In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin)

Our screen for tubulin-binding small molecules that do not depolymerize bulk cellular microtubules, but based upon structural features of well known microtubule-depolymerizing colchicine and podophyllotoxin, revealed tubulin binding anti-cancer property of noscapine (Ye et al. in Proc Natl Acad Sci USA 95:2280–2286, 1998). Guided by molecular modelling calculations and structure–activity relationships we conjugated at C9 of noscapine, a folate group—a ligand for cellular folate receptor alpha (FRα). FRα is over-expressed on some solid tumours such as ovarian epithelial cancers. Molecular docking experiments predicted that a folate conjugated noscapine (Targetin) accommodated well inside the binding cavity (docking score −11.295 kcal/mol) at the interface between α- and β-tubulin. The bulky folate moiety of Targetin is extended toward lumen of microtubules. The binding free energy (ΔG _bind) computed based on molecular mechanics energy minimization was −221.01 kcal/mol that revealed favourable interaction of Targetin with the receptor. Chemical synthesis, tubulin-binding experiments, and anti-cancer activity in vitro corroborate fully well with the molecular modelling experiments. Targetin binds tubulin with a dissociation constant (K _d value) of 149 ± 3.0 μM and decreases the transition frequencies between growth and shortening phases of microtubule assembly dynamics at concentrations that do not alter the total polymer mass. Cancer cells in general were more sensitive to Targetin compared with the founding compound noscapine (IC₅₀ in the range of 15–40 μM). Quite strikingly, ovarian cancer cells (SKOV3 and A2780), known to overexpress FRα, were much more sensitive to targetin (IC₅₀ in the range of 0.3–1.5 μM).     

Preparation and properties of glucose isomerase immobilized on Indion 48-R

Partially purified glucose isomerase fromStreptomyces thermonitrificans when coupled to glutaraldehyde-activated Indion 48-R, retained 30–40% activity of the soluble enzyme. However, an approximately twofold increase in the activity could be achieved by binding the enzyme in the presence of glucose. Binding the enzyme to matrices presaturated with either glucose or fructose and influence of lysine modification on the activity of the soluble enzyme revealed that the comparatively low activity observed in case of the enzyme bound in the absence of substrate is the result of the nonspecific binding of either substrate or product to the matrix. Immobilization did not affect the pH and temperature optima of the enzyme, but it lowered the temperature stability. Immobilization resulted in a marginal increase in theK _m and a threefold decrease in theV _max . Substrate concentrations as high as 36% glucose could be converted to 18.5% fructose in 5 h, at pH 7.0 and 70‡C. The bound enzyme, however, showed inferior stability to repeated use and lost approx 40% of its initial activity after five cycles of use. Indion 48-R bound glucose isomerase could be stored, in wet state, for 30 d without any apparent loss in its initial activity.     

Conformational properties of <Emphasis Type="Italic">ortho</Emphasis>-nitrobenzenesulfonamide in gas and crystalline phases. Intra- and intermolecular hydrogen bond

A combined gas-phase electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pvtz, MP2/cc-pvtz) study of molecular structure of 2-nitrobenzenesulfonamide (2-NBSA) was carried out. Quantum chemical calculations showed that 2-NBSA has four conformers, two of which are stabilized by intramolecular hydrogen bond. The latter (with the S–N bond in a close to orthogonal position around the phenyl ring and differing from each other by staggered or eclipsed positions of the N–H and S=O bonds in the SO₂NH₂ group) presented in a saturated vapor over 2-NBSA at T = 433 (3) K in commensurable amounts. Experimental internuclear distances (Ǻ) for the staggered conformer are (?): r _h1(C–H)_av. = 1.071(9), r _h1(C–C)_av. = 1.390(4), r _h1(C–S) = 1.789(8), r _h1(S=O)_av. = 1.427(6), r _h1(S–N) = 1.644(6), r _h1(N–O)_av. = 1.221(4), r _h1(C′–N) = 1.487(8), r _h1(N–H)_av. = 1.014. Calculations at B3LYP/cc-pvtz level were performed to determine the structure and the energies of the transition states between conformers. It was shown that the conformer structures of free molecule differ from those of a molecule stabilized by intermolecular hydrogen bonds in a crystal. Influence of a substituent X (X = –CH₃, –NO₂) on conformational features of the ortho-substituted benzenesulfonamide was established.     

A comprehensive study on the inclusion mechanism of benzophenone into supramolecular nanoassemblies prepared using two water-soluble associative polymers

In this study, the entrapment of benzophenone (BZ) into supramolecular nanoassemblies prepared by mixing two water-soluble associative polymers (i.e. polymerized β-CD (pβ–CD) and dextran grafted with lauryl-side chains (MD)) has been investigated by using isothermal titration microcalorimetry (ITC) and molecular modeling. ITC experiments have been performed at various temperatures (4 °C (277 K), 25 °C (298 K), and 37 °C (310 K)) to evaluate the interaction of BZ with pβ–CD in comparison with β-CD. The inclusion complexation for both β-CD/BZ and pβ–CD/BZ interactions was entropy-driven (|ΔH| < |TΔS|) when the temperature of the experiment was low (4 °C) and enthalpy-driven (|ΔH| > |TΔS|) with minor entropic contribution when the temperature was increased (25 and 37 °C). Using all the thermodynamic data obtained for β-CD/BZ and pβ–CD/BZ interactions when the temperature of the experiment was varied, the \Updelta H   =   f(T\Updelta S ) \Updelta H\; = \;f(T\Updelta S ) plot was perfectly linear, which reflected an enthalpy–entropy compensation process. Finally, the combination of ITC data with molecular modeling provided consistent information in regard to the location of MD side chains and BZ inside the cyclodextrin cavity, as well as concerning the stability of the nanoassemblies loaded with BZ.     

Effect of DNA and bivalent metal ions on the interaction of thermostable DNA polymerase <Emphasis Type="Italic">Tte</Emphasis> with dNTPs

The interaction of DNA polymerase Tte from Thermus thermophilus B35 with dUTP analog containing a fluorescein residue bound to C(5) of the base (Flu-dUTP) was studied by fluorescence titration. The dissociation constants of the enzyme—substrate complexes in the absence and in the presence of a DNA duplex containing an extended template and bivalent metal ions and the kinetic parameters of polymerization by DNA polymerase Tte in the presence of Flu-dUTP were determined. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1268–1272, May, 2005.     

Intensification of Biocatalytical Processes by Synergistic Substrate Conversion. Fungal Peroxidase Catalyzed <Emphasis Type="Italic">N</Emphasis>-Hydroxy Derivative Oxidation in Presence of 10-Propyl Sulfonic Acid Phenoxazine

Many industrial pollutants, xenobiotics, and industry-important compounds are known to be oxidized by peroxidases. It has been shown that highly efficient peroxidase substrates are able to enhance the oxidation of low reactive substrate by acting as mediators. To explore this effect, the oxidation of two N-hydroxy derivatives, i.e., N-hydroxy-N-phenyl-acetamide (HPA) and N-hydroxy-N-phenyl-carbamic acid methyl ester (HPCM) catalyzed by recombinant Coprinus cinereus (rCiP) peroxidase has been studied in presence of efficient substrate 3-(4a,10a-dihydro- phenoxazin-10-yl)-propane-1-sulfonic acid (PPSA) at pH 8.5. The bimolecular constant of PPSA cation radical reaction with HPA was estimated to be (2.5 ± 0.2)·10⁷ M⁻¹ s⁻¹ and for HPCM was even higher. The kinetic measurements show that rCiP-catalyzed oxidation of HPA and HPCM can increase up to 33,000 times and 5,500 times in the presence of equivalent concentration of high reactive substrate PPSA. The mathematical model of synergistic rCiP-catalyzed HPA–PPSA and HPCM–PPSA oxidation was proposed. Experimentally obtained rate constants were in good agreement with those calculated from the model confirming the synergistic scheme of the substrate oxidation. In order to explain the different reactivity of substrates, the docking of substrates in the active site of the enzyme was calculated. Molecular dynamic calculations show that the enzyme–substrate complexes are structurally stable. The high reactive PPSA exhibited higher affinity to enzyme active site than HPA and HPCM. Furthermore, the orientation of HPA and HPCM was not favorable for proton transfer to the distal histidine, and different substrate reactivity was explained by these diversities.     

A one-pot synthesis of alkyl acylcarbamodithioates from acid chlorides, thiols, and ammonium thiocyanate

Abstract  

An efficient synthesis of alkyl acylcarbamodithioates by reaction of acid chlorides with ammonium thiocyanate in the presence of thiols is described. The unusually large values of ⁵ J _FH = 12–15 Hz, observed for alkyl (2-fluorobenzoyl)carbamodithioates provide information about Ar–C–N–H torsion in these compounds.     

The influence of humic acid on the pH-dependent sorption of americium(III) onto kaolinite

This work investigates the sorption of americium [Am(III)] onto kaolinite and the influence of humic acid (HA) as a function of pH (3–11). It has been studied by batch experiments (V/m = 250:1 mL/g, C _Am(III) = 1 × 10⁻⁵ mol/L, C _HA = 50 mg/L). Results showed that the Am(III) sorption onto the kaolinite in the absence of HA was typical, showing increases with pH and a distinct adsorption edge at pH 3–5. However in the presence of HA, Am sorption to kaolinite was significantly affected. HA was shown to enhance Am sorption in the acidic pH range (pH 3–4) due to the formation of additional binding sites for Am coming from HA adsorbed onto kaolinite surface, but reduce Am sorption in the intermediate and high pH above 6 due to the formation of aqueous Am-humate complexes. The results on the ternary interaction of kaolinite–Am–HA are compared with those on the binary system of kaolinite–HA and kaolinite–Am and adsorption mechanism with pH are discussed. Effect of different molecular weight of HA, with three HA fractions separated by ultrafiltration techniques, on the Am sorption to kaolinite were also studied. The results showed that the enhancement of the sorption of Am onto kaolinite at the acidic pH conditions (pH 3–4) was higher with HA fractions of higher molecular weight. Also, the Am sorption over a pH range from 6 to 10 decreased with decreasing molecular weight of HA.     

Quantitative study of hydration of C<Subscript>3</Subscript>S and C<Subscript>2</Subscript>S by thermal analysis

This research is part of a European project (namely, CODICE project), main objective of which is modelling, at a multi-scale, the evolution of the mechanical performance of non-degraded and degraded cementitious matrices. For that, a series of experiments were planned with pure synthetic tri-calcium silicate (C₃S) and bi-calcium silicate (C₂S) (main components of the Portland cement clinker) to obtain different calcium–silicate–hydrate (C–S–H) gel structures during their hydration. The characterization of those C–S–H gels and matrices will provide experimental parameters for the validation of the multi-scale modelling scheme proposed. In this article, a quantitative method, based on thermal analyses, has been used for the determination of the chemical composition of the C–S–H gel together with the degree of hydration and quantitative evolution of all the components of the pastes. Besides, the microstructure and type of silicate tetrahedron and mean chain length (MCL) were studied by scanning electron microscopy (SEM) and ²⁹Si magic-angle-spinning (MAS) NMR, respectively. The main results showed that the chemical compositions for the C–S–H gels have a CaO/SiO₂ M ratio almost constant of 1.7 for both C₃S and C₂S compounds. Small differences were found in the gel water content: the H₂O/SiO₂ M ratio ranged from 2.9 ± 0.2 to 2.6 ± 0.2 for the C₃S (decrease) and from 2.4 ± 0.2 to 3.2 ± 0.2 for the C₂S (increase). The MCL values of the C–S–H gels, determined from ²⁹Si MAS NMR, were 3.5 and 4 silicate tetrahedron, for the hydrated C₃S and C₂S, respectively, remaining almost constant at all hydration periods.     

The influence of steric hindrance on conformation properties and molecular structure of 2,4,6-trinitrobenzenesulfonic acid: gas electron diffraction and quantum chemical calculations

A combined gas-phase electron diffraction and quantum chemical (B3LYP/cc-pVTZ, MP2/cc-pVDZ) study of molecular structure of 2,4,6-trinitrobenzenesulfonic acid (2,4,6-tri-NBSA) was carried out. Quantum chemical calculations showed that 2,4,6-tri-NBSA possesses six conformers, which form three pairs of enantiomers with the relative energy of 0, 4.4/3.9, and 2.5/2.5 kcal/mol. It was experimentally established that at T = 444(5) K a saturated vapor over 2,4,6-tri-NBSA is, predominantly (up to 93 mol.%), represented by a low-energy enantiomers II and II′ characterized by intramolecular hydrogen bond between an H atom of the hydroxyl group and one of the O atoms of the NO₂ group. Experimental internuclear distances for the low-energy enantiomers are (?): r _h1(C–C)_av. = 1.387(4), r _h1(C–S) = 1.811(6), r _h1(S=O)_av. = 1.424(4), r _h1(S–O) = 1.579(4), r _h1(N–O)_av. = 1.214(3), r _h1(C–N)_av. = 1.491(5). Geometry of the conformer II points on existance of strong steric interactions between SO₂OH group and two ortho-nitro groups. Analysis of the orbital interactions between the substituents and benzene ring was carried out. Geometric parameters and energies of transition states between conformers were calculated (B3LYP).     

Different coordination modes of the dimethyldisulfide ligand in trimethylplatinum(IV) complexes

The reaction of [PtMe₃(bpy)(Me₂CO)](BF₄) (2) (prepared from [PtMe₃I(bpy)] (1) plus Ag(BF₄)) with MeSSMe resulted in the formation of [PtMe₃(bpy)(MeSSMe-κS)](BF₄) (3). A single-crystal X-ray diffraction analysis revealed in the octahedral Pt(IV) complex (configuration index: OC-6-33), a conformation of the monodentately κS bound MeSSMe ligand (C–S–S–C 92.7(4)°) being very close to that in non-coordinated MeSSMe, thus allowing some hyperconjugative interaction stabilizing the S–S bond. The reaction of [K(18C6)][(PtMe₃)₂(μ-I)(μ-pz)₂] (4; 18C6 = 18-crown-6, Hpz = pyrazole) with Ag(BF₄) and MeSSMe resulted in the formation of dinuclear complexes [(PtMe₃)₂(μ-pz)₂(μ-MeSSMe)] existing at room temperature in acetone solution as different fast interconverting isomers. At –40 °C, two isomers with a μ-1κS:2κS (5a) and a μ-1κS:2κS′ (5b) coordinated MeSSMe ligand in the ratio 2:1 could be identified ¹H NMR spectroscopically. DFT calculations of type 5 complexes revealed the existence of two conformers with a μ-MeSSMe-1κS:2κS ligand, which differ mainly in the C–S–S–C dihedral angle (66.4 vs. 180.0° 6a/6a′). They have essentially the same energy and a very low activation barrier in acetone as solvent (1.3 kcal/mol) for their mutual interconversion. A further equilibrium structure was identified to be an isomer having a μ-MeSSMe-1κS:2κS′ ligand (6b) that proved to be only 1.9 kcal/mol higher in energy than 6a/6a′.     

Influence of Amino Acid Composition and Phosphorylation on the Ion Yields of Peptides in MALDI-MS

The influence of arginine (Arg), lysine (Lys), and phenylalanine (Phe) residues and phosphorylation on the molecular ion yields of model peptides have been quantitatively studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry in both positive- and negative-ion mode. The results obtained from these experiments have been interpreted from the standpoint of two different components, namely, desorption and ionization, on the basis of the physicochemical properties of constituent amino acids of the model peptides. The presence of basic residues such as Arg and Lys enhanced the ion yields of protonated molecules [M + H]⁺. An N-terminal rather than a C-terminal Arg residue was advantageous for the formation of both [M + H]⁺ and [M – H]^–. The presence of the Phe residue resulted in the increase of the ion yields of both [M + H]⁺ and [M – H]^–. In contrast, the presence of phosphate group(s) contributed to the suppression of the yields of both [M + H]⁺ and [M – H]^– due to the loss of phosphate group. The detection limits for both [M + H]⁺ and [M – H]^– of model peptides have been evaluated.     

Modeling Ar and Kr matrix effect on the ν s (Cl–H) and ν l (Cl–H) of Cl–H···NH3 by the IEF-PCM method

Ar and Kr matrix effect on the geometry and Cl–H stretching (ν _s (Cl–H)) and librational (ν _l (Cl–H)) frequencies of the hydrogen-bonded complex Cl–H···NH₃ are simulated within the framework of polarizable continuum model with integral equation formalism (IEF-PCM) at B3LYP and MP2 levels of theory with the basis set 6-311++G(2df,2pd). Within the framework of B3LYP and IEF-PCM, the simulated gas phase, Ar, and Kr matrix ν _s (Cl–H) of the complex are 2140, 1684, and 1550 cm⁻¹, respectively, which deviate from the experimental values (~2200, 1371, and 1218 cm⁻¹) by −60, 313, and 332 cm⁻¹. Within the framework of MP2 and IEF-PCM, the gas phase, Ar, and Kr matrix ν _s (Cl–H) are calculated as 2366, 2037, and 1957 cm⁻¹ by the harmonic approximation, and as 2177, 1876, and 1665 cm⁻¹ by the full-dimensional anharmonic correction. The matrix effect modeling is of greater importance than the anharmonic correction in accounting for the large experimental gas phase to Ar or Kr matrix shift of the ν _s (Cl–H) (−829 or −982 cm⁻¹). Our calculations do not support the assignment of the 733.8 and 736.9 cm⁻¹ bands to the Ar and Kr matrix ν _l (Cl–H).     

Rational design,synthesis and biological evaluations of amino-noscapine: a high affinity tubulin-binding noscapinoid

Noscapine and its derivatives are important microtubule-interfering agents shown to have potent anti-tumor activity. The binding free energies (ΔG _bind) of noscapinoids computed using linear interaction energy (LIE) method with a surface generalized Born (SGB) continuum solvation model were in agreement with the experimental ΔG _bind with average root mean square error of 0.082 kcal/mol. This LIE–SGB model guided us in designing a novel derivative of noscapine, amino-noscapine [(S)-3-((R)-9-amino-4-methoxy-6-methyl-5,6,7,8-tetrahydro [1, 3] dioxolo[4,5-g]isoquinolin-5-yl)-6,7-dimethoxy isobenzo-furan-1(3H)-one] that has higher tubulin binding activity (predicted ΔG _bind = −6.438 kcal/mol and experimental ΔG _bind = −6.628 kcal/mol) than noscapine, but does not significantly change the total extent of the tubulin subunit/polymer ratio. The modes of interaction of amino-noscapine with the binding pocket of tubulin involved three hydrogen bonds and are distinct compared to noscapine which involved only one hydrogen bond. Also the patterns of non-bonded interactions are albeit different between both the lignads. The ‘blind docking’ approach (docking of ligand with different binding sites of a protein and their evaluations) as well as the reasonable accuracy of calculating ΔG _bind using LIE–SGB model constitutes the first evidence that this class of compounds binds to tubulin at a site overlapping with colchicine-binding site or close to it. Our results revealed that amino-noscapine has better anti-tumor activity than noscapine.     

What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2-oxoglutarate dependent Jumonji-C (JmjC) Nϵ-methyl lysine histone demethylases also have N-methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N-methyl arginine demethylation by human KDM4E and compare the results with those reported for N-methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen-bond between the substrate Ser1 and Tyr178. The calculations imply that in either C−H or N−H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N-methyl arginine demethylation, electron transfer occurs via a σ-channel; the transition state for the N−H pathway is ∼10 kcal/mol higher than for the C−H pathway due to the higher bond dissociation energy of the N−H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier-lowering effect on the C−H pathway, by contrast, such EEFs inhibit the N−H activation rate. The overall results imply that KDM4 catalyzed N-methyl arginine demethylation and N-methyl lysine demethylation occur via similar C−H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates.     

Density functional computations of alkynylation of nitrones catalyzed by chiral zinc(II)-complexes

The alkynylation of nitrones catalyzed by chiral zinc(II)-complexes was studied by means of the density functional theory (DFT). All the intermediates and transition states were optimized completely at B3LYP/6-31G(d,p) level. Calculation results confirm that this alkynylation of nitrones was endothermic and the total absorbed energy was about 14 kJ/mol. The formation of the M5 complexes was the rate-determining step and the chirality-limiting step for this alkynylation. The transition states TS3-re involve a H(8)–O(2)–Zn(6)–C(9)–C(14)–N(13)–O(12) 7-membered ring, and thus the transition states TS3-si involve a Zn(6)–C(9)–C(14)–N(13)–O(12) 5-membered ring. The dominant reaction is the attack of nitrones from the re-surface of M4. The reactivity of anti-nitrones was stronger than that of syn-nitrones for zinc-catalyzed alkynylation of nitrones. The dominant reaction channel was cata → TS1b → M1b → M2 → M3b → TS2b → M4b → TS3b1-anti-re → M5b1-anti-re → Pro-R. The dominant products predicted theoretically were of R-chirality, (2R)-N-hydroxy-N-methylpent-3-yn-2-amine. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic Engineering of Caulobacter crescentus for Removal of Cadmium from Water

Hexa-histidine (6His) peptide was inserted to a permissive site of the surface layer (S-layer) protein RsaA of Caulobacter crescentus. The recombinant strain JS4022/p723–6H, expressing RsaA-6His fusion protein was examined for its ability to sequester Cd(II) from the bacterial growth medium. When mixed with 1 ppm CdCl₂, JS4022/p723–6H removed 94.3 ∼ 99.9% of the Cd(II), whereas the control strain removed only 11.4 ∼ 37.0%, depending on experimental conditions. The effective contact time of the cells and Cd(II) was as short as 15 min. When higher concentrations of CdCl₂ were tested, JS4022/p723–6H consistently demonstrated enhanced binding capacity over the control strain. At 15 ppm of Cd(II), each gram of JS4022/p723–6H dry cells retrieved 16.0 mg of Cd(II), comparing to 11.6 mg g⁻¹ achieved by the control strain. This work provides a potential cost-effective solution toward bioremediation of heavy metals from aqueous systems.     

Heparin-immobilized microspheres for the capture of cytokines

The preparation and characterization of heparin-immobilized microspheres which were used to bind acidic fibroblast growth factor (aFGF), vascular endothelial growth factor (VEGF), monocyte chemoattractant protein 1 (MCP-1/CCL2), and regulation upon activation normal T cell express sequence (RANTES/CCL5) is described. These beads were used as trapping agents in microdialysis sampling experiments in a separate study. Both free heparin and a synthesized heparin–albumin conjugate were immobilized onto microspheres and compared for their effectiveness. The heparin–albumin conjugate microspheres exhibited significant nonspecific adsorption which appeared to be due to the albumin content. The prepared heparin-immobilized microspheres were stable for 3 months at 4 °C. A bead-based flow cytometric assay was developed to study the binding capacity and specificity of the heparin-immobilized microspheres to cytokines. These heparin-immobilized microspheres exhibited broad dynamic ranges for binding to the four cytokines (aFGF, 1.0–1,000 ng/mL; VEGF, 0.5–1,000 ng/mL; CCL2, 1.95–1,000 ng/mL; CCL5, 1.95–500 ng/mL). Fast binding kinetics of the cytokines to the heparin-immobilized beads suggests that these beads may be useful as affinity agents in microfluidic flow systems.     

Experimental and Theoretical Investigation of the Proton-Bound Dimer of Lysine

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol^–1) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol^–1, respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol^–1, respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.     

All-electron relativistic calculations on hydrogen atom adsorption onto small copper clusters

An all-electron scalar relativistic calculation on Cu _n H (n = 1–13) clusters has been performed by using density functional theory with the generalized gradient approximation at the PW91 level. Our results reveal that the hydrogen atom prefers to occupy the two fold coordination site for Cu _n H (n = 2, 4–6, 8, 10–13) clusters, the single fold coordination site for Cu _n H (n = 1, 3, 7) and the three fold coordination site for Cu₉H cluster. For all Cu _n H clusters, only the Cu₁₁ structure in Cu₁₁H is distorted obviously. After adsorption, the Cu–Cu bond is strengthened and the Cu–H bond of odd-numbered Cu _n H clusters is relatively stronger than that of adjacent even-numbered Cu _n H clusters. The Cu–Cu bond-length and Cu–H bond-length for all Cu _n H clusters of our work are significantly shorter than those of previous work. This discrepancy can be explained in terms of the scalar relativistic effect. The most favorable adsorption between small copper clusters and hydrogen atom takes place in the case that hydrogen atom is adsorbed onto an odd-numbered pure Cu _n cluster and becomes Cu _n H cluster with even number of valence electrons. The odd–even alteration of magnetic moments is observed in Cu _n H clusters and may provide the material with tunable code capacity of “0” and “1” by adsorbing a hydrogen atom onto odd- or even-numbered copper clusters.