Trans Arrangement Research Articles

2D holodirected lead(II) halide coordination polymers based on rigid N,N′-bis(4-pyridylmethylidyne) phenylene-1,4-diamine ligand: Syntheses, crystal structures, NBO studies and luminescence properties

To investigate the influence of the different halides on coordination parameters and exploitable properties, a series of isostructural lead(II) coordination polymers, namely, [Pb(µ-L)(µ-X)2]n (X=Cl (1), Br (2), I (3)) based on rigid ligand N,N′-bis(4-pyridylmethylidyne) phenylene-1,4-diamine (L) were synthesized successfully. The structures of these compounds were elucidated by FT-IR spectroscopy, and single crystal X-ray diffraction crystallography. Single crystal X-ray analyses revealed that these compounds have a 2D net structure containing PbX4N2 centers in which lead(II) ions bridged by both halide anions and L ligands in trans arrangement. Moreover, natural bond orbital (NBO) calculations were employed to obtain atomic charge distributions, hybridizations and the strength of interactions between lead ion and halides via second-order perturbation energies. All materials display a blue luminescence in the solid state at room temperature. Also, there is an obvious relationship between the NBO findings and observed red shift order in these compounds. Finally the results of thermal behavior studies of compounds 1–3 have been discussed.

Ferromagnetic Coupling in the Heterospin Bis-Catecholato-Manganese(IV) Complex with Pyridine Substituted by Nitronyl-nitroxide.

A new bis(3,6-di-tert-butyl-catecholato)manganese complex with two 4-NIT-Py ligands was synthesized and characterized [4-NIT-Py = pyridine substituted at position 4 with nitronyl-nitroxide radical, 2-(pyridin-4-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl]. X-ray diffraction indicated an octahedral environment of the manganese atom with a trans arrangement of ligands. Bonds lengths in the inner coordination core of the metal and in the chelate cycles that are representative of the charge distribution between the metal and ligands displayed a Mn(IV)(Cat2-)2 charge distribution. Variable-temperature magnetic susceptibility measurements detected intramolecular ferromagnetic coupling between the Mn(IV) S = 3/2 spins and spins of nitronyl-nitroxyls and intermolecular ferromagnetic interactions of spins of adjacent nitronyl-nitroxide fragments in a chain of molecules at low temperatures. The last phenomenon is revealed by short contacts between nitronyl-nitroxide radicals of adjacent complex molecules.

Cobalt(II) chloride adducts with acetonitrile, propan-2-ol and tetrahydrofuran: considerations on nuclearity, reactivity and synthetic applications.

High-spin cobalt(II) complexes are considered useful building blocks for the synthesis of single-molecule magnets (SMM) because of their intrinsic magnetic anisotropy. In this work, three new cobalt(II) chloride adducts with labile ligands have been synthesized from anhydrous CoCl2, to be subsequently employed as starting materials for heterobimetallic compounds. The products were characterized by elemental, spectroscopic (EPR and FT-IR) and single-crystal X-ray diffraction analyses. trans-Tetrakis(acetonitrile-κN)bis(tetrahydrofuran-κO)cobalt(II) bis[(acetonitrile-κN)trichloridocobaltate(II)], [Co(C2H3N)4(C4H8O)2][CoCl3(C2H3N)]2, (1), comprises mononuclear ions and contains both acetonitrile and tetrahydrofuran (thf) ligands, The coordination polymer catena-poly[[tetrakis(propan-2-ol-κO)cobalt(II)]-μ-chlorido-[dichloridocobalt(II)]-μ-chlorido], [Co2Cl4(C3H8O)4], (2'), was prepared by direct reaction between anhydrous CoCl2 and propan-2-ol in an attempt to rationalize the formation of the CoCl2-alcohol adduct (2), probably CoCl2(HOiPr)m. The binuclear complex di-μ-chlorido-1:2κ4Cl:Cl-dichlorido-2κ2Cl-tetrakis(tetrahydrofuran-1κO)dicobalt(II), [Co2Cl4(C4H8O)4], (3), was obtained from (2) after recrystallization from tetrahydrofuran. All three products present cobalt(II) centres in both octahedral and tetrahedral environments, the former usually less distorted than the latter, regardless of the nature of the neutral ligand. Product (2') is stabilized by an intramolecular hydrogen-bond network that appears to favour a trans arrangement of the chloride ligands in the octahedral moiety; this differs from the cis disposition found in (3). The expected easy displacement of the bound solvent molecules from the metal coordination sphere makes the three compounds good candidates for suitable starting materials in a number of synthetic applications.

Pseudohalides regulated diverse helicity in copper(II) coordination polymers derived from a bis(aminoethoxy) ligand

This paper reports the syntheses and structural characterization of three new Cu(II) coordination polymers, namely [Cu(BAEE)(N3)2]∝ (1), [Cu(BAEE)(NCO)2]∝ (2) and [Cu(BAEE)(NCS)2]∝ (3), where BAEE is 1,2-bis(2-aminoethoxy)ethane. Compound 1 is a one-dimensional (1D) single-stranded normal helical structure, while compounds 2 and 3 are extraordinary single-stranded meso-helical polymers. The influence of pseudohalides in these systems is observed as the azide ions are cis coordinated in 1 and the thiocyanate ions are trans coordinated in 3, while alternate metal centers are either cis or trans coordinated with cyanate ions in 2. These geometrical preferences play a crucial role in the diverse helicity in these chain structures, where the cis arrangement (in 1) favors a uniform helicity in the structure and the trans arrangement (in 2 and 3) of the pseudohalide ligands around the copper(II) center brings meso-helicity in the chains. The energetic difference of the cis/trans isomers and the formation energies of the different assemblies using DFT calculations suggest that the different H-bond acceptor ability of the thiocyanate ion determines the different architecture observed in 3. Our results highlight how the geometrical preferences of the pseudohalides around the copper(II) center influence the helical diversity in these systems and thereby provide a clue toward the development of uncommon coordination polymers with amazing meso-helical character.

Synthesis, crystal structure, and luminescent properties of silver complexes with 2-methylquinoline

The complexes [AgL2(NO3)] (I) and [AgL2(CH3SO3)] · H2O (II) (L is 2-methylquinoline, C10H9N) have been synthesized and structurally characterized by single-crystal X-ray diffraction. Crystals of I are monoclinic, space group P21/n, a = 9.296(1) A, b = 13.495(1) A, c = 14.931(1) A, β = 95.06(1)°, V = 1865.8(3) A3, ρcalc = 1.624 g/cm3, Z = 4. Crystals of II are monoclinic, space group P21/n, a = 13.147(1) A, b = 11.767(1) A, c = 13.814(1) A, β = 96.06(1)°, V = 2124.3(3) A3, ρcalc = 1.599 g/cm3, Z = 4. Compounds I and II are composed of discrete complexes of similar structure but with different orientation of the methyl groups of ligand L (trans and cis arrangement, respectively). Both anions, NO3- and CH3SO3- function as a chelating weakly bound ligand for the Ag+ ion. The presence of water molecules in II is favorable for the formation of dimeric supramolecular moieties between the centrosymmetrically arranged Ag+ complexes with 2-methylquinoline. The luminescence spectra of solid complexes I and II showed a bathochromic shift as compared to the spectrum of L in acetonitrile. Complexes I and II have been characterized by 1H and 13C{H} NMR spectra in CD3CN.

The properties of the Lewis acid-base complexes of boron trifluoride with some carbon dioxide analogues. An ab initio study

The properties of nine binary Lewis acid-base complexes, formed between boron trifluoride, on the one hand, and the carbon dioxide analogues XCY (X, Y = O, S, Se) on the other, have been investigated by means of ab initio calculations. The properties of most interest are the structures, the interaction energies, the vibrational spectra and the natural orbital population changes. The structures of the complexes bound through either a sulphur or a selenium atom are remarkably similar, and feature a FB … XC fragment in a trans arrangement, with FB … X and B … XC angles close to 90°. The adducts bound through oxygen have quite different structures, with a B … OC angle close to 150° in the case of BF3·OCO and with linear B … OCS and B … OCSe moieties in the other two cases. The binding energies of all nine complexes span a very narrow range, and are all less than 10 kJ mol−1. The changes of the intramolecular BF, XC and CY bond lengths are small, but they vary in a systematic way with the strength of interaction. The wavenumber shifts of the modes of the BF3 and XCY fragments are also fairly insignificant, except for the symmetric bending mode of the BF3 molecule, where the shifts are found to be in the range from −20 to −40 cm−1. The similarities and differences in the properties of the three families of adducts have been rationalized by reference to the redistribution of the natural orbital populations resulting from complex formation.

Synthesis, crystal structures, EPR and DFT studies of first row transition metal complexes of lignin model compound ethylvanillin

The transition metal complexes of ethylvanillin [Mn(L)2(H2O)2] (1), [Co(L)2(H2O)2] (2), [Ni(L)2(H2O)2] (3), and [Zn(L)2(H2O)2] (4) have been synthesized. The geometric and electronic structure of 1, 2, 3 and 4 has been solved by X-ray diffraction analysis and EPR spectroscopy. They are octahedral complexes with a cis arrangement of the two water molecules. All the structures were calculated by DFT methods at the level of theory B3P86/6-311g. The EPR spectra of 1 are isotropic both at 298 and 77K with g values at 2.034±0.010 and 2.040±0.010, respectively indicating Mn(II) ion (3d5) with a S=5/2 spin. 1 shows a hyperfine structure with six strong absorptions, corresponding to the |−1/2, m>→|1/2, m> ‘allowed’ transitions (ΔM=±1, Δm=0), and five pairs of ‘forbidden’ absorptions (ΔM=±1, Δm=±1), between the Δm=0 hyperfine transitions in an organic solvent such as DMF, DMSO and CH3CN. EPR spectroscopy and DFT calculations suggest that in the temperature range 77–298K 2 presents a high-spin S=3/2 state, whereas the low-spin state S=1/2 begins to be populated at temperatures higher than 77K(liquid nitrogen temperature). In 3, the weak signal due to a small amount of an octahedral Ni(III) complex (NiL3), is characterized by a rhombic spectrum. DFT simulations on 4 indicate that the octahedral structure with a cis arrangement of the two water ligands is more stable than the octahedral one with a trans arrangement and the tetrahedral geometry.

Synthesis, X-ray structures, and characterization of hexafluoro-iso-propoxide group 3 and lanthanide precursors

A series of hydrated hexafluoro-iso-propoxide (hfip) lanthanide complexes was synthesized from the amide-alkoxide exchange reaction of the lanthanide bis-trimethylsilyl amide dissolved in toluene and an excess amount of H-hfip. The products were isolated and identified by single crystal X-ray diffraction as: [cis-(H2O)2(hfip)2Ln(μ-hfip)]2 (Ln=Ce, Pr, Nd, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Y), [trans-(H2O)2(hfip)2Sc(μ-hfip)]2 (Sc), [(H2O)2(hfip)2La2(μ-hfip)3(μ3-OH)]2 (La-OH), and [(H2O)(hfip)2Sc(μ-hfip)(μ-OH)(μ3-OH)Sc(H2O)(hfip)]2 (Sc-OH). All species were found to have bound H2O molecules thought to be present in the hfip. For the non-oxo species, dinuclear species were formed with one bridging and two terminal hfip ligands. The waters were cis-oriented for all samples but the smallest derivative, Sc, where they were located in trans arrangement. Oxo species were formed by ‘aged’ hfip and generated tetranuclear species (La-OH and Sc-OH) that possessed different ligand sets. Initial efforts to determine these compounds utility for LnF3 nanomaterial production were undertaken using amine solvent in solvothermal (SOLVO) or solution precipitation (SPPT) routes. LnF3 phases were noted but often this was mixed with the Ln(O,F) or Ln2O3 phases.

Unusual traits of cis and trans-2,3-dibromo-1,1-dimethylindane on the way from 1,1-dimethylindene to 2-bromo-, 3-bromo-, and 2,3-dibromo-1,1-dimethylindene.

Do not rely on the widely accepted rule that vicinal, sp3-positioned protons in cyclopentene moieties should always have more positive 3J NMR coupling constants for the cis than for the trans arrangement: Unrecognized exceptions might misguide one to wrong stereochemical assignments and thence to erroneous mechanistic conclusions. We show here that two structurally innocent-looking 2,3-dibromo-1,1-dimethylindanes violate the rule by means of their values of 3J(cis) = 6.1 Hz and 3J(trans) = 8.4 Hz. The stereoselective formation of the trans diastereomer from 1,1-dimethylindene was improved with the tribromide anion (Br3−) as the brominating agent in place of elemental bromine; the ensuing, regiospecific HBr elimination afforded 3-bromo-1,1-dimethylindene. The addition of elemental bromine to the latter compound, followed by thermal HBr elimination, furnished 2,3-dibromo-1,1-dimethylindene, whose Br/Li interchange reaction, precipitation, and subsequent protolysis yielded only 2-bromo-1,1-dimethylindene.

Oxidorhenium(V) Complexes with Tetradentate Iminophenolate Ligands: Influence of Ligand Flexibility on the Coordination Motif and Oxygen-Atom-Transfer Activity.

The synthesis of oxidorhenium(V) complexes 1-3 coordinated by tetradentate iminophenolate ligands H2L1-H2L3 bearing backbones of different rigidity (alkyl, cycloalkyl, and phenyl bridges) allows for the formation of distinct geometric isomers, including a symmetric trans-oxidochlorido coordination motif in complex 3. The complex employing a cycloalkyl-bridged ligand (2) of intermediate rigidity exhibits an interesting solvent- and temperature-dependent equilibrium between a symmetric (trans) isomer and an asymmetric (cis) isomer in solution. The occurrence of a symmetric isomer for 2 and 3 is confirmed by single-crystal X-ray diffraction analysis. Chlorido abstraction from 2 with AgOTf yields the corresponding cationic complex 2a, which does not exhibit an isomeric equilibrium in solution but adopts the isomeric form predominant for 2 in a given solvent. All complexes were, furthermore, employed in three benchmark oxygen-atom-transfer (OAT) reactions, namely, the reduction of perchlorate, the epoxidation of cyclooctene, and OAT from dimethyl sulfoxide (DMSO) to triphenylphosphane (PPh3), to assess the influence of the isomeric structure on the reactivity in these reactions. In perchlorate reduction, a clear structural influence was observed, where the trans arrangement in 3 led to the complete absence of activity. In the epoxidation reaction, all complexes led to comparable epoxide yields, albeit higher catalytic activity but lower overall stability of the catalysts with a trans arrangement was observed. In OAT from DMSO to PPh3, also a clear structural dependence was observed, where the trans complex 3 led to full phosphane conversion with an excess of oxidant, while the cis compound 1 was completely inactive.

Crystal structure of new carboxylate phosphabetaines and phosphonium salts conjugated with them

Earlier unknown crystalline forms of three carboxylate phosphabetaines and conjugated with them phosphonium salts differing by β substituent with respect to the carboxylate group were studied. The structure of studied compounds in crystal is determined by intermolecular electrostatic interactions. This leads to the trans arrangement of the carboxylate and the phosphonium groups.

Synthesis and structural characterization of organotin(IV) complexes with ferrocenyldithiophosphonate ligands

The reaction of ammonium salts of benzylferrocenyldithiophosphonate ligands [NH4][S2P(OR)(Fc)] [R = Bz (1), 4-(iPr)-Bz (2), 4-(tBu)-Bz (3), 4-(Ph)-Bz (4), 3-(OBz)-Bz (5); Bz = benzyl, Fc = ferrocenyl] with organotin(IV) chlorides Ph2SnCl2, nBu2SnCl2 and Ph3SnCl, gave the corresponding organotin(IV) benzylferrocenyldithiophosphonates [Ph2Sn{S2P(OR)(Fc)}2] [R = Bz (6), 4-(iPr)-Bz (7), 4-(tBu)-Bz (8), 4-(Ph)-Bz (9), 3-(OBz)-Bz (10)], [nBu2Sn{S2P(OR)(Fc)}2] [R = Bz (11), 4-(Ph)-Bz (12)] and [Ph3Sn{S2P(OBz)(Fc)}] (13). Compounds 6–13 were characterized by elemental analyses, infrared, 1H, 13C{1H},31P{1H} and 119Sn{1H}NMR spectroscopy and ESI mass spectrometry, while complexes 6, 11 and 13 were also characterized by single-crystal X-ray diffraction studies. The dithiophosphonate ligands display an anisobidentate coordination mode upon interaction with the metal center. The solid-state structures of the disubstituted complexes 6 and 11 exhibit a trans arrangement for the ferrocenyl groups from the dithiophosphonate ligands.

Electrocatalytic Hydrogen Production by a Nickel(II) Complex with a Phosphinopyridyl Ligand

AbstractA novel nickel(II) complex [Ni(L)2Cl]Cl with a bidentate phosphinopyridyl ligand 6‐((diphenylphosphino)methyl)pyridin‐2‐amine (L) was synthesized as a metal‐complex catalyst for hydrogen production from protons. The ligand can stabilize a low Ni oxidation state and has an amine base as a proton transfer site. The X‐ray structure analysis revealed a distorted square‐pyramidal NiII complex with two bidentate L ligands in a trans arrangement in the equatorial plane and a chloride anion at the apex. Electrochemical measurements with the NiII complex in MeCN indicate a higher rate of hydrogen production under weak acid conditions using acetic acid as the proton source. The catalytic current increases with the stepwise addition of protons, and the turnover frequency is 8400 s−1 in 0.1 m [NBu4][ClO4]/MeCN in the presence of acetic acid (290 equiv) at an overpotential of circa 590 mV.

Electrocatalytic Hydrogen Production by a Nickel(II) Complex with a Phosphinopyridyl Ligand.

A novel nickel(II) complex [Ni(L)2 Cl]Cl with a bidentate phosphinopyridyl ligand 6-((diphenylphosphino)methyl)pyridin-2-amine (L) was synthesized as a metal-complex catalyst for hydrogen production from protons. The ligand can stabilize a low Ni oxidation state and has an amine base as a proton transfer site. The X-ray structure analysis revealed a distorted square-pyramidal Ni(II) complex with two bidentate L ligands in a trans arrangement in the equatorial plane and a chloride anion at the apex. Electrochemical measurements with the Ni(II) complex in MeCN indicate a higher rate of hydrogen production under weak acid conditions using acetic acid as the proton source. The catalytic current increases with the stepwise addition of protons, and the turnover frequency is 8400 s(-1) in 0.1 m [NBu4 ][ClO4 ]/MeCN in the presence of acetic acid (290 equiv) at an overpotential of circa 590 mV.

Structural Preferences in Phosphanylthiolato Platinum(II) Complexes.

Invited for this month's cover picture are the groups of Prof. Alfonso Polo and Dr. Albert Poater at the Universitat de Girona, as well as their collaborators from the Universitat Autònoma de Barcelona and the Institute of Chemical Research of Catalonia. The cover picture shows phosphanylthiolate ligand coordination on a platinum(II) center to give only the bischelate cis ‐P,P isomer when the ligand/Pt ratio is 2, whereas a trinuclear unexpected complex is achieved with a ligand/Pt ratio of 1. Here, the synthesis and structural determination is combined with density functional theory (DFT) calculations to rationalize the reaction mechanistically and through conceptual DFT. The exciting point of this study is that it opens the door to test new experimental pathways to monitor the preferred cis or trans arrangement of bidentate ligands to platinum. (Legend: H‐white, C‐black, P‐purple, S‐yellow, Cl‐green, Pt‐blue.) For more details, see the Full Paper on p. 51 ff.

Mechanistic investigation of trimethylamine-N-oxide reduction catalysed by biomimetic molybdenum enzyme models.

In this paper, we report a theoretical investigation of the reduction reaction mechanism of Me3NO using molybdenum containing systems that are functional and structural analogues of trimethylamine N-oxide reductase mononuclear molybdenum enzyme. The reactivity of the monooxomolybdenum(IV) benzenedithiolato complex and its derivatives to carbamoyl (t-BuNHCO) and acylamino (t-BuCONH) substituents on the benzene rings in both cis and trans arrangements was explored. The calculated energy profiles describing the steps of two mechanisms of attack considered viable (named cis- and trans-attack) by the Me3NO substrate at cis and trans positions with respect to the oxo ligand show that the attack on cis is energetically more favourable than the attack on trans. Along the pathway for the cis-attack the first step of the reaction, that is rate-determining for all the studied compounds, is the approach of the substrate to the Mo centre in cis to the oxo ligand that causes a distortion of the initial square-pyramidal geometry of the complex. The reaction steps involved in the trans position attack were also explored. Calculations confirm that, as previously suggested, the introduction of ligands able to form intramolecular NH···S hydrogen bonds accelerates the reduction of the Me3NO substrate and contributes to the tuning of the reactivity of molybdoenzyme models.

The impact of modular substitution on crystal packing: the tale of two ureas

A small library of 13 (3a–m) compounds with modular positioning of iodide and urea/thiourea groups was synthesized in excellent yields in a single step synthetic protocol. The existence of the anticipated (thio)urea derivatives was unambiguously established using a combination of 1–2D NMR spectroscopy, ESI-MS and single crystal X-ray diffraction studies. These (thio)urea compounds were classified into four classes as follows: a) mono-substituted urea, b) di-substituted urea, c) di-substituted thiourea and d) electronically tailored di-substituted thiourea. The changes in molecular conformation and crystal packing due to the change in the relative positioning of the iodo group at the phenyl ring attached to one of the N atoms and different substituents at other N atoms in urea and thiourea derivatives have been discussed. The urea derivatives, in general, display the chain association through one-dimensional three-centered N–H⋯O hydrogen bonding interactions due to the trans–trans orientation of both NH protons with respect to the carbonyl group, whereas the thiourea compounds exhibit a centrosymmetric dimeric assembly via the complementary N–H⋯S interactions because of the trans–cis arrangement of the NH protons leading to either a helical or a sheet pattern. The presence of a nitro group at the para position of the thiourea derivative leads to trans–trans arrangement of both NH protons with respect to the thiocarbonyl groups, thus yielding a chain assembly through one-dimensional three-centered N–H⋯S interactions similar to urea derivatives. Associations of these chains or sheets in urea/thiourea derivatives through halogen bonding interactions (hal⋯hal, hal⋯π, hal⋯S etc.) generate a 2D assembly.

A new route for the synthesis of phosphate esters: 2,2'-[benzene-1,2-diylbis(oxy)]bis(5,5-dimethyl-1,3,2-dioxaphosphinane) 2,2'-dioxide.

Podand-type ligands are an interesting class of acyclic ligands which can form host-guest complexes with many transition metals and can undergo conformational changes. Organic phosphates are components of many biological molecules. A new route for the synthesis of phosphate esters with a retained six-membered ring has been used to prepare 2,2'-[benzene-1,2-diylbis(oxy)]bis(5,5-dimethyl-1,3,2-dioxaphosphinane) 2,2'-dioxide, C6H4{O[cyclo-P(O)OCH2CMe2CH2O]}2 or C16H24O8P2, (1), 2-[(2'-hydroxybiphenyl-2-yl)oxy]-5,5-dimethyl-1,3,2-dioxaphosphinane 2-oxide, [cyclo-P(O)OCH2CMe2CH2O](2,2'-OC6H4-C6H4OH), (2), and oxybis(5,5-dimethyl-1,3,2-dioxaphosphinane) 2,2'-dioxide, O[cyclo-P(O)OCH2CMe2CH2O]2, (3). Compound (1) is novel, whereas the results for compounds (2) and (3) have been reported previously, but we record here our results for compound (3), which we find are more precise and accurate than those currently reported in the literature. In (1), two cyclo-P(O)OCH2CMe2CH2O groups are linked through a catechol group. The conformations about the two catechol O atoms are quite different, viz. one C-C-O-P torsion angle is -169.11 (11)° and indicates a trans arrangement, whereas the other C-C-O-P torsion angle is 92.48 (16)°, showing a gauche conformation. Both six-membered POCCCO rings have good chair-shape conformations. In both the trans and gauche conformations, the catechol O atoms are in the axial sites and the short P=O bonds are equatorially bound.

New trans-dichloropalladium(II) complexes of 7-azaindole: Crystal and molecular structures, FT-IR, FT-Raman and DFT studies

New complexes of Pd(II) with 7-azaindole (7AI), trans-[PdCl2(7AI)2] (1) and 1⋅DMF were synthesized. A single crystal X-ray diffraction of 1⋅DMF has shown that the complex crystallizes in the monoclinic system (space group P21/n with a = 7.65743 (13), b = 11.9426 (2), c = 13.3870 (2) Å, β = 91.2583 (16)°, V = 1223.94 (3) (Å3) and Z = 2). Palladium is bound to two pyridine nitrogen atoms of the 7AI ligands and to two chloride ions, in a square-planar trans arrangement. The FT-Raman and infrared spectra of 1 were recorded in the 3600–50 cm−1 range. The molecular structure of 1 was confirmed by elemental analysis and vibrational spectra. Comprehensive theoretical calculations (including the optimized structural parameters, the HOMO–LUMO energy gap, harmonic frequencies and vibrational intensities) were performed for 1 by using the B3LYP and PBE0 density functional methods with the 6-311G++(d,p)/LanL2DZ basis sets. A natural bond orbital (NBO) analysis was carried out. A detailed assignment of the experimental vibrational spectra was performed on the basis of the potential energy distribution (PED). The Pd–Cl stretching vibrations were assigned to bands at 339 (IR) and 292 cm−1 (Raman). The bands at 273 and 260 cm−1 (IR) and 195 cm−1 (Raman) correspond to the Pd–N(pyridine) stretching vibrations. The unequivocal assignment of these modes is necessary for the structural characterization of other Pd(II) and Pt(II) complexes with the pyridine-based ligands, by using vibrational spectroscopy.

Aldehydic nature and conformation of 3,6-anhydro-L-galactose monomer

We investigated the aldehydic nature and conformation of 3,6-anhydro-L-galactose (L-AnG) by using enzymes that bind L-AnG in a reactive conformation. We found that L-AnG, but not L-galactose, can be oxidized by E. coli L-lactaldehyde dehydrogenase (Ec_LADH); this observation suggests that L-AnG is an aldehyde belonging to the a-hydroxyaldehyde family. Because the native enzyme that catalyzes oxidation of L-AnG to its carboxylate is LAnG dehydrogenase (L-AnGDH), we compared the crystal structure and amino-acid sequences of Ec_LADH with those of L-AnGDHs. This analysis revealed that the two oxygen atoms in the a-hydroxyaldehyde moiety of L-AnG are essential for the reactions of Ec_LADH and LAnGDHs. A chemical database search indicated that two configurations of L-AnG are possible: a trans arrangement in which C-2 and C-5 hydroxyl groups are on the opposite side and a cis arrangement in which these groups are on the same side. Manual docking of the two forms of L-AnG into the active site of Pseudoalteromonas atlantica LAnGDH (Pa_L-AnGDH) revealed that only the trans LAnG configuration can be fitted into the active site of Pa_L-AnGDH. The identification of trans L-AnG suggests the existence of three L-AnG conformations: bicyclic pyranose, opened pyranose, and open-chain aldehyde. The conformation of L-AnG monomer (open-chain aldehyde) differs from that in agarose (bicyclic pyranose) or agarobiose (opened pyranose) because a five-membered anhydro ring is free to move and can find its most stable conformation. This study validates the assumption of trans-type open-chain aldehyde conformation of L-AnG that was applied in our previous studies.