Accurate Molecular Structure Research Articles

Enhanced spectral reconstruction of ultrafast spatiotemporal encoded 2D NMR spectroscopy

BackgroundNuclear Magnetic Resonance (NMR) is extensively utilized in research as a non-invasive technique for investigating molecular structures and composite components. The spatiotemporal encoding (SPEN) technique effectively accelerates multi-dimensional NMR experiments. In ultrafast SPEN NMR, the acquired data are divided into odd and even segments corresponding to the positive and negative gradients during the decoding stage, respectively. However, the interlaced Fourier transform (FT) method used to reconstruct a full-width spectrum from these segments often suffers from severe noise contamination, necessitating the development of a more effective spectrum reconstruction method. ResultsIn this work, we analyze the noise amplification effect of the interlaced FT and find that the noise is most significant in two edge regions of the spectrum along the indirect dimension due to the relatively small time offset differences between odd and even segments in those regions. Consequently, we develop an iterative optimization method to obtain the full-width spectrum while mitigating the noise. The proposed method incorporates the odd and even data segments into an objective function with sparsity regularization to simplify the spectrum, which is then refined iteratively during the optimization. As a result, the reconstructed spectrum is significantly cleaner and maintains the full spectral width. Experimental results demonstrate a remarkable improvement in the readability and interpretability of SPEN data, evidenced by clearer signal peaks and reduced background noise. SignificanceThe proposed reconstruction method provides a reliable approach for processing SPEN 2D NMR data, effectively addressing the low sensitivity issue in the joint reconstruction on odd and even segments. Combining SPEN's ultrafast data acquisition with the proposed high-sensitivity spectrum reconstruction method enhances the utility of NMR for more accurate molecular structure analysis and component identification in composite samples, particularly promoting NMR research in rapid reaction systems.

Design of self-healing and anticorrosion epoxy coating with active multiple hydrogen bonds based on grafted polyetheramine

The healing of epoxy coatings in damaged areas significantly influences their service life and protection quality. Intrinsic self-healing coatings, which enable multiple healing cycles without the need for additional functional carriers, have emerged as a promising coating technology. Nevertheless, the cross-linked structure of thermoset epoxy coating system restricts the large-scale migration of molecular chains, posing a significant challenge to achieve intrinsic healing of resin without compromising its mechanical properties. In this study, we report a design scheme for epoxy coating with intrinsic self-healing properties based on active multiple hydrogen bonds. Grafting aminobenzothiazole at the end of polyetheramine D230 chain, the grafted polyetheramine (GD230) was synthesized and served as the auxiliary curing agent, whose accurate molecular structure has been confirmed by different characterizations. The self-healing coating with reversible dynamics network based on hydrogen bonds was prepared by crosslinking through epoxy resin and mixed curing agent of polyetheramine D230 and GD230. Various measurements have been adopted to evaluate the self healing and anticorrosion performance. Results showed that the functional coating with a ratio of 8:2 for D230 to GD230 has satisfied both performances on the steel substrate. After immersion in 3 wt% NaCl solution for 120 days, the impedance value of functional coating still remains about 1010 Ω cm2. After the coating was scratched and immersion for 96 h, the impedance value of functional coating increased by about two orders of magnitude compared to that in blank coating. Mechanical testing and theoretical calculations were used to support dynamic crosslinking model to reveal the self-healing mechanism.

Study on low-rank coal flotation collector screening and performance based on molecular polarity index.

Extensive studies using a trial-and-error approach have been conducted on low-rank coal flotation collectors. However, screening efficient collectors remains a considerable challenge due to the lack of suitable screening principles. It has proven that polar compounds such as carboxylic acids and esters are effective collectors for low-rank coal flotation. In this work, the effects of carboxylic acid, alcohol, and methyl ester on the floatability of low-rank coal were compared, the flotation performance of the polar collector was evaluated with theoretical calculations, a suitable evaluation parameter was determined and a screening principle based on this parameter was determined. The results show that the enhancement effects of polar collectors on low-rank coal floatability follow the order of methyl decanoate > methyl laurate > methyl octanoate > sec-octanol > methyl oleate (or methyl oleate > sec-octanol) > n-octanoic acid. Compared with the molecular polarity index, the hydrophobicity indices log P and dipole moment cannot be used to accurately evaluate different types of collectors and the same type of collectors, respectively. At room temperature, liquid polar compounds with molecular polarity indices in the range of 6.0 ~ 8.0kcal/mol effectively enhance the floatability of low-rank coal. The molecular polarity index of the collector is used for the first time to screen effective collectors of low-rank coal in this work. This parameter is anticipated to be highly important for the development and research of low-rank coal and other mineral collectors. To obtain reasonable and accurate molecular structure, geometry optimization and frequency calculations of the studied collectors were conducted via the Gaussian 09 software package based on density functional theory at the B3LYP/6-311 + G (d, p) level. The integral equation formalism for the polarizable continuum model (IEF-PCM) was utilized with water as the solvent (dielectric constant = 78.36, T = 298K) for all the calculations. Then, the atomic charge distributions (MPA and NPA) and electrostatic potential maps, the dipole moment and molecular polarity index, and the log P and water solubilities of studied collectors were shown or calculated by Gauss View 5.0, Mutiwfn program and website ( https://www.molsoft.com/mprop/mprop.cgi ), respectively.

Single-cluster Functionalized TiO2 Nanotube Array for Boosting Water Oxidation and CO2 Photoreduction to CH3OH.

Solar-driven CO2 reduction and water oxidation to liquid fuels represents a promising solution to alleviate energy crisis and climate issue, but it remains a great challenge for generating CH3OH and CH3CH2OH dominated by multi-electron transfer. Single-cluster catalysts with super electron acceptance, accurate molecular structure, customizable electronic structure and multiple adsorption sites, have led to greater potential in catalyzing various challenging reactions. However, accurately controlling the number and arrangement of clusters on functional supports still faces great challenge. Herein, we develop a facile electrosynthesis method to uniformly disperse Wells-Dawson- and Keggin-type polyoxometalates on TiO2 nanotube arrays, resulting in a series of single-cluster functionalized catalysts P2M18O62@TiO2 and PM12O40@TiO2 (M=Mo or W). The single polyoxometalate cluster can be distinctly identified and serves as electronic sponge to accept electrons from excited TiO2 for enhancing surface-hole concentration and promote water oxidation. Among these samples, P2Mo18O62@TiO2-1 exhibits the highest electron consumption rate of 1260 μmol g-1 for CO2-to-CH3OH conversion with H2O as the electron source, which is 11 times higher than that of isolated TiO2 nanotube arrays. This work supplied a simple synthesis method to realize the single-dispersion of molecular cluster to enrich surface-reaching holes on TiO2, thereby facilitating water oxidation and CO2 reduction.

Single‐cluster Functionalized TiO2 Nanotube Array for Boosting Water Oxidation and CO2 Photoreduction to CH3OH

AbstractSolar‐driven CO2 reduction and water oxidation to liquid fuels represents a promising solution to alleviate energy crisis and climate issue, but it remains a great challenge for generating CH3OH and CH3CH2OH dominated by multi‐electron transfer. Single‐cluster catalysts with super electron acceptance, accurate molecular structure, customizable electronic structure and multiple adsorption sites, have led to greater potential in catalyzing various challenging reactions. However, accurately controlling the number and arrangement of clusters on functional supports still faces great challenge. Herein, we develop a facile electrosynthesis method to uniformly disperse Wells‐Dawson‐ and Keggin‐type polyoxometalates on TiO2 nanotube arrays, resulting in a series of single‐cluster functionalized catalysts P2M18O62@TiO2 and PM12O40@TiO2 (M=Mo or W). The single polyoxometalate cluster can be distinctly identified and serves as electronic sponge to accept electrons from excited TiO2 for enhancing surface‐hole concentration and promote water oxidation. Among these samples, P2Mo18O62@TiO2‐1 exhibits the highest electron consumption rate of 1260 μmol g−1 for CO2‐to‐CH3OH conversion with H2O as the electron source, which is 11 times higher than that of isolated TiO2 nanotube arrays. This work supplied a simple synthesis method to realize the single‐dispersion of molecular cluster to enrich surface‐reaching holes on TiO2, thereby facilitating water oxidation and CO2 reduction.

Molecular Gas-Phase Conformational Ensembles.

Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.

Reticular Electrochemiluminescence Nanoemitters: Structural Design and Enhancement Mechanism.

ConspectusElectrochemiluminescence (ECL) is a powerful transduction technique, which depends critically on the formation of the excited emitter through the charge transfer between the electrochemical reaction intermediates of the emitter and the co-reactant/emitter. The exploration of ECL mechanisms for conventional nanoemitters is limited due to the uncontrollable charge transfer process. With the development of molecular nanocrystals, reticular structures such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) have been utilized as atomically precise semiconducting materials. The long-range order in crystalline frameworks and the tunable coupling among building blocks promote the quick development of electrically conductive frameworks. Especially, the reticular charge transfer can be regulated by both interlayer electron coupling and intralayer topology-templated conjugation. By modulating intramolecular or intermolecular charge mobility, reticular structures could serve as promising candidates for enhancing ECL. Thus, reticular crystalline nanoemitters with different topologies provide a confined platform to understand ECL fundamentals for designing next-generation ECL devices.Aiming at exploring the mechanism of ECL emission, our group has developed a series of ECL nanoemitters as well as enhancement strategies of ECL emission in the past 20 years. A series of water-soluble ligand-capped quantum dots were introduced as ECL nanoemitters to create sensitive analytical methods for detecting and tracing biomarkers. The functionalized polymer dots were also designed as ECL nanoemitters for imaging of membrane proteins with signal transduction strategies of dual resonance energy transfer and dual intramolecular electron transfer. To decode the ECL fundamental and enhancement mechanisms, an electroactive MOF with accurate molecular structure was first constructed with two redox ligands as a highly crystallized ECL nanoemitter in aqueous medium. Through the mixed-ligand approach, luminophores and co-reactants were integrated into one MOF structure for self-enhanced ECL. Furthermore, several donor-acceptor COFs were developed as efficient ECL nanoemitters with tunable intrareticular charge transfer. The atomically precise structure of conductive frameworks established clear correlations between the structure and charge transport in these materials. Therefore, reticular materials as crystalline ECL nanoemitters have demonstrated both proof of concept and mechanistic innovation.In this Account, taking advantage of reticular materials with accurate molecular structure, we survey the design of the electroactive reticular materials including MOFs and COFs as crystalline ECL nanoemitters at the molecular level. The enhancement mechanisms of ECL emission of various topology frameworks are discussed via the regulation of reticular energy transfer and charge transfer and the accumulation of anion/cation radicals. Our perspective on the reticular ECL nanoemitters is also discussed. This Account provides a new avenue for designing molecular crystalline ECL nanoemitters and decoding the fundamentals of ECL detection methods.

Insights into the Diels-Alder Reaction of Furan with Maleic Anhydride from Its Prereactive Intermediate.

The prereactive intermediate in the furan-maleic anhydride cycloaddition, a classical Diels-Alder reaction, has been captured and characterized in pulsed jets by Fourier transform microwave spectroscopy for the first time. The observed species is stabilized by the π-π* interaction between the two moieties, which connects to the endo channel of the cycloaddition. The secondary interactions between the C=C and C=O in the observed isomer are accountable for its lower energy with respect to the one with the exo channel. The present study tries to fill the significant void of the experimental information on prereactive intermediates as the first stage of Diels-Alder cycloadditions, by outlining the stability of the prereactive intermediate and its accurate molecular structure and by emphasizing the role of the π-π* interaction in governing the stereochemical outcome of the reaction.

DNA Supramolecular Assembly on Micro/Nanointerfaces for Bioanalysis.

Facing increasing demand for precision medicine, materials chemistry systems for bioanalysis with accurate molecular design, controllable structure, and adjustable biological activity are required. As a genetic biomacromolecule, deoxyribonucleic acid (DNA) is created via precise, efficient, and mild processes in life systems and can in turn precisely regulate life activities. From the perspective of materials chemistry, DNA possesses the characteristics of sequence programmability and can be endowed with customized functions by the rational design of sequences. In recent years, DNA has been considered to be a potential biomaterial for analysis and has been applied in the fields of bioseparation, biosensing, and detection imaging. To further improve the precision of bioanalysis, the supramolecular assembly of DNA on micro/nanointerfaces is an effective strategy to concentrate functional DNA modules, and thus the functions of DNA molecules for bioanalysis can be enriched and enhanced. Moreover, the new modes of DNA supramolecular assembly on micro/nanointerfaces enable the integration of DNA with the introduced components, breaking the restriction of limited functions of DNA materials and achieving more precise regulation and manipulation in bioanalysis. In this Account, we summarize our recent work on DNA supramolecular assembly on micro/nanointerfaces for bioanalysis from two main aspects. In the first part, we describe DNA supramolecular assembly on the interfaces of microscale living cells. The synthesis strategy of DNA is based on rolling-circle amplification (RCA), which generates ultralong DNA strands according to circular DNA templates. The templates can be designed with complementary sequences of functional modules such as aptamers, which allow DNA to specifically bind with cellular interfaces and achieve efficient cell separation. In the second part, we describe DNA supramolecular assembly on the interfaces of nanoscale particles. DNA sequences are designed with functional modules such as targeting, drug loading, and gene expression and then are assembled on interfaces of particles including upconversion nanoparticles (UCNPs), gold nanoparticles (AuNPs), and magnetic nanoparticle (MNPs). The integration of DNA with these functional particles achieves cell manipulation, targeted tumor imaging, and cellular regulation. The processes of interfacial assembly are well controlled, and the functions of the obtained bioanalytical materials can be flexibly regulated. We envision that the work on DNA supramolecular assembly on micro/nanointerfaces will be a typical paradigm for the construction of more bioanalytical materials, which we hope will facilitate the development of precision medicine.

Molecular structure of 5-fluorouracil from gas-phase electron diffraction data and quantum-chemical calculations

The accurate equilibrium molecular structure of a canonical tautomer of 5-fluorouracil was determined by electron diffraction taking into account anharmonic vibrational corrections calculated with ab initio force field. This structure was applied to benchmark the results of CCSD(T) computations used for the analysis of substitution effects in uracil derivatives.

Diving for Accurate Structures in the Ocean of Molecular Systems with the Help of Spectroscopy and Quantum Chemistry.

The prediction and interpretation of structural properties are the starting points for a deep understanding of thermochemistry, kinetics, and spectroscopic signatures of molecular systems. To give an example, detailed knowledge of the conformational behavior of the main building blocks of biomolecules in the gas phase (i.e., without the perturbing effect of the environment) is a mandatory prerequisite toward the understanding of the role played by different interactions in determining the biological activity in terms of structure-activity relationships. The first step to take is an unambiguous definition of molecular structure. We address the so-called Born-Oppenheimer equilibrium structure, which is defined in a rigorous manner and isotopically independent, and the target accuracy. For the latter, we aim at so-called "spectroscopic" accuracy, which implies uncertainties of a few milliangstroms for bond lengths and smaller than a tenth of degree for angles. If on one side the continuous enhancements of the experimental techniques give access to new and unprecedented spectroscopic determinations, on the other side they require increasing efforts for an unbiased interpretation and analysis. Among the pieces of information, accurate molecular structures play a particularly important role. Indeed, there is a strong relationship between the experimental outcome and the electronic structure of the system. Spectroscopic techniques, in particular those exploited in the gas phase, are therefore accurate and reliable sources for structural information. However, it is seldom straightforward to derive molecular structures directly from the experimental information. Indeed, even in the favorable case of investigations in the gas phase, vibrational effects are always present, and disentangling their contributions requires collection of information for all vibrational modes, a nearly impossible task. To overcome these limitations, joint theory-spectroscopy strategies can be identified, which are referred to as "top-down" and "bottom-up". The first approach, denoted as the semiexperimental approach, relies on extracting from experimental outcomes the equilibrium structure by using quantum-chemical computations to recover vibrational effects. The bottom-up approach consists in verifying the computed equilibrium geometry by means of a comparison between calculated and experimental spectroscopic parameters that probe structural characteristics. In this contribution, we try to review the most important challenges in accurate molecular structure determinations, with particular emphasis on the "solution" provided by a joint theoretical-experimental approach and on the current state of the art. Starting from the illustration of different strategies, we proceed by addressing the increasing complexity in the derivation of equilibrium geometries: we start from the construction of a database of accurate structures, we then face the problem of extending the dimension of the systems amenable to accurate structural determinations, and finally we move to the challenge of understanding the nature of intermolecular interactions.

CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments.

Accurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ∼300-residue long α-helical coiled coil which cannot be assessed by either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases. Here we present CCFold, a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence only. The algorithm is based on a statistical analysis of experimentally determined structures and can handle any hydrophobic repeat patterns in addition to the most common heptads. We demonstrate that CCFold outperforms general-purpose computational folding in terms of accuracy, while being faster by orders of magnitude. By combining the CCFold algorithm and Rosetta folding we generate representative dimer models for all IF protein classes. The source code is freely available at https://github.com/biocryst/IF; a web server to run the program is at http://pharm.kuleuven.be/Biocrystallography/cc. Supplementary data are available at Bioinformatics online.

Spin-resolved state-selective electron capture in C5+-H collisions

The electron capture processes in the C5+(1s)+H(1s) collision system are investigated by the quantum-mechanical molecular orbital close-coupling (QMOCC) method in the energy range of 10−5–10 keV u−1. Accurate molecular structure calculations are performed by the ab initio multireference single- and double-excitation configuration interaction method. The electron translational effects are included in the calculations. The total and spin-resolved state-selective cross sections are presented and compared with the available experimental and theoretical data. The present results have a good agreement with the experimental measurements. Our calculations show that the electron translation factors play a very important role for energies above 0.1 keV u−1 leading to significant differences between the present and the previous QMOOC cross section results of Nolte et al 2012 (J. Phys. B: At. Mol. Opt. Phys. 45 245202). The effects of the core electron also cannot be ignored below 2 keV u−1. Model potential calculations, in which the core electron is treated as frozen, cannot give accurate spin-resolved cross sections.

Facile Probe Design: Fluorescent Amphiphilic Nucleic Acid Probes without Quencher Providing Telomerase Activity Imaging Inside Living Cells.

Nowadays, the probe with fluorophore but no quencher is promising for its simple preparation, environmental friendliness, and wide application scope. This study designs a new amphiphilic nucleic acid probe (ANAP) based on aggregation-caused quenching (ACQ) effect without any quencher. Upon binding with targets, the dispersion of hydrophobic part (conjugated fluorene, CF) in ANAP is enhanced as a signal-on model for proteins, nucleic acids, and small molecules detection or the aggregation of CF is enhanced as a signal-off model for ion detection. Meanwhile, because of the high specificity of ANAP, a one-step method is developed powerfully for monitoring the telomerase activity not only from the cell extracts but also from 50 clinic urine samples (positive results from 45 patients with bladder cancer and negative results from 5 healthy people). ANAPs can also readily enter into cells and exhibit a good performance for distinguishing natural tumor cells from the tumor cells pretreated by telomerase-related drugs or normal cells. In contrast to our previous results ( Anal. Chem. 2015 , 87 , 3890 - 3894 ), the present CF is a monomer which is just the structure unit of the previous fluorescent polymer. Since the accurate molecular structure and high DNA/CF ratio of the present CF, these advanced experiments obtain an easier preparation of probes, an improved sensitivity and specificity, and broader detectable targets.

Resonant charge transfer in slow Li+−Li(2s) collisions**Project supported by the National Natural Science Foundation of China (Grant Nos. 11179041, 11474032, and 11474033) and the NSAF (Grant No. U1330117).

The resonant charge transfer process for Li+−Li(2s) collision is investigated by the quantum-mechanical molecular orbital close-coupling (QMOCC) method and the two-center atomic-orbital close-coupling (AOCC) method in an energy range of 1.0 eV/u–104 eV/u. Accurate molecular structure data and charge transfer cross sections are given. Both the all-electron model (AEM) and one-electron model (OEM) are used in the QMOCC calculations, and the discrepancies between the two models are analyzed. The OEM calculation can also give a reliable prediction of the cross sections for energies below 1 keV/u.

An accurate molecular structure of phenyl, the simplest aryl radical.

The phenyl radical (C6H5(·)) is the prototypical σ-type aryl radical and one of the most common aromatic building blocks for larger ring molecules. Using a combination of rotational spectroscopy of singly substituted isotopic species and vibrational corrections calculated theoretically, an extremely accurate molecular structure has been determined. Relative to benzene, the phenyl radical has a substantially larger C-Cipso-C bond angle [125.8(3)° vs. 120°], and a shorter distance [2.713(3) Å vs. 2.783(2) Å] between the ipso and para carbon atoms.

An Accurate Molecular Structure of Phenyl, the Simplest Aryl Radical

AbstractThe phenyl radical (C6H5.) is the prototypical σ‐type aryl radical and one of the most common aromatic building blocks for larger ring molecules. Using a combination of rotational spectroscopy of singly substituted isotopic species and vibrational corrections calculated theoretically, an extremely accurate molecular structure has been determined. Relative to benzene, the phenyl radical has a substantially larger C‐Cipso‐C bond angle [125.8(3)° vs. 120°], and a shorter distance [2.713(3) Å vs. 2.783(2) Å] between the ipso and para carbon atoms.

Simulation of Crystalline and Amorphous Copper Phthalocyanine: Force Field Development and Analysis of Thermal Transport Mechanisms

The thermal conductivities of crystalline and amorphous CuPc structures have been studied using molecular dynamics simulations. To this end, a Hybrid-COMPASS force field for the CuPc molecule has been developed and parametrized using ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio calculation results, and the van der Waals (vdW) parameters were derived by comparing MD simulations of CuPc crystal structures to experimentally determined characteristics. The resulting force field successfully predicts accurate molecular structure, crystal structure, and vibration density of states (VDOS) of CuPc molecule in isolation and in condensed phase. Thermal conductivities calculated using the Green–Kubo formalism show a significant difference between crystalline and amorphous CuPc. Further analysis of the thermal conductivity spectral modes reveals that this difference mainly stems from the scattering of acoustic phonons, and t...

Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study.

The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

Accurate molecular structure of nickel phthalocyanine (NiN8C32H16): Gas-phase electron diffraction and quantum-chemical calculations

The molecular structure of the nickel phthalocyanine (NiPc) was determined using the combination of gas-phase electron diffraction (GED), mass spectrometry and quantum chemical calculations. The DFT calculations with employing different functionals and basis sets found the molecular structure with D4h symmetry that agrees satisfactorily to the one found in experiment at 776±5K. The important bond lengths and bond angles according to GED (total errors in parentheses) are: rh1(Ni–N)=1.913(5)Å, rh1(N–Cp)=1.385(4)Å, rh1(Cp–Nm)=1.327(5)Å, rh1(Cp–Cp)=1.462(6)Å, rh1(Cp–C)=1.399(3)Å, rh1(C–C)=1.395(3)Å, ∠NiNCp=126.6(2)°, ∠NCpNm=128.4(4)°, ∠CpNmCp=120.1(5)°, ∠NCpCp=110.0(4)°, ∠CpCpC=121.2(1)°. The nickel–nitrogen bond distance obtained is by 0.04Å longer than the one found for this compound in the literature. The structures of the crystalline and gaseous NiPc complex are compared. The effect of the metal (Ni, Cu, Zn) on structural features of the MPc complexes is discussed. Using NBO-analysis, the correlation between the metal–ligand bond distance and the total energy of donor–acceptor orbital interactions per one M–N bond was found in the MPc complexes.