Quantum Mechanical DFT Calculations Research Articles

In situ crystallization of methanesulfonic acid, CH3SO3H, and serendipitous single crystal formation of its anhydride, (CH3)2S2O5

Methanesulfonic acid, CH3SO3H, has been crystallized using an in situ technique on a single crystal diffractometer. The crystal structure is monoclinic (P21/c, Z = 4, a = 842.07(4) pm, b = 582.20(3) pm, c = 820.38(4) pm, β = 106.459(2)°) and stamped by the presence of strong hydrogen bonds. Single crystals of the anhydride of methanesulfonic acid, (CH3)2S2O5, formed as a side product in the reaction of bis‐trimethylsilyl‐sulfate, [(CH3)3SiO]2SO2 with SO3 in a sealed glass ampoule. The monoclinic crystal structure (P21/n, Z = 12, a = 1794.5(2) pm, b = 831.75(7) pm, 1383.4(1) pm, β = 110.630(4)°) shows three crystallographically different (CH3)2S2O5 molecules in the unit cell. According to the orientation of the CH3 groups with respect to each other the (CH3)2S2O5 molecule appears as the so‐called trans‐conformer. The structure of both molecules is corroborated by quantum mechanical DFT calculations.

Rhodium(I)-Catalyzed Annulation of Bicyclo[1.1.0]butyl-Substituted Dihydroquinolines and Dihydropyridines.

Bicyclo[1.1.0]butane-containing compounds feature a unique chemical reactivity, trigger "strain-release" reaction cascades, and provide novel scaffolds with considerable utility in the drug discovery field. We report the synthesis of new bicyclo[1.1.0]butane-linked heterocycles by a nucleophilic addition of bicyclo[1.1.0]butyl anions to 8-isocyanatoquinoline, or, alternatively, iminium cations derived from quinolines and pyridines. The resulting bicyclo[1.1.0]butanes are converted with high regioselectivity to unprecedented bridged heterocycles in a rhodium(I)-catalyzed annulative rearrangement. The addition/rearrangement process tolerates a surprisingly large range of functional groups. Subsequent chemo- and stereoselective synthetic transformations of urea, alkene, cyclopropane, and aniline moieties of the 1-methylene-5-azacyclopropa[cd]indene scaffolds provide several additional new heterocyclic building blocks. X-ray structure-validated quantum mechanical DFT calculations of the reaction pathway indicate the intermediacy of rhodium carbenoid and metallocyclobutane species.

Organometallic tin monochalcogenides [SnX (X = O, S, Se, and Te)] as alternative ligands for carbonyls: A DFT study

Quantum mechanical DFT calculations were performed on the Fe(CO)5 and for the axial and equatorial isomers of [Fe(CO)4(SnX)] (X = O, S, Se, Te) complexes. The equatorial isomer of [Fe(CO)4(SnX)] complexes is more stable than the axial isomer using energetic values. These complexes' bonding nature is analysed by NPA and EDA results. The bond index of the bond between Fe and SnX is provided by the WBI analysis. The FMO studies of these complexes show lesser HOMO-LUMO energy gaps in the values of 4.00 to 4.76 eV than that of [Fe(CO)5]. From the NBO analysis, the contribution to the bond formation of the Sn atom to the Fe-Sn bond is greater than that of the Fe atom. Similar contributions are seen in the carbonyl group (in the Fe-C bond), although the contribution of the carbon atom is larger than that of the tin atom.

Fine-tuning of organic optical double-donor NLO chromophores with DA-supported functional groups.

New strategic chromophores with updated fine-tuning of previously reported BLD1 and BLD3 chromophores were designed. BLD1 and BLD3 have silicon functional groups on the donor unit, and the bridge has a good chance of self-assembling, so in the present study we fine-tuned the isolating groups to the bulky cyclic alkene to improve their dipole moment and organic electro-optic (OEO) properties as well. To demonstrate the impact of cyclic alkenes on the electron-donating groups in sensible NLO chromophore designs, a thorough analysis and comparison of the chromophore synthesis, UV-Vis calculations, solvatochromic behavior of the chromophore, DFT quantum mechanical calculations, thermal stabilities, and much lower dipole moments was conducted.

Facile Synthesis of an Octagermacubane with Two Three‐Coordinate Germanium(0) Atoms and its Unique Radical Anion

AbstractThermolysis of a 1 : 1 mixture of tris(di‐tert‐butylmethylsilyl)germane 9 and bis(di‐tert‐butylmethylsilyl)germane 17 at 100 °C produces unexpectedly octagermacubane 18, having two 3‐coordinate Ge0 atoms (40 % yield). 18 was characterized by X‐ray crystallography and it is a singlet biradical (according to DFT quantum mechanical calculations and the absence of an EPR signal). Reactions of 18 with CH2Cl2 and H2O yield the novel dichloro‐octagermacubane 24 and hydroxy‐octagermacubane 25, respectively. Reduction of 18 with tBuMe2SiNa in THF produces an isolable octagermacubane radical anion 26‐Na. Based on X‐ray crystallography, EPR spectroscopy and DFT quantum mechanical calculations, 26‐Na is classified as a Ge‐centered radical anion.

Facile Synthesis of an Octagermacubane with Two Three-Coordinate Germanium(0) Atoms and its Unique Radical Anion.

Thermolysis of a 1 : 1 mixture of tris(di-tert-butylmethylsilyl)germane 9 and bis(di-tert-butylmethylsilyl)germane 17 at 100 °C produces unexpectedly octagermacubane 18, having two 3-coordinate Ge0 atoms (40 % yield). 18 was characterized by X-ray crystallography and it is a singlet biradical (according to DFT quantum mechanical calculations and the absence of an EPR signal). Reactions of 18 with CH2 Cl2 and H2 O yield the novel dichloro-octagermacubane 24 and hydroxy-octagermacubane 25, respectively. Reduction of 18 with tBuMe2 SiNa in THF produces an isolable octagermacubane radical anion 26-Na. Based on X-ray crystallography, EPR spectroscopy and DFT quantum mechanical calculations, 26-Na is classified as a Ge-centered radical anion.

The Versatile Photo-Thermal Behaviour of a 2-Hydroxyazobenzene.

Photochromic compounds are employed in implementing neuron surrogates. They will boost the development of neuromorphic engineering in wetware. In this work, the photochromic behaviours of (E)-3,4,6-trichloro-2-(p-diazenil)-phenol (t-DZH) and its conjugated phenoxide base (t-DZ) have been investigated experimentally in three different media: (1) pure acetonitrile, (2) in water and acetonitrile mixed in a 1/1 volume ratio, and (3) in an aqueous micellar solution of 3-(N,N-Dimethylmyristylammonio)propanesulfonate (SB3-14). The analysis of the spectral and kinetic features of t-DZH and t-DZ has been supported by quantum-mechanical DFT calculations, the maximum entropy method, and the determination of their colourability (C). The versatility of t-DZH and t-DZ makes them promising molecular probes of micro-environments and potential ingredients of photochemical oscillators required for implementing pacemaker neurons capable of communicating through optical signals in wetware.

Zn(II) complex with pyridine based 1,3-selenazolyl-hydrazone: Synthesis, structural characterization and DFT study

An octahedral complex of Zn(II) with a ligand from a class of pyridine- based 1,3-selenazolyl-hydrazones was synthesized and characterized by IR and NMR spectroscopy and single crystal X-ray diffraction analysis. The purity of the complex was confirmed by elemental analysis. Two ligands are coordinated in the neutral NNN-tridentate form forming a complex cation, while the positive charge is neutralized by [ZnCl4]2-. Complex crystallizes in monoclinic C2/c space group with the Zn atoms situated in a special position. The packing features of the novel complex were analyzed using Hirshfeld surfaces, construction of 2D pseudosymmetric plot and DFT quantum mechanical calculations and compared with the previously published sulfur-based isostere. The key difference in the structures, imposed by replacement of sulfur with selenium, were identified.

How mono- and diphosphine ligands alter regioselectivity of the Rh-catalyzed annulative cleavage of bicyclo[1.1.0]butanes

Rh(I)-catalyzed cycloisomerizations of bicyclo[1.1.0]butanes provide a fruitful approach to cyclopropane-fused heterocycles. Products and stereochemical outcome are highly dependent on catalyst. The triphenylphosphine (PPh3) ligand provides pyrrolidines, placing substituents anti to the cyclopropyl group. The 1,2-bis(diphenylphosphino)ethane (dppe) ligand yields azepanes with substituents syn to the cyclopropyl group. In this work, quantum mechanical DFT calculations pinpoint a reversal of regio- and diastereoselectivity, suggesting a concerted (double) C−C bond cleavage and rhodium carbenoid formation, driven by strain-release. The ligand-influenced cleavage step determines the regioselectivity of carbometalation and product formation, and suggests new applications of bicyclobutanes.

Computational Analysis of the Behavior of BODIPY Decorated Monofunctional Platinum(II) Complexes in the Dark and under Light Irradiation

Dual-action drugs are occupying an important place in the scientific landscape of cancer research owing to the possibility to combine different therapeutic strategies into a single molecule. In the present work, the behavior of two BODIPY-appended monofunctional Pt(II) complexes, one mononuclear and one binuclear, recently synthesized and tested for their cytotoxicity have been explored both in the dark and under light irradiation. Quantum mechanical DFT calculations have been used to carry out the exploration of the key steps, aquation and guanine attack, of the mechanism of action of Pt(II) complexes in the dark. Due to the presence of the BODIPY chromophore and the potential capability of the two investigated complexes to work as photosensitizers in PDT, time dependent DFT has been employed to calculate their photophysical properties and to inspect how the sensitizing properties of BODIPY are affected by the presence of the platinum “heavy atom”. Furthermore, also the eventual influence on of the photophysical properties due to the displacement of chlorido ligands by water and of water by guanine has been taken into consideration.

Phosphorus–nitrogen compounds. Part 58. Syntheses, structural characterizations and biological activities of 4-fluorobenzyl-spiro(N/O)cyclotriphosphazene derivatives

The starting compound, tetrachloro-4-fluorobenzyl-spiro(N/O)cyclotriphosphazene (2), was synthesized from the substitution reaction of hexachlorocyclotriphosphazatriene (N3P3Cl6; trimer; HCCP) with sodium 3-(4-fluorobenzylamino)-1-propanoxide (1). Reactions of spiro (2) with excess 1-(2-aminoethyl)-piperidine, 4-(2-aminoethyl)-morpholine, 1-(2-hydroxyethyl)piperidine and 4-(2-aminoethyl)morpholine yielded the fully substituted cyclotriphosphazene derivatives (2a–2d), respectively. Elemental analysis, mass spectrometry (ESI-MS), FTIR, 1H-, 13C- and 31P-NMR data confirmed the structure of the new cyclotriphosphazenes (2a–2d); and the crystal structure of 2 was also identified by X-ray crystallography. The quantum mechanical DFT calculations of 2 were performed to estimate the geometry optimization, total energy, orientation of frontier molecular orbitals (HOMOs and LUMOs), and chemical parameters. In addition, antibacterial and antifungal activities of the fully substituted 4-fluorobenzyl-spiro(N/O)cyclotriphosphazenes (2a–2d) were investigated against G(+) and G(−) bacteria and fungi. Using agarose gel electrophoresis, the DNA cleavage activities of these phosphazenes on double-stranded plasmid DNA were evaluated. To evaluate the abilities of compounds 2a–2d to inhibit cell proliferation in different concentrations, the antiproliferative and antimigrative activities against prostate adenocarcinoma (PC3), breast cancer (MCF7) and colon cancer (HT29) cell lines were studied in vitro; and the compound 2c was determined to be the most efficient against the three cancer cells. Communicated by Ramaswamy H. Sarma

Azo-hydrazone molecular switches: Synthesis and NMR conformational investigation.

A series of five intramolecularly hydrogen-bonded arylhydrazone (aryl = phenol, p-nitrophenol, anisole, quinoline) derived molecular switches have been synthesized and characterized by NMR and HRMS techniques. It was found that the compounds exist as different isomers in solution. An investigation of both conformational and/or configurational changes of the azo-hydrazone compounds was carried out by 1D 1 H- and 13 C- spectra, 2D NOESY, COSY, HSQC, and HMBC techniques. It was found that these stimuli-responsive molecular switches exist mainly in the E form by intramolecularly hydrogen bonded between NH and the pyridine nitrogen at equilibrium. Deprotonation of the neutral E form yields the E' deprotonated isomer. Prediction of 13 C-NMR chemical shifts was achieved by DFT quantum mechanical calculations. Anions have traditionally been difficult to calculate correctly, so calculations of the anion using different functionals, basis sets, and solvent effects are also included. Deuterium isotope effects on the 13 C-NMR chemical shifts were employed in the assignments and furthermore utilized as indicators of intramolecular hydrogen bonding. Studies in various organic solvents including CDCl3 , CD3 CN, and DMSO-d6 were also performed aiming to monitor dynamic changes over several days. The effect of the hydrogen bonded solvents leads to Z forms.

Synthesis, isolation and characterization of a stable lithium stannenolate. A keto or an enol tautomer?

The synthesis and isolation of the first stable lithium stannenolate is reported. Structural and spectroscopic data, in combination with DFT quantum-mechanical calculations, indicate that the stannenolate adopts the keto tautomeric structure.

A High Yield Synthesis of an Octastannacubane and a Bis(silyl) Stannylene via Reductive Elimination of a Silane.

Thermolysis of tris(silyl) tin hydride 2 at 70 °C for 3 hours results in elimination of tBu2 MeSiH and generation of bis(silyl) stannylene 3 which dimerizes instantaneously yielding distannene 4. Compound 3 can be trapped by NHCMe yielding stannylene-NHCMe complex 5. Upon heating (70 °C, 24 h) 4 yields stannyl radical 8 along with pentastannatricyclo[2.1.0.02, 5 ]pentane 10 (ca. 30 %) and traces (ca. 5 %) of the novel octastannacubane 9. Remarkably, octastannacubane 9 is produced in 70 % yield by mild heating (50 °C) of 1,1,2,2-tetrasilyldistannane 11, along with tBu2 MeSiH. Octastannacubane 9 was characterized by X-ray crystallography, NMR and UV/Vis spectroscopy. Based on DFT quantum-mechanical calculations the 11 → 9 transformation occurs via reductive elimination of two tBu2 MeSiH molecules from 11 yielding a distannyne, (or its bis-stannylene isomer), followed by its tetramerization.

Synthesis of Stable Dianionic Cyclic Silenolates and Germenolates.

In this contribution a convenient synthetic method to obtain the previously unknown dianionic cyclic silenolates and germenolates is described. These dianions 2a,b and 4a,b are easily accessible via a one-pot synthetic protocol in high yields. Their structural properties were analyzed by a combination of NMR, single-crystal X-ray crystallography, and DFT quantum mechanical calculations. Moreover, the reactivity of 2a,b and 4a,b with selected examples of electrophiles was investigated. 2a and 4a were reacted with ClSiiPr3 to give new examples of polysilanes and polygermanes with exocyclic double bonds. The reaction of 2b with ClSiMe2SiMe2Cl led to the formation of the acyl bicyclo[2.2.2]octasilane 6. Moreover, the reaction of 2a,b and 4a,b with MeI, as an example of a carbon-centered electrophile, led to selective alkylation reactions at the negatively charged silicon and germanium atoms. The corresponding methylated structures 9a,b and 10a,b were formed in nearly quantitative yields. The competitive reactivity of the silyl and silenolate anion toward 1 equiv of ClSiMe3 showed that the outcome of the reaction was strongly influenced by the substituent at the carbonyl moiety. 2a reacted with 1 equiv of ClSiMe3 to give the corresponding cyclic silenolate S1a, which demonstrated that the silyl anion is more nucleophilic than the silenolate with attached aromatic groups. 2b, on the other hand, reacted with 1 equiv of ClSiMe3 to give the bicyclic compound 11via an intramolecular sila-Peterson alkenation reaction. These findings clearly showed that the alkyl-substituted silenolate is more nucleophilic than the silyl anion. This paper demonstrates that 2a,b and 4a,b have the potential to be used as unique building blocks for complex polysilane and polygermane frameworks.

Solvent Effects and Aggregation Phenomena Studied by Vibrational Optical Activity and Molecular Dynamics: The Case of Pantolactone.

Raman and Raman optical activity (ROA), IR, and vibrational circular dichroism (VCD) spectra of (R)- and (S)-pantolactone have been recorded in three solvents. ROA has been employed on water and DMSO solutions, VCD on DMSO and CCl4 solutions. In the last solvent, monomer–dimer equilibrium is present. Due to the low conformational flexibility of the isolated molecule and to the possibility of aggregation, this compound has been used here to test different protocols for computation of the spectroscopic responses taking into account solvent effects. Molecular dynamics (MD) simulations have been carried out together with statistical clustering methods based on collective variables to extract the structures needed to calculate the spectra. Quantum mechanical DFT calculations based on PCM are compared with approaches based on different representations of the solvent shell (MM or QM level). Appropriate treatment of the solvent permits obtaining of good band-shapes, with the added advantage that the MD analysis allows one to take into account flexibility of dimeric structures justifying the broadness of observed bands and the absence of intense VCD couplets in the carbonyl and OH stretching regions.

A multi-methodological inquiry of the behavior of cisplatin-based Pt(IV) derivatives in the presence of bioreductants with a focus on the isolated encounter complexes.

The study of Pt(IV) antitumor prodrugs able to circumvent some drawbacks of the conventional Pt(II) chemotherapeutics is the focus of a lot of attention. This paper reports a thorough study based on experimental methods (reduction kinetics, electrochemistry, tandem mass spectrometry and IR ion spectroscopy) and quantum-mechanical DFT calculations on the reduction mechanism of cisplatin-based Pt(IV) derivatives having two hydroxido (1), one hydroxido and one acetato (2), or two acetato ligands (3) in axial position. The biological reductants glutathione and ascorbic acid were taken into consideration. The presence of a hydroxido ligand resulted to play an important role in the chemical reduction with ascorbic acid, as verified by 15N-NMR kinetic analysis using 15N-enriched complexes. The reactivity trend (1 > 2 > 3) does not reflect the respective reduction peak potentials (1 < 2 < 3), an inverse relationship already documented in similar systems. Turning to a simplified environment, the Pt(IV) complexes associated with a single reductant molecule (corresponding to the encounter complex occurring along the reaction coordinate in bimolecular reactions in solution) were characterized by IR ion spectroscopy and sampled for their reactivity under collision-induced dissociation (CID) conditions. The complexes display a comparable reduction reactivity ordering as that observed in solution. DFT calculations of the free energy pathways for the observed fragmentation reactions provide theoretical support for the CID patterns and the mechanistic hypotheses on the reduction process are corroborated by the observed reaction paths. The bulk of these data offers a clue of the intricate pathways occurring in solution.Graphic abstract.

Structure characterization and biological activity of 2-arylbenzofurans from an Indonesian plant, Sesbania grandiflora (L.) Pers

A new 2-arylbenzofuran, sesbagrandiflorain C (1), together with four known compounds, 2-(3,4-dihydroxy-2-methoxyphenyl)-4-hydroxy-6-methoxybenzofuran-3-carbaldehyde (2), 2-(4-hydroxy-2-methoxyphenyl)-5,6-dimethoxybenzofuran-3-carboxaldehyde (3), sesbagrandiflorain A (4) and sesbagrandiflorain B (5), have been isolated from the stem bark of an Indonesian plant, Sesbania grandiflora (L.) Pers. The chemical structure of compound 1 was elucidated by UV, IR, MS, and NMR spectroscopic techniques. The proton and carbon NMR resonances of 1 were also compared with the predicted chemical shifts obtained from DFT quantum mechanical calculations with Gaussian. None of the compounds showed antibacterial activity against Bacillus subtilis, Escherichia coli, Mycobacterium smegmatis, Pseudomonas aeruginosa, and Staphylococcus aureus in an agar diffusion assay. However, sesbagrandiflorains A (4) and B (5) exhibited moderate activity against Mycobacterium tuberculosis H37Rv. In addition, compounds 1 – 5 have moderate cytotoxicity against HeLa, HepG2, and MCF-7 cancer cell lines.

Experimental and theoretical study of Aspartic acid

The aim of this research is to detect zwittterionic structure of the aspartic acid and confirm the experimental spectra with quantum chemical calculations. The experimental IR and Raman spectra of aspartic acid powder show no vibrational bands of OH and NH stretching in expected spectral region. We assume that zwitterionic structure of aspartic acid is responsible for lowering the frequencies of these vibrations. An extensive experimental and computational research supports this assumption. Our DFT calculation strongly suggests the need for the dielectric environment in order to stabilize the zwitterionic structure of a single molecule. The network of intermolecular hydrogen bonding between aspartic acid molecules provides this dielectric environment. The DFT quantum mechanical calculations corroborate this assumption by optimizing a four-member group of molecules, which also gives an explanation of broad IR spectrum lines.

Anharmonic Vibrational States of Solids from DFT Calculations. Part I: Description of the Potential Energy Surface.

A computational approach is presented to compute anharmonic vibrational states of solids from quantum-mechanical DFT calculations by taking into explicit account phonon-phonon couplings via the vibrational configuration interaction (VCI) method. The Born-Oppenheimer potential energy surface (PES) is expanded in a Taylor's series in terms of harmonic normal coordinates, centered at the equilibrium nuclear configuration, is truncated to quartic order, and contains one-mode, two-mode, and three-mode interatomic force constants. The description of the anharmonic terms of the PES involves the numerical evaluation of high-order energy derivatives (cubic and quartic in our case) with respect to nuclear displacements and constitutes the most computationally demanding step in the characterization of anharmonic vibrational states of materials. Part I is devoted to the description of the PES. Four different numerical approaches are presented for the description of the potential, all based on a grid representation of the PES in the basis of the normal coordinates, that require different ingredients (energy and/or forces) to be evaluated at each point (i.e., nuclear configuration) of the grid. The numerical stability and relative computational efficiency of the various schemes for the description of the PES are discussed on two molecular systems (water and methane) and two extended solids (Ice-XI and MgH2). All the presented algorithms are implemented into a developmental version of the Crystal program.