyridine imine) and L_B=N, N-ethylenebis(2-benzoylpyridine imine), have been isolated. The complexes were characterized by elemental analyses, conductivity measurements, t.g./d.t.g. methods, magnetic susceptibilities and spectroscopic (i.r., far-i.r., ligand field,¹Hn.m.r.) studies. Monomeric pseudo-octahedral stereochemistries for the Co^II, Ni^II and Cu^II complexes andcis square planar structures for the compounds [ML_BX₂] (M=Pd or Pt; X=Cl or Br) are assigned in the solid state. The molecules L_A and L_B behave as tetradentate chelate ligands in the Co^II, Ni^II, Cu^II and Magnus-type Pd^II and Pt^II complexes, bonding through both the pyridine and methine nitrogen atoms. A bidentateN-methine coordination of the Schiff base L_B is assigned in the [ML_BX₂] complexes (M=Pd or Pt; X=Cl or Br). The anomalous magnetic moment values of the Co^II complexes are discussed.     

Theoretical prediction of ionization potential,electron affinity,and electronic spectrum of the S2N radical

Ab initio MRD –CI calculations using a basis set of near Hartree–Fock quality have been carried out to calculate the ground-state electronic structure of S₂N⁺, S₂N, and S₂N^? and the ionization potential, electron affinity, and vertical electronic spectrum of S₂N. At the highest level of theory (estimated full CI or FCI ), S₂N⁺ is predicted to have a linear structure with r(N? S) = 1.51 Å. For S₂N and S₂N^?, the minimum in energy at the FCI level corresponds to a quasi-linear [with a barrier height to linearity of about 2.0 kcal mol^?1, ] and a bent structure , respectively. The adiabatic/vertical ionization potential and electron affinity of S₂N are predicted to be 7.26/7.82 and 1.60/0.79 eV, respectively. Of the several electronic transitions in S₂N considered, the ones with the excitation energy of 1.87 eV (X² A₁ → ²B₂) and 2.87 eV (X²A₁ → ²B₂) are somewhat intense (? = 0.005 and 0.002) and likely to be observed.     

MRSDCI studies of low-lying electronic states of the CF 2 + ion

Summary The equilibrium geometries, excitation energies, force constants and vibrational frequencies for four low-lying electronic statesX ² A ₁,² B ₁,² B ₂ and² A ₂ of the CF ₂ ⁺ ion have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated excitation energies for these states and vibrational frequencies for the ground state are in good agreement with experimental data via photoelectron spectroscopy of the CF₂ radical (carbene). The electronic transition dipole moments, oscillator strengths for the² B ₁ X ² A ₁ and² B ₂ X ² A ₁ transitions, radiative lifetimes for the² B ₁ and² B ₂ states and the spin properties for theX ² A ₁ state are calculated based on the MRSDCI wavefunctions.     

Mechanism of the Tyrosine Ammonia Lyase Reaction—Tandem Nucleophilic and Electrophilic Enhancement by a Proton Transfer

Quantum mechanics/molecular mechanics calculations in tyrosine ammonia lyase (TAL) ruled out the hypothetical Friedel–Crafts (FC) route for ammonia elimination from L ‐tyrosine due to the high energy of FC intermediates. The calculated pathway from the zwitterionic L ‐tyrosine‐binding state (0.0 kcal mol^?1) to the product‐binding state ((E)‐coumarate+H₂N? MIO; ?24.0 kcal mol^?1; MIO=3,5‐dihydro‐5‐methylidene‐4H‐imidazol‐4‐one) involves an intermediate (IS, ?19.9 kcal mol^?1), which has a covalent bond between the N atom of the substrate and MIO, as well as two transition states (TS1 and TS2). TS1 (14.4 kcal mol^?1) corresponds to a proton transfer from the substrate to the N1 atom of MIO by Tyr300? OH. Thus, a tandem nucleophilic activation of the substrate and electrophilic activation of MIO happens. TS2 (5.2 kcal mol^?1) indicates a concerted C? N bond breaking of the N‐MIO intermediate and deprotonation of the pro‐S β position by Tyr60. Calculations elucidate the role of enzymic bases (Tyr60 and Tyr300) and other catalytically relevant residues (Asn203, Arg303, and Asn333, Asn435), which are fully conserved in the amino acid sequences and in 3D structures of all known MIO‐containing ammonia lyases and 2,3‐aminomutases.     

HCF(X~1A’)+SO2反应的动力学研究

用激光光解-激光诱导荧光方法研究了室温下(T＝293 K) HCF(X^~1A^’)自由基与SO₂分子的反应动力学. 实验中HCF(X^~1A^’)自由基是由213 nm激光光解HCFBr₂产生的, 用激光诱导荧光(LIF)检测HCF(X^~1A^’)自由基的相对浓度随着反应时间的变化, 得到此反应的二级反应速率常数为: k＝(1.81±0.15)×10^－12 cm³&#8226;molecule^－1&#8226;s^－1, 体系总压为1862 Pa. 高精度理论计算表明, HCF(X^~1A^’)和SO₂分子反应的机理是典型的加成-消除反应. 我们运用RRKM-TST理论计算了此二级反应速率常数的温度效应和压力效应, 计算结果和室温下测定的二级反应速率常数符合得较好.     

Secondary inter­actions in gold(I) complexes with thione ligands. 5. Two ionic compounds of the form bis­(thione)gold(I) bis(4‐halobenzene­sulfon­yl)amide

Bis(1,3‐thia­zolidine‐2‐thione‐κS²)gold(I) bis­(4‐chloro­benzene­sulfonyl)amide, [Au(C₃H₅NS₂)₂](C₁₂H₈Cl₂NS₂O₄), has no imposed symmetry. Classical N—H⋯N and N—H⋯O hydrogen bonds link the residues to form chains parallel to the b axis. Weaker inter­actions involve C—H⋯O, C—H⋯Au and a number of X⋯Cl contacts (X = Cl, S or Au) clustered in the region y ≃ . In bis­(1‐methyl­imidazolidine‐2‐thione‐κS²)gold(I) bis­(4‐iodo­benzene­sulfonyl)amide, [Au(C₄H₈N₂S)₂](C₁₂H₈I₂NS₂O₄), the Au atom of the cation and the N atom of the anion lie on the twofold axis (0, y, ) in the space group C2/c. The formula unit forms a self‐contained ring with two symmetry‐equivalent N—H⋯O hydrogen bonds, and weak C—H⋯X (X = O, I or S), Au⋯I and I⋯I contacts are observed. In both compounds, the anions display extended conformations.