C2v Geometry Research Articles

Influence of proline and hydroxyproline as antimicrobial and anticancer peptide components on the silver(I) ion activity: structural and biological evaluation with a new theoretical and experimental SAR approach.

Silver(I) complexes with proline and hydroxyproline were synthesized and structurally characterized and crystal structure analysis shows that the formulas of the compounds are {[Ag2(Pro)2(NO3)]NO3}n (AgPro) (Pro = L-proline) and {[Ag2(Hyp)2(NO3)]NO3}n (AgHyp) (Hyp = trans-4-hydroxy-L-proline). Both complexes crystallize in the monoclinic lattice with space group P21 with a carboxylate bidentate-bridging coordination mode of the organic ligands Pro and Hyp (with NH2+ and COO- groups in zwitterionic form). Both complexes have a distorted seesaw (C2v) geometry around one silver(I) ion with τ4 values of 58% (AgPro) and 51% (AgHyp). Moreover, the results of spectral and thermal analyses correlate with the structural ones. 1H and 13C NMR spectra confirm the complexes species' presence in the DMSO biological testing medium and their stability in the time range of the bioassays. In addition, molar conductivity measurements indicate complexes' behaviour like 1 : 1 electrolytes. Both complexes showed higher or the same antibacterial activity against Bacillus cereus, Pseudomonas aeruginosa and Staphylococcus aureus as AgNO3 (MIC = 0.063 mM) and higher than silver(I) sulfadiazine (AgSD) (MIC > 0.5 mM) against Pseudomonas aeruginosa. In addition, complex AgPro exerted a strong cytotoxic effect against the tested MDA-MB-231 and Jurkat cancer cell lines (IC50 values equal to 3.7 and 3.0 μM, respectively) compared with AgNO3 (IC50 = 6.1 (5.7) μM) and even significantly higher selectivity than cisplatin (cisPt) against MDA-MB-231 cancer cell lines (SI = 3.05 (AgPro); 1.16 (cisPt), SI - selectivity index). The binding constants and the number of binding sites (n) of AgPro and AgHyp complexes with bovine serum albumin (BSA) were determined at four different temperatures, and the zeta potential of BSA in the presence of silver(I) complexes was also measured. The in ovo method shows the safety of the topical and intravenous application of AgPro and AgHyp. Moreover, the complexes' bioavailability was verified by lipophilicity evaluation from the experimental and theoretical points of view.

Slow magnetic relaxation in a heteroleptic anilate-based DyIII metal-organic framework.

Novel heteroleptic anilate-based lanthanide MOFs (LnIII = Tb, Dy, Ho) have been obtained under hydrothermal conditions by the ancillary ligand synthetic strategy. These structurally isomorphous species contain octacoordinated LnIII ions with coordination polyhedra approaching an ideal D2d symmetry, best described by a distorted biaugmented trigonal prismatic C2v geometry. In the whole series, only the Dy-MOF exhibits SMM behaviour.

Comment on "Theoretical study of the NO3 radical reaction with CH2ClBr, CH2ICl, CH2BrI, CHCl2Br, and CHClBr2" by I. Alkorta, J. M. C. Plane, J. Elguero, J. Z. Dávalos, A. U. Acuña and A. Saiz-Lopez, Phys. Chem. Chem. Phys. 2022, 24, 14365.

This comment addresses a systematic error in the potential energy surfaces of the title reactions presented in the original article by Alkorta et al. The NO3 radical has D3h symmetry in the electronic ground state while the M08HX functional employed in the original article predicts an incorrect C2v geometry and energy. By combining thermodynamic data for the OH + HNO3 → H2O + NO3 reaction with spectroscopic data and results from M08HX calculations on HNO3, H2O and the OH radical, the ground state NO3 radical energy is estimated to be 37 kJ mol-1 lower than reported for the C2v geometry.

CO activation by the heterobinuclear transition metal-iron clusters: A photoelectron spectroscopic and theoretical study

Spectroscopic characterization of CO activation on multiple metal-containing catalysts remains an important and challenging goal for identifying the structure and nature of active site in many industrial processes such as Fischer-Tropsch chemistry and alcohol synthesis. Here, we use mass-selected photoelectron velocity-map imaging spectroscopy and quantum chemical calculations to study the reactions of CO molecules with several heterobinuclear transition metal-iron clusters M–Fe (M = Ti, V, Cr). The mass spectra reveal the favorable formation of MFe(CO)4− with relatively high thermodynamic stability. The MFe(CO)4− (M = Ti, V, Cr) complexes are established to have a metal–Fe bonded M–Fe(CO)4 structure with C3v geometry. While the positive charge and unpaired electrons are mainly located on the M atom, the natural charge of Fe(CO)4 is about −2e. The MFe(CO)4− (M = Ti, V, Cr) can be seen as being formed via the interactions between the M+ fragment and the [Fe(CO)4]2− core, which satisfies the 18-electron rule. The CO molecules are remarkably activated in these MFe(CO)4−. These results shed insight into the structure–reactivity relationship of heterobinuclear transition metal carbonyls and would have important implications for understanding of CO activation on alloy surfaces.

Ultrafast imaging of spontaneous symmetry breaking in a photoionized molecular system

The Jahn-Teller effect is an essential mechanism of spontaneous symmetry breaking in molecular and solid state systems, and has far-reaching consequences in many fields. Up to now, to directly image the onset of Jahn-Teller symmetry breaking remains unreached. Here we employ ultrafast ion-coincidence Coulomb explosion imaging with sub-10 fs resolution and unambiguously image the ultrafast dynamics of Jahn-Teller deformations of {{rm{CH}}}_{4}^{+} cation in symmetry space. It is unraveled that the Jahn-Teller deformation from C3v to C2v geometries takes a characteristic time of 20 ± 7 fs for this system. Classical and quantum molecular dynamics simulations agree well with the measurement, and reveal dynamics for the build-up of the C2v structure involving complex revival process of multiple vibrational pathways of the {{rm{CH}}}_{4}^{+} cation.

Mechanisms of CO2 reduction into CO and formic acid on Fe (100): a DFT study

Understanding the mechanism of CO2 reduction on iron is crucial for the design of more efficient and cheaper iron electrocatalyst for CO2 conversion. In the present study, we have employed spin-polarized density functional theory calculations within the generalized gradient approximation (DFT-GGA) to elucidate the mechanism of CO2 reduction into carbon monoxide and formic acid on the Fe (100) facet. We also sort to understand the transformations of the other isomers of adsorbed CO2 on iron as earlier mechanistic studies are centred on the transformations of the C2v geometry alone and not the other possible conformations i.e., flip-C2v and Cs modes. Two alternative reduction routes were considered i.e., the direct CO2 dissociation against the hydrogen-assisted CO2 transformation through formate and carboxylate into CO and formic acid. Our results show that CO2 in the C2v mode is the precursor to the formation of both products i.e., CO and formic acid. Both the formation and transformation of CO2 in the Cs and flip-C2v is challenging kinetically and thermodynamically compared to the C2v mode. The formic acid formation is favoured over CO via the reverse water gas shift reaction mechanism on Fe (100). Both formic acid formation and CO formation will proceed via the carboxylate intermediate since formate is a stable intermediate whose transformation into formic acid is challenging both kinetically and thermodynamically.Graphic abstract

Optical, third order non-linear optical and electrochemical properties of dipolar, centrosymmetric and C2v organoimido polyoxometalate derivatives.

A family comprising seven arylimido-polyoxometalate (POM) hybrid chromophores (three of which are new), with linear dipolar, C2v and linear centrosymmetric geometries have been synthesised and studied by electronic absorption spectroscopy, electrochemistry, Z-scans (two photon absorption, TPA) and computation (DFT/TD-DFT). These reveal that POM acceptor units are an effective basis for TPA materials: the centrosymmetric bis-POM chromophores produce significant cross sections (δ up to 82 GM) from a single aryl bridge, a similar performance to larger dipolar π-systems combining carbazole or diphenylamino donors with the imido-POM acceptor. DFT/TD-DFT calculations indicate strong communication between POM and organic components is responsible for the linear and non-linear optical behaviour of these compounds, while electrochemical measurements reveal class II mixed valence behaviour resulting from an interplay of through-bond and through-space effects.

Beyond Born-Oppenheimer constructed diabatic potential energy surfaces for F + H2 reaction.

First principles based beyond Born-Oppenheimer theory has been implemented on the F + H2 system for constructing multistate global diabatic Potential Energy Surfaces (PESs) through the incorporation of Nonadiabatic Coupling Terms (NACTs) explicitly. The spin-orbit (SO) coupling effect on the collision process of the F + H2 reaction has been included as a perturbation to the non-relativistic electronic Hamiltonian. Adiabatic PESs and NACTs for the lowest three electronic states (12A', 22A', and 12A″) are determined in hyperspherical coordinates as functions of hyperangles for a grid of fixed values of the hyperradius. Jahn-Teller (JT) type conical intersections between the two A' states translate along C2v and linear geometries in F + H2. In addition, A' and A″ states undergo Renner-Teller (RT) interaction at collinear configurations of this system. Both JT and RT couplings are validated by integrating NACTs along properly chosen contours. Subsequently, we have solved adiabatic-to-diabatic transformation (ADT) equations to evaluate the ADT angles for constructing the diabatic potential matrix of F + H2, including the SO coupling terms. The newly calculated diabatic PESs are found to be smooth, single-valued, continuous, and symmetric and can be invoked for performing accurate scattering calculations on the F + H2 system.

Spin-polarized cation monovacancies in wurtzite structure semiconductors: first-principles study

We study spin-polarized cation vacancies in wurtzite structure semiconductors (BeO, ZnO, ZnS, CdS, BN, AlN, GaN and GaP) by using first-principles calculations based on the density functional theory. We find that C3v geometries are the most stable and are spin-polarized. Two majority spin electrons occupying the defect E level lead to the magnetic moment of 2 μB in the case of II–VI semiconductors. On the contrary, in the case of III–V semiconductors, three majority spin electrons occupying the defect E and A1 levels induce the magnetic moment of 3 μB. The spin polarization of cation vacancies in oxides and nitrides are found to be stable compared with other cation vacancies in II–VI and III–V semiconductors, respectively. We clarify that the effect of the symmetry lowering from C3v to Cs is small and thus confirm that the spin polarized C3v geometries are the most stable.

The unusual symmetry of hexafluoro-o-xylene-A microwave spectroscopy and computational study.

The rotational constants and quartic centrifugal distortion coefficients of hexafluoro-o-xylene were precisely derived from the 8 GHz to 18 GHz gas phase microwave spectrum. In addition, the rotational constants of all singly substituted 13C isotopologues were determined. Instead of the intuitively expected symmetry of C2v, as in o-xylene, calculations with a variety of methods (B3LYP, CAM-B3LYP, ωB97XD, MP2, and coupled-cluster singles, doubles, and perturbative triples) predict a C2 symmetry structure in which the two CF3 groups rotate in opposite directions by about 16°. While the experimental results in this study are not capable of proving this unusual symmetry, they can support future microwave, gas phase electron diffraction or nuclear magnetic resonance studies. From the presented data, a preliminary r0 structure was determined, reproducing the experimental rotational constants with deviations of no more than 15 kHz. Analysis of the interactions between the two CF3 groups using an effective fragment potential approach identifies two major contributions to their interaction, due to exchange-repulsion and electrostatic repulsion, with electrostatic repulsion responsible for the barrier at the C2v geometry.

Spectrophotometric study of the gaseous species over molten HoCl3, LiCl-HoCl3 and CsCl-HoCl3 at temperature up to 1500K

Electronic absorption spectroscopy is used in the temperature range 1180–1480 K, to study the vapor species over molten HoCl3, and 1:1 molten mixtures of MCl: HoCl3 (M = Li, Cs). Emphasis is given on the f ← f hypersensitive transition of Ho(III) and the effect of the chloride coordination geometries on the splitting of the most intense hypersensitive transition 5G6 ← 5I8. The absorbance measurements permit the determination of the enthalpies of vaporization of the species formed over the melts studied: ΔHvap.(HoCl3) = 240 ± 9 kJ mol−1, ΔHvap.(LiHoCl4) = 193 ± 4 kJ mol−1 and ΔHvap.(CsHoCl4) = 202 ± 8 kJ mol−1. The volatility enhancement of Ho(III) due to the formation of the MHoCl4 vapor species is calculated at different temperatures. A three-fold and a four-fold coordination of Ho(III) is anticipated for the HoCl3 (g) and the MHoCl4 (g) species, respectively. The molar absorptivities (ε) and oscillator strengths (f) increase as the coordination decreases from the ‘‘octahedral’’ HoCl63− (ε = 9 L mol−1 cm−1; f = 15 × 106) to the distorted tetrahedral HoCl4− (ε = 84 L mol−1 cm−1; f = 102 × 10−6) to the trigonal HoCl3 (ε = 105 L mol−1 cm−1; f = 110 × 10−6). The vapor spectra support the view for a trigonal (most likely C3v) geometry for HoCl3(g) and a C2v symmetry for the MHoCl4(g) (M = Li, Cs) with the Ho(III) in a distorted HoCl4 tetrahedral symmetry. At high kT values, due to the higher mobility of Li+, the LiHoCl4(g) structure has a nearly D4h like symmetry with the Ho(III) possessing a pseudo-like inversion center.

Quadruple bonding of bare group-13 atoms in transition metal complexes.

Density functional theory calculations at the M06-D3/def2-TZVPPD level of the group-13 anion complexes EFe(CO)3- (E = B-Tl) and the isoelectronic neutral and charged boron adducts BTM(CO)3q (TMq = Fe-, Ru-, Os-, Co, Rh, Ir, Ni+, Pd+, Pt+) give tetrahedral (C3v) geometries in the 1A1 electronic ground state as equilibrium structures. The analysis of the bonding situation with the energy decomposition analysis in combination with natural orbital for chemical valence method suggests that the E-TM(CO)3q bonds possess four bonding components: (a) one strong electron-sharing σ bond E-TM(CO)3q; (b) two π backdonations E⇇TM(CO)3q and (c) one weak σ donation E→TM(CO)3q. The relative strength of the four bonding components depends on the charge of the system, the transition metal TM and the group-13 atom E. The σ donation E→TM(CO)3q is in all systems rather weak while the associated charge migration is not negligible. A similar situation of the bonding of terminal group-13 atoms Ga and In is found in Ga-TM(GaCp)4+ and E-Pt(PMe3)3+ (TM = Ni, Pd, Pt; E = Ga, In), which are model compounds for the stable complexes GaTM(GaCp*)4+ (TM = Ni, Pt) and InPt(PPh3)3+. The quadruple bonds E→TML2 are hybrids of electron-sharing and dative bonds.

Accurate global adiabatic potential energy surfaces for three low-lying electronic states of AlH2 free radicals.

In order to obtain the all-round molecular properties of the AlH2 system and the corresponding dynamical characteristics of the Al + H2 (v = 0, j = 0) → H + AlH reaction, three significant global adiabatic potential energy surfaces of AlH2 (X2A1, 2B1, and 2B2) free radicals were constructed for the first time. Ab initio energies were calculated under the multi-reference configuration interaction method and the aug-cc-pV(T,Q)Z basis sets; then the ab initio energies were extrapolated to the complete basis sets limit. The three adiabatic potential energy surfaces were constructed by the many-body expansion theory. The maximum root-mean square error was just 50 cm-1, which was small enough to ensure that the potential energy surfaces were accurate. The concerned T-type insertion topographical features, dissociation schemes, C2v geometry reaction mechanisms, and minimum energy curve paths were investigated and are discussed in detail. Several differences from previous studies are also pointed out. Eventually, the integral cross-sections of Al + H2 (v = 0, j = 0) → H + AlH reaction as calculated by quasi-classical trajectory method were employed to predict the dynamical properties of AlH2, providing the most reliable theoretical reference of the dynamical characteristics known thus far for such a reaction. These new potential energy surfaces can be treated as a reliable basis for investigation of the dynamics and as a component for constructing larger aluminum-/hydrogen-containing systems.

Pseudo-Jahn-Teller effect on the lowest triplet state of para-benzoquinone involving inequivalent carbonyl bonds

Various experiments have suggested the symmetry distortion of para-benzoquinone (PBQ) at the lowest triplet (n-π*) state. The vibronic coupling of electronic states known as the pseudo-Jahn-Teller effect could be the origin of the symmetry distortion. However, previous quantum chemical calculations could not provide reliable evidence for the symmetry distortion. Here we show the pseudo-Jahn-Teller distortion is an intrinsic property of PBQ due to the vibronic coupling between two low-lying n-π* states. Consequently, PBQ takes a C2v geometry having inequivalent two carbonyl groups, but the molecule remains planar. This state involves an inequivalent n-π* electronic transition and yields a mixed-valence state.

Synthesis and 4f 4f absorption studies of tris(acetylacetonato)praseodymium(III) and holmium(III) complexes with imidazole and pyrazole in non-aqueous solvents. Structure elucidation by Sparkle / PM7

The complexes [Pr(acac)3(im)2], [Pr(acac)3(pz)], [Ho(acac)3(im)] and [Ho(acac)3(pz)] (acac is the anion of acetylacetone, im is imidazole and pz is pyrazole) were synthesized and characterized by elemental and thermal analyses, IR and NMR spectroscopy. The ground state molecular structures were obtained using semi-empirical Sparkle/PM7 method. The optimized structures reflect the effect of lanthanide contraction along the lanthanide series as the average Ho—O and Ho—N distances are found shorter than the average Pr—O and Pr—N distances. The size of the lanthanide also affects the overall geometry of the complex. It can be seen in the homologous [Pr(acac)3(pz)] and [Ho(acac)3(pz)] complexes with pentagonal bipyramidal (D5h) and capped trigonal prism (C2v) geometries, respectively. The 4f 4f absorption spectra of the complexes recorded in different non-aqueous solvents are presented and analyzed. The oscillator strength of 3P2 ← 3H4,1D2 ← 3H4 transitions in the case of Pr(III) complexes and 5G6 ← 5I8 transition in the case of Ho(III) complexes, show remarkable changes upon a change in the ancillary ligand and/or solvent. The band shape of 3P2 ← 3H4 transition of both the Pr(III) complexes in pyridine show remarkable change and suggests influence of pyridine in changing the inner-coordination sphere of the complexes. The band shape of the hypersensitive 5G6 ← 5I8 transition of the Ho(III) complexes show appreciable change on changing the ligand/solvent. The paramagnetic shift obtained for these complexes are predominantly dipolar in nature.

Beyond Oxides: Nitride as a Ligand in a Neutral IrIXNO3 Molecule Bearing a Transition Metal at High Oxidation State

Theoretical calculations utilizing relativistic ZORA Hamiltonian point to the conceivable existence of an IrNO3 molecule in C3v geometry. This minimum is shown to correspond to genuine nonavalent iridium nitride trioxide, which is a neutral analogue of cationic [IrO4 ]+ species detected recently. Despite the presence of nitride anion, the molecule is protected by substantial barriers exceeding 200 kJ mol-1 against transformations leading, for example, to global minimum (O=)2 Ir-NO, which contains metal at a lower formal oxidation state.

One‐ and Two‐Photon‐Induced Photochemistry of Iron Pentacarbonyl [Fe(CO)5]: Insights from Coupled Cluster Response Theory

AbstractWe present herein the first comprehensive study of the one‐ and two‐photon absorption of Fe(CO)5 utilising a hierarchy of linear‐ and quadratic‐response coupled cluster (LR‐ and QR‐CC) methodologies to provide an in‐depth characterisation, as well as potential energy curves for axial and equatorial bond dissociations, highlighting the state crossings leading from the bright 1A2′′ state through to the dissociative 1E′ state. We have characterised a range of metal‐to‐ligand charge transfer (MLCT) and ligand field (LF) states that are in agreement with both previous studies and experiment, including the identification of a series of E′ states that present Rydberg character in the 5.9–7.2 eV region. Due to the rapid excited state dissociation of Fe(CO)5 through the low lying 1E′ and 2E′′ ligand‐field states, we have also included an LR‐CCSD analysis of the major dissociative product, Fe(CO)4. Analysis of the C2v geometry of Fe(CO)4 reveals four accessible ligand field states at 1.085, 1.684, 1.958, and 2.504 eV respectively, reinforcing the highly unstable nature of Fe(CO)4 along with a strong MLCT band between 4.300 and 5.573 eV. This band overlaps with one in the spectra of Fe(CO)5 suggesting that full fragmentation could proceed by two paths: two‐photon excitation leading to dissociation, or through sequential one‐photon absorption events, the first causing dissociation to and the second initiating further fragmentation of the complex.

Alkali Metal Covalent Bonding in Nickel Carbonyl Complexes ENi(CO)3.

The alkali metal-nickel carbonyl anions ENi(CO)3 - with E=Li, Na, K, Rb, Cs have been produced and characterized by mass-selected infrared photodissociation spectroscopy in the gas phase. The molecules are the first examples of 18-electron transition metal complexes with alkali atoms as covalently bonded ligands. The calculated equilibrium structures possess C3v geometry, where the alkali atom is located above a nearly planar Ni(CO)3 - fragment. The analysis of the electronic structure reveals a peculiar bonding situation where the alkali atom is covalently bonded not only to Ni but also to the carbon atoms.

Alkali Metal Covalent Bonding in Nickel Carbonyl Complexes ENi(CO)3−

AbstractThe alkali metal‐nickel carbonyl anions ENi(CO)3−with E=Li, Na, K, Rb, Cs have been produced and characterized by mass‐selected infrared photodissociation spectroscopy in the gas phase. The molecules are the first examples of 18‐electron transition metal complexes with alkali atoms as covalently bonded ligands. The calculated equilibrium structures possessC3vgeometry, where the alkali atom is located above a nearly planar Ni(CO)3−fragment. The analysis of the electronic structure reveals a peculiar bonding situation where the alkali atom is covalently bonded not only to Ni but also to the carbon atoms.

Structure‐Activity Relationships for Poly(phenylene)vinylene Derivatives as Antibacterial Agents

AbstractA series of poly(phenylene)vinylene (PPV) derivatives with different geometries and peripheral functional groups have been synthesized by Horner‐Wadsworth‐Emmons reaction. Compounds bearing carboxylic acid or quaternary ammonium functional groups prepared by this metal‐free protocol were weakly active against both Gram‐negative and Gram‐positive bacteria, which is in contrast to previously reported results. The activity of polyanionic derivatives was higher for Gram‐negative bacteria and showed bacteriostatic behavior, whereas polycationic derivatives were clearly more active against Gram‐positive bacteria and behaved as bactericidal agents. The spatial disposition of the active groups seems to play a key role, with the highest activity observed for a C3v geometry. The presence of quaternary ammonium functional groups also facilitated the internalization of the molecules into the bacteria. Levels of cytotoxicity similar to that of the solvent were obtained for most compounds against COS‐1 and VERO cells.