scholarly journals Metal–Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy

Materials ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 55 ◽  
Author(s):  
Vytor P. Oliveira ◽  
Bruna L. Marcial ◽  
Francisco B. C. Machado ◽  
Elfi Kraka
Keyword(s):  
Density Functional ◽  
Halogen Bonding ◽  
Fine Tuning ◽  
Mode Analysis ◽  
Planar Geometry ◽  
Local Mode ◽  
Special Role ◽  
Bonded Materials ◽  
Local Vibrational Mode ◽  
Donor And Acceptor

Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y2)(NC5H4X-3)2 with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC5H4X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles

2017 ◽  
Vol 73 (3) ◽  
pp. 157-167 ◽  
Author(s):  
Patrick M. J. Szell ◽  
Shaina A. Gabriel ◽  
Russell D. D. Gill ◽  
Shirley Y. H. Wan ◽  
Bulat Gabidullin ◽  
...  
Keyword(s):  
Solid State ◽  
Density Functional ◽  
Halogen Bond ◽  
Chemical Shifts ◽  
Halogen Bonding ◽  
Structural Features ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
X Ray ◽  
Donor And Acceptor

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P21/c space group: acridine–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C13H9N, 1,10-phenanthroline–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C12H8N2, and 2,3,5,6-tetramethylpyrazine–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C8H12N2. 13C and 19F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from 19F to 13C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional 1H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental 13C and 19F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

scholarly journals Halogen Bonding Involving I2 and d8 Transition-Metal Pincer Complexes

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 373
Author(s):  
Marek Freindorf ◽  
Seth Yannacone ◽  
Vytor Oliveira ◽  
Niraj Verma ◽  
Elfi Kraka
Keyword(s):  
Charge Transfer ◽  
Transition Metal ◽  
Bond Strength ◽  
Oxidative Addition ◽  
Halogen Bonding ◽  
Mode Analysis ◽  
Pincer Complexes ◽  
Local Mode ◽  
Electronic Effects ◽  
Pincer Complex

We systematically investigated iodine–metal and iodine–iodine bonding in van Koten’s pincer complex and 19 modifications changing substituents and/or the transition metal with a PBE0–D3(BJ)/aug–cc–pVTZ/PP(M,I) model chemistry. As a novel tool for the quantitative assessment of the iodine–metal and iodine–iodine bond strength in these complexes we used the local mode analysis, originally introduced by Konkoli and Cremer, complemented with NBO and Bader’s QTAIM analyses. Our study reveals the major electronic effects in the catalytic activity of the M–I–I non-classical three-center bond of the pincer complex, which is involved in the oxidative addition of molecular iodine I2 to the metal center. According to our investigations the charge transfer from the metal to the σ* antibonding orbital of the I–I bond changes the 3c–4e character of the M–I–I three-center bond, which leads to weakening of the iodine I–I bond and strengthening of the metal–iodine M–I bond, facilitating in this way the oxidative addition of I2 to the metal. The charge transfer can be systematically modified by substitution at different places of the pincer complex and by different transition metals, changing the strength of both the M–I and the I2 bonds. We also modeled for the original pincer complex how solvents with different polarity influence the 3c–4e character of the M–I–I bond. Our results provide new guidelines for the design of pincer complexes with specific iodine–metal bond strengths and introduce the local vibrational mode analysis as an efficient tool to assess the bond strength in complexes.

scholarly journals A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Sensors ◽  
2020 ◽  
Vol 20 (8) ◽  
pp. 2358 ◽  
Author(s):  
Niraj Verma ◽  
Yunwen Tao ◽  
Wenli Zou ◽  
Xia Chen ◽  
Xin Chen ◽  
...  
Keyword(s):  
Electric Field ◽  
Stark Effect ◽  
Comprehensive Evaluation ◽  
Critical Evaluation ◽  
Normal Modes ◽  
Mode Analysis ◽  
Local Mode ◽  
Underlying Assumption ◽  
Local Vibrational Mode ◽  
Internal Coordinates

Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.

scholarly journals Vibrational Analysis of Benziodoxoles and Benziodazolotetrazoles

Physchem ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 45-68
Author(s):  
Seth Yannacone ◽  
Kapil Dev Sayala ◽  
Marek Freindorf ◽  
Nicolay V. Tsarevsky ◽  
Elfi Kraka
Keyword(s):  
Energetic Materials ◽  
Substituent Effects ◽  
Vibrational Analysis ◽  
Mode Analysis ◽  
Hypervalent Iodine ◽  
Local Mode ◽  
Explosive Decomposition ◽  
Local Vibrational Mode ◽  
Bond Strengths ◽  
The Stability

Tetrazoles are well known for their high positive enthalpy of formation which makes them attractive as propellants, explosives, and energetic materials. As a step towards a deeper understanding of the stability of benziodazolotetrazole (BIAT)-based materials compared to their benziodoxole (BIO) counterparts, we investigated in this work electronic structure features and bonding properties of two monovalent iodine precursors: 2-iodobenzoic acid and 5-(2-iodophenyl)tetrazole and eight hypervalent iodine (III) compounds: I-hydroxybenzidoxolone, I-methoxybenziodoxolone, I-ethoxybenziodoxolone, I-iso-propoxybenziodoxolone and the corresponding I-hydroxyben ziodazolotetrazole, I-methoxybenziodazolotetrazole, I-ethoxybenziodazolotetrazole and I-iso- propoxybenziodazolotetrazole. As an efficient tool for the interpretation of the experimental IR spectra and for the quantitative assessment of the I−C, I−N, and I−O bond strengths in these compounds reflecting substituent effects, we used the local vibrational mode analysis, originally introduced by Konkoli and Cremer, complemented by electron density and natural bond orbital analyses. Based on the hypothesis that stronger bonds correlate with increased stability, we predict that, for both series, i.e., substituted benziodoxoles and benziodazolotetrazoles, the stability increases as follows: I-iso-propoxy < I-ethoxy < I-methoxy < I-hydroxy. In particular, the I−N bonds in the benziodazolotetrazoles could be identified as the so-called trigger bonds being responsible for the initiation of explosive decomposition in benziodazolotetrazoles. The new insight gained by this work will allow for the design of new benziodazolotetrazole materials with controlled performance or stability based on the modulation of the iodine bonds with its three ligands. The local mode analysis can serve as an effective tool to monitor the bond strengths, in particular to identify potential trigger bonds. We hope that this article will foster future collaboration between the experimental and computational community being engaged in vibrational spectroscopy.

Investigation of Adsorption Effect of Carbon Monoxide on Coniine: A DFT Study

2021 ◽  
Vol 17 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Mehrnoosh Khaleghian ◽  
Marina Murashko ◽  
Mahin Ahmadianarog ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Gap ◽  
Adsorption Effect ◽  
Chemical Shift Tensors ◽  
Solvent Water ◽  
Donor And Acceptor ◽  
Before And After ◽  
Electron Donor And Acceptor

: For the first time in the present study, the non-bonded interaction of the Coniine (C8H17N) with carbon monoxide (CO) was investigated by density functional theory (DFT/M062X/6-311+G*) in the gas phase and solvent water. The adsorption of the CO over C8H17N was affected on the electronic properties such as EHOMO, ELUMO, the energy gap between LUMO and HOMO, global hardness. Furthermore, chemical shift tensors and natural charge of the C8H17N and complex C8H17N/CO were determined and discussed. According to the natural bond orbital (NBO) results, the molecule C8H17N and CO play as both electron donor and acceptor at the complex C8H17N/CO in the gas phase and solvent water. On the other hand, the charge transfer is occurred between the bonding, antibonding or nonbonding orbitals in two molecules C8H17N and CO. We have also investigated the charge distribution for the complex C8H17N/CO by molecular electrostatic potential (MEP) calculations using the M062X/6-311+G* level of theory. The electronic spectra of the C8H17N and complex C8H17N/CO were calculated by time dependent DFT (TD-DFT) for investigation of the maximum wavelength value of the C8H17N before and after the non-bonded interaction with the CO in the gas phase and solvent water. Therefore, C8H17N can be used as strong absorbers for air purification and reduce environmental pollution.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

High resolution spectroscopic study of H2 Se (40+,0) A1 and (40-,0) B2 stretching states: normal mode and local mode analysis

1997 ◽  
Vol 92 (6) ◽  
pp. 1073-1082 ◽  
Author(s):  
By ZE-YI ZHOU ◽  
XIAO-GANG WANG ◽  
ZHONG-PING ZHOU ◽  
OLEG N. ULENIKOV ◽  
GALINA A. ONOPENKO ◽  
...  
Keyword(s):  
High Resolution ◽  
Spectroscopic Study ◽  
Normal Mode ◽  
Mode Analysis ◽  
Local Mode ◽  
Local Mode Analysis

scholarly journals Adenine as a Halogen Bond Acceptor: A Combined Experimental and DFT Study

Crystals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 224 ◽  
Author(s):  
Yannick Roselló ◽  
Mónica Benito ◽  
Elies Molins ◽  
Miquel Barceló-Oliver ◽  
Antonio Frontera
Keyword(s):  
Density Functional ◽  
Halogen Bond ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Adenine Ring ◽  
Bonding Interaction ◽  
Donor Ability ◽  
Adenine Derivative

In this work, we report the cocrystallization of N9-ethyladenine with 1,2,4,5-tetrafluoro-3,6-diiodobenzene (TFDIB), a classical XB donor. As far as our knowledge extends, this is the first cocrystal reported to date where an adenine derivative acts as a halogen bond acceptor. In the solid state, each adenine ring forms two centrosymmetric H-bonded dimers: one using N1···HA6–N6 and the other N7···HB6–N6. Therefore, only N3 is available as a halogen bond acceptor that, indeed, establishes an N···I halogen bonding interaction with TFDIB. The H-bonded dimers and halogen bonds have been investigated via DFT (Density Functional Theory) calculations and the Bader’s Quantum Theory of Atoms In Molecules (QTAIM) method at the B3LYP/6-311+G* level of theory. The influence of H-bonding interactions on the lone pair donor ability of N3 has also been analyzed using the molecular electrostatic potential (MEP) surface calculations.

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