Correspondence on "Beyond the Dimer and Trimer: Tetraspiro[2.1.25.1.29.1.213.13]hexadecane-1,3,5,7-tetraone - the Cyclic Tetramer of Carbonylcyclopropane".

The International Union of Pure and Applied Chemistry (IUPAC) name given in the title is incorrect. The correct IUPAC name for this molecule is tetraspiro[2.1.25.1.29.1.213.13]hexadecane-4,8,12,16-tetraone. The incorrect name given in the title, unfortunately, makes the carbon atom hexavalent at two different (3 and 5) positions. In addition, the two other keto groups (at positions 1 and 7) would appear on two of the cyclopropane rings if one adopts to the incorrect name. Nevertheless, this wrong name is a good example to discuss the importance of IUPAC nomenclature in the classroom with students.

Theoretical Studies on the Isomerization Kinetics of Low-Lying Isomers of the SiC4H2 System.

The low-lying isomers of SiC4H2 are investigated to understand the kinetics of isomerization pathways using density functional theory. In our earlier work, we studied the various possible isomers (J. Phys. Chem. A, 2020, 124, 987-1002) and the chemical bonding of low-lying isomers of SiC4H2 (J. Phys. Chem. A, 2022, 126, 9366-9374). Among them, four isomers, 1-ethynyl-3-silacycloprop-1-en-3-ylidene (1), 3-silapent-1,4-diyn-3-ylidene (2), 1-silapent-1,2,3,4-tetraen-1-ylidene (4), and 1-silapent-2,4-diyn-1-ylidene (5) have already been identified in the laboratory. The previously known theoretical isomer 2-methylene-1-silabicyclo[1.1.0]but-1(3)-en-4-ylidene (3) and the newly identified unknown isomer through the present kinetic studies 5-silabicyclo[2.1.0]pent-1(4),2-dien-5-ylidene (N6) remain elusive in the laboratory to date. The isomerization pathways of the low-lying isomers of SiC4H2 are predicted through the transition state structures. Intrinsic reaction coordinate analysis identifies the minimum energy reaction pathways connecting the transition state from one isomer to another of the investigated system. The present kinetic data reveal the isomerization of global minimum energy isomer 1 to thermodynamically stable low-lying isomers, 2 and 5. Interestingly, isomer 3 interconverts to the experimentally known low-energy isomer 4, the second most thermodynamically stable isomer among them. The thermodynamic and kinetic parameters of the low-lying isomers of SiC4H2 are also documented in this work. The rate coefficient and equilibrium constant for isomerization reactions are calculated using the Rice-Ramsperger-Kassel-Marcus theory. The equilibrium constant delineates the difficulties in forming N6 and 3 through the isomerization pathways. Furthermore, ab initio molecular dynamics studies dictate the stability of low-lying isomers of SiC4H2 within the time scale of the simulation.

Energetic and Spectroscopic Properties of Astrophysically Relevant MgC4H Radicals Using High-Level Ab Initio Calculations.

Considering the importance of magnesium-bearing hydrocarbon molecules (MgCnH; n = 2, 4, and 6) in the carbon-rich circumstellar envelopes (e.g., IRC+10216), a total of 28 constitutional isomers of MgC4H have been theoretically investigated using density functional theory (DFT) and coupled-cluster methods. The zero-point vibrational energy corrected relative energies at the ROCCSD(T)/cc-pCVTZ level of theory reveal that the linear isomer, 1-magnesapent-2,4-diyn-1-yl (1, 2Σ+), is the global minimum geometry on the MgC4H potential energy surface. The latter has been detected both in the laboratory and in the evolved carbon star, IRC+10216. The calculated spectroscopic data for 1 match well with the experimental observations (error ∼ 0.78%) which validates our theoretical methodology. Plausible isomerization processes happening among different isomers are examined using DFT and coupled-cluster methods. CASPT2 calculations have been performed for a few isomers exhibiting multireference characteristics. The second most stable isomer, 1-ethynyl-1λ3-magnesacycloprop-2-ene-2,3-diyl (2, 2A1, µ = 2.54 D), is 146 kJ mol-1 higher in energy than 1 and possibly the next promising candidate to be detected in the laboratory or in the interstellar medium in future.

CCSD(T) Rotational Constants for Highly Challenging C5H2 Isomers-A Comparison between Theory and Experiment.

We evaluate the accuracy of CCSD(T) and density functional theory (DFT) methods for the calculation of equilibrium rotational constants (Ae, Be, and Ce) for four experimentally detected low-lying C5H2 isomers (ethynylcyclopropenylidene (2), pentatetraenylidene (3), ethynylpropadienylidene (5), and 2-cyclopropen-1-ylidenethenylidene (8)). The calculated rotational constants are compared to semi-experimental rotational constants obtained by converting the vibrationally averaged experimental rotational constants (A0, B0, and C0) to equilibrium values by subtracting the vibrational contributions (calculated at the B3LYP/jun-cc-pVTZ level of the theory). The considered isomers are closed-shell carbenes, with cumulene, acetylene, or strained cyclopropene moieties, and are therefore highly challenging from an electronic structure point of view. We consider both frozen-core and all-electron CCSD(T) calculations, as well as a range of DFT methods. We find that calculating the equilibrium rotational constants of these C5H2 isomers is a difficult task, even at the CCSD(T) level. For example, at the all-electron CCSD(T)/cc-pwCVTZ level of the theory, we obtain percentage errors ≤0.4% (Ce of isomer 3, Be and Ce of isomer 5, and Be of isomer 8) and 0.9-1.5% (Be and Ce of isomer 2, Ae of isomer 5, and Ce of isomer 8), whereas for the Ae rotational constant of isomers 2 and 8 and Be rotational constant of isomer 3, high percentage errors above 3% are obtained. These results highlight the challenges associated with calculating accurate rotational constants for isomers with highly challenging electronic structures, which is further complicated by the need to convert vibrationally averaged experimental rotational constants to equilibrium values. We use our best CCSD(T) rotational constants (namely, ae-CCSD(T)/cc-pwCVTZ for isomers 2 and 5, and ae-CCSD(T)/cc-pCVQZ for isomers 3 and 8) to evaluate the performance of DFT methods across the rungs of Jacob's Ladder. We find that the considered pure functionals (BLYP-D3BJ, PBE-D3BJ, and TPSS-D3BJ) perform significantly better than the global and range-separated hybrid functionals. The double-hybrid DSD-PBEP86-D3BJ method shows the best overall performance, with percentage errors below 0.5% in nearly all cases.

In Silico Drug Design and Analysis of Dual Amyloid-Beta and Tau Protein-Aggregation Inhibitors for Alzheimer's Disease Treatment.

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disorder that gradually leads to the state of dementia. The main features of AD include the deposition of amyloid-beta peptides (Aß), forming senile plaques, and the development of neurofibrillary tangles due to the accumulation of hyperphosphorylated Tau protein (p-tau) within the brain cells. In this report, seven dual-inhibitor molecules (L1-7) that can prevent the aggregation of both Aß and p-tau are suggested. The drug-like features and identification of the target proteins are analyzed by the in silico method. L1-7 show positive results in both Blood-Brain Barrier (BBB) crossing and gastrointestinal absorption, rendering to the results of the permeation method. The molecular docking test performed for L1-7 shows binding energies in the range of -4.9 to -6.0 kcal/mol towards Aß, and -4.6 to -5.6 kcal/mol for p-tau. The drug's effectiveness under physiological conditions is assessed by the use of solvation models on the investigated systems. Further, the photophysical properties of L1-3 are predicted using TD-DFT studies.

Planar pentacoordinate carbon in [XC7H2]2+ (X = Be and Mg) and its derivatives.

The planar pentacoordinate carbon (ppC) atom is theoretically established here in [XC7H2]2+ and [XSi2C5H2]2+, where X = Be and Mg, using density functional theory. Inclusion compounds with alkali and alkaline earth metal ions are identified with the monomer units of tricyclic C7H2 and Si2C5H2 isomers with a planar tetracoordinate carbon (ptC) atom. While all alkali and some alkaline earth metals (Ca2+, Sr2+, and Ba2+) stabilize the ptC isomer in both cases, Be2+ and Mg2+ ions form a bond directly with the ptC atom, thus making it a ppC atom. The theoretical binding energies computed at the PBE0-D3/def2-TZVP level of theory are ∼-9.68, -10.42, -5.85, and -5.47 eV for [BeC7H2]2+, [BeSi2C5H2]2+, [MgC7H2]2+, and [MgSi2C5H2]2+, respectively.

Why an integrated approach between search algorithms and chemical intuition is necessary?

Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C12O2Mg2 system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.

From Molecules with a Planar Tetracoordinate Carbon to an Astronomically Known C5H2 Carbene.

Ethynylcyclopropenylidene (2), an isomer of C5H2, is a known molecule in the laboratory and has recently been identified in Taurus Molecular Cloud-1 (TMC-1). Using high-level coupled-cluster methods up to the CCSDT(Q)/CBS level of theory, it is shown that two isomers of C5H2 with a planar tetracoordinate carbon (ptC) atom, (SP-4)-spiro[2.2]pent-1,4-dien-1,4-diyl (11) and (SP-4)-spiro[2.2]pent-1,4-dien-1,5-diyl (13), serve as the reactive intermediates for the formation of 2. Here, a theoretical connection has been established between molecules containing ptC atoms (11 and 13) and a molecule (2) that is present nearly 430 light years away, thus providing evidence for the existence of ptC species in the interstellar medium. The reaction pathways connecting the transition states and the reactants and products have been confirmed by intrinsic reaction coordinate calculations at the CCSDT(Q)/CBS//B3LYP-D3BJ/cc-pVTZ level. While isomer 11 is non-polar (µ = 0), isomers 2 and 13 are polar, with dipole moment values of 3.52 and 5.17 Debye at the CCSD(T)/cc-pVTZ level. Therefore, 13 is also a suitable candidate for both laboratory and radioastronomical studies.

Why Are MgC3H Isomers Missing in the Interstellar Medium?

Considering the recent findings of linear doublet (2Σ+) MgCnH isomers (n = 2, 4, and 6) in the evolved carbon star IRC+10216, various structural isomers of MgC3H and MgC3H+ are theoretically investigated here. For MgC3H, 11 doublet and 8 quartet stationary points ranging from 0.0 to 71.8 and 0.0 to 110.1 kcal mol-1, respectively, have been identified initially at the UωB97XD/6-311++G(2d,2p) level. To get accurate relative energies, further energy evaluations are carried out for all isomers with coupled cluster methods and thermochemical modules such as G3//B3LYP, G4MP2, and CBS-QB3 methods. Unlike the even series, where the global minima are linear molecules with a Mg atom at one end, in the case of MgC3H, the global minimum geometry turns out to be a cyclic isomer, 2-magnesabicyclo[1.1.0]but-1,3,4-triyl (1, C2v, 2A1). In addition, five low-lying isomers, magnesium-substituted cyclopropenylidene (2, Cs, 2A'), 1-magnesabut-2,3-dien-1-yl-4-ylidene (3, Cs, 2A″), 1-magnesabut-2-yn-1-yl-4-ylidene (4, Cs, 2A″), 2λ3-magnesabicyclo[1.1.0]but-1,3-diyl-4-ylidene (5, C2v;, 2A1), and 1-magnesabut-2,3-dien-2-yl-4-ylidene (6, C∞v, 2Σ+), were also identified. The doublet linear isomer of MgC3H, 1-magnesabutatrienyl (10, C∞v, 2Σ+) turns out to be a minimum but lies 54.1 kcal mol-1 above 1 at the ROCCSD(T)/cc-pVTZ level. The quartet (4Σ+) electronic state of 10 was also found to be a minimum, but it lies 8.0 kcal mol-1 above 1 at the same level. Among quartets, isomer 10 is the most stable molecule. The next quartet electronic state (of isomer 11) is 34.4 kcal mol-1 above 10, and all other quartet electronic states of other isomers are not energetically close to low-lying doublet isomers 2 to 6. Overall, the chemical space of MgC3H contains more cyclic isomers (1, 2, and 3) on the low-energy side unlike their even-numbered MgCnH counterparts (n = 2, 4, and 6). Though the quartet electronic state of 10 is linear, it is not the global minimum geometry on the MgC3H potential energy surface. Isomerization pathways among the low-lying isomers (doublets of 1-4 and a quartet of 10) reveal that these molecules are kinetically stable. For the cation, MgC3H+, the cyclic isomers (1+, 2+, and 3+) are on the low-energy side. The singlet linear isomer, 10+, is a fourth-order saddle point. The low-lying cations are quite polar, with dipole moment values of >7.00 D. The current theoretical data would be helpful to both laboratory astrophysicists and radioastronomers for further studies on the MgC3H0/+ isomers.

Six Low-Lying Isomers of C11H8 Are Unidentified in the Laboratory-A Theoretical Study.

Isomers of C11H8 have been theoretically examined using density functional theory and coupled-cluster methods. The current investigation reveals that 2aH-cyclopenta[cd]indene (2), 7-ethynyl-1H-indene (6), 4-ethynyl-1H-indene (7), 6-ethynyl-1H-indene (8), 5-ethynyl-1H-indene (9), and 7bH-cyclopenta[cd]indene (10) remain elusive till date in the laboratory. The puckered low-lying isomer 2 lies at 9 kJ mol-1 below the experimentally known molecule, cyclobuta[de]naphthalene (3), at the fc-CCSD(T)/cc-pVTZ//fc-CCSD(T)/cc-pVDZ level of theory. 2 lies at 36 kJ mol-1 above the thermodynamically most stable and experimentally known isomer, 1H-cyclopenta[cd]indene (1), at the same level. It is identified that 1,2-H transfer from 1 yields 2H-cyclopenta[cd]indene (14) and subsequent 1,2-H shift from 14 yields 2. Appropriate transition states have been identified, and intrinsic reaction coordinate calculations have been carried out at the B3LYP/6-311+G(d,p) level of theory. Recently, 1-ethynyl-1H-indene (11) has been detected using synchrotron-based vacuum ultraviolet ionization mass spectrometry. 2-Ethynyl-1H-indene (4) and 3-ethynyl-1H-indene (5) have been synthetically characterized in the past. While the derivatives of 7bH-cyclopenta[cd]indene (10) have been isolated elsewhere, the parent compound remains unidentified till date in the laboratory. Although C11H8 is a key elemental composition of astronomical interest for the formation of polycyclic aromatic hydrocarbons in the interstellar medium, none of its low-lying isomers have been characterized by rotational spectroscopy though they are having a permanent dipole moment (µ ≠ 0). Therefore, energetic and spectroscopic properties have been computed, and the present investigation necessitates new synthetic studies on C11H8, in particular 2, 6-10, and also rotational spectroscopic studies on all low-lying isomers.

Si2C5H2 isomers - search algorithms versus chemical intuition.

The pros and cons of using search algorithms alone in identifying new geometries have been discussed by using the Si2C5H2 elemental composition as an example. Within 30 kcal mol-1 at the CCSD(T)/def2-TZVP//PBE0/def2-TZVP level of theory, the coalescence kick and cuckoo methods postulate merely four isomers (1, 3, 6, and 7) for Si2C5H2 (O. Yañez et. al., Chem. Commun., 2017, 53, 12112). On the contrary, chemical intuition yields fourteen (2, 4, 5, and 8-18) new isomers within the same energy range at the B3LYP/6-311++G(2d,2p) level of theory. Based on the relative energies of the first eleven isomers of Si2C5H2 (1, C2v, 0.00; 2, Cs, 21.39; 3, Cs, 21.95; 4, Cs, 22.76; 5, Cs, 24.74; 6, Cs, 25.34; 7, Cs, 25.64; 8, Cs, 25.79; 9, Cs, 27.20; 10, C2v, 28.59; and 11, C2v, 29.16 kcal mol-1) calculated at the CCSD(T)/cc-pVTZ level of theory, it is evident that the search algorithms had missed at least seven isomers in the same energy range. The relative energy gaps of isomers 12-18 fall in the range of 30-40 kcal mol-1 at the latter level of theory. Consequentially, this scenario triggers a speculation going forward with search algorithms alone in the search of all new isomers. While one cannot underestimate the power of these algorithms, the role of chemical intuition may not be completely neglected. Retrospectively, the fourteen new isomers found by chemical intuition may help in writing better search algorithms. All eighteen isomers - including the most stable isomer with a planar tetracoordinate carbon atom 1- remain elusive in the laboratory to date. Thus, structural and spectroscopic parameters have been presented here, which may possibly aid the future experimental studies.

Theoretical Studies of SiC4H2 Isomers Delineate Three Low-Lying Silylidenes Are Missing in the Laboratory.

Eleven isomers of SiC4H2 lying within 50 kcal mol-1 have been theoretically investigated using density functional theory and high-level coupled-cluster methods. Among them, four isomers, 1-ethynyl-3-silacycloprop-1(2)-en-3-ylidene (1), diethynylsilylidene (2), 1-sila-1,2,3,4-pentatetraenylidene (4), and 1,3-butadiynylsilylidene (5), have already been identified in the laboratory. The current investigation reports three low-lying (<1 eV) silylidenes [2-methylenesilabicyclo[1.1.0]but-1(3)-en-4-ylidene (3), 4-sila-2-methylenebicyclo[1.1.0]but-1(3)-en-4-ylidene (6), and 3-ethynyl-1-silapropadienylidene (7)] and three high-lying (>1 eV) silylidenes [2-sila-(didehydrovinylidene)cyclopropene (8), an isomer with a planar tetracoordinate carbon (ptC) atom (10), and 1-ethynyl-1-silapropadienylidene (11)], which remain elusive in the laboratory to date. Isomer 9 also contains a ptC atom, which turned out to be a transition state at all levels. Though all isomers are polar (µ ≠ 0), rotational spectrum is available only for 4. Using matrix isolation, three isomers (1, 2, and 5) have been trapped in the laboratory at 10 K. Considering the astrochemical relevance of silicon-carbide clusters in the interstellar medium, the current theoretical data demand new molecular spectroscopic studies on SiC4H2. Surprisingly, unlike the isovalent C5H2 isomers, where the bent carbenes are yet to be identified in the laboratory, the bent silylidenes (2 and 5) have been trapped in the case of SiC4H2. In both the cases, molecules with transannular C-C and/or Si-C bonds remain elusive, though they lie in the low-lying region. Using suitable precursors, whether these peculiar geometries (especially 3 and 6) would be identified or not in the laboratory needs to be addressed by molecular spectroscopists. The present investigation documents structural and spectroscopic information of SiC4H2 isomers, which may compliment future molecular spectroscopic observations including radioastronomical searches.

MgC6H2 Isomers: Potential Candidates for Laboratory and Radioastronomical Studies.

Eighty three stationary points of MgC6H2 isomers spanning from 0 to 215 kcal mol-1 have been theoretically identified using density functional theory at the B3LYP/6-311++G(2d,2p) level of theory. Among them, four low-lying isomers lying within 23.06 kcal mol-1 (1 eV) have been further characterized in detail using high-level coupled-cluster (CC) methods. The thermodynamically most stable isomer turns out to be 1-magnesacyclohepta-4-en-2,6-diyne (1). The other three isomers, 3-magnesahepta-1,4,6-triyne (2), 1-magnesacyclohepta-2,3,4-trien-6-yne (3), and 1-magnesahepta-2,4,6-triyne (4) lie 8.24, 19.76, and 21.36 kcal mol-1, respectively, above 1 at the ae-CCSD(T)/cc-pCVTZ level of theory. All the four isomers are polar with a permanent electric dipole moment (µ ≠ 0). Hence, they are potential candidates for rotational spectroscopic studies. Considering the recent identification of magnesium-bearing hydrocarbons such as, MgC2H and MgC4H in IRC+10216, it is believed that the current theoretical data may be of relevance to laboratory molecular spectroscopic and radioastronomical studies on MgC6H2 isomers. The energetic and spectroscopic information gathered in this study would aid the detection of low-lying MgC6H2 isomers in the laboratory, which are indispensable for radioastronomical studies. It is also noted here that neither the National Institute of Standards and Technology Chemistry WebBook nor the Kinetic Database for Astrochemistry lists any isomer of MgC6H2 at the moment. Therefore, these isomers are studied here theoretically for the very first time.

Theoretical Studies of Two Key Low-Lying Carbenes of C5H2 Missing in the Laboratory.

The equilibrium geometries and spectroscopic properties of two key singlet carbenes, buta-1,3-diynylcarbene (6) and 2-methylenebicyclo[1.1.0]but-1(3)-en-4-ylidene (9), which have not been experimentally observed to date, are investigated using high-level coupled-cluster (CC) methods. The current theoretical study necessitates new experimental data on C5H2 isomers considering the relevance of these molecules to interstellar chemistry. Bent-pentadiynylidene (4) has been missing in the laboratory and the prime focus of our earlier theoretical work. The present theoretical study indicates that isomers 6 and 9 are also viable experimental targets. Apart from ethynylcyclopropenylidene (2), pentatetraenylidene (3), ethynylpropadienylidene (5), and 3-(didehydrovinylidene)cyclopropene (8), which are identified by Fourier transform microwave spectroscopy, the dipole moments of elusive 4, 6, and 9 are also nonzero (µ ≠ 0). The relative energies of these isomers, calculated at the CCSDT(Q)/CBS level of theory, with respect to linear triplet pentadiynylidene (1) reveal that they all lie within 25.1 kcal mol-1. Therefore, geometric, energetic, aromatic, and spectroscopic parameters are reported here, which may assist the efforts of molecular spectroscopists in the future. Anharmonic vibrational calculations on isomers 6 and 9 indicate that the former is loosely bound and would be challenging to be detected experimentally. Among the undetected carbenes, 9 may be considered as a potential target molecule considering its higher polarity and aromatic nature.

From High-Energy C7H2 Isomers with A Planar Tetracoordinate Carbon Atom to An Experimentally Known Carbene.

In this work, we use high-level ab initio procedures to show that the high-energy isomers of C7H2 with a planar tetracoordinate carbon (ptC) atom serve as reactive intermediate leading to the formation of an experimentally known ring-chain carbene, 1-(buta-1,3-diynyl)cyclopropenylidene (2). Among the experimentally known isomers of C7H2, the latter is the only low-lying ring-chain carbene identified by Fourier-transform microwave spectroscopy. Here we investigate the ring-opening pathways of C-C single bonds connected to the ptC atom in three different C7H2 isomers using coupled-cluster and density functional theory methods. These three isomers [ptC1 ( C2 v; X̃1A1), ptC2 ( C s; X̃1A'), and ptC3 ( C s; X̃1A')] are found to be local minima on the C7H2 potential-energy surface at both CCSD(T)/cc-pVTZ and B3LYP/6-311+G(d,p) levels of theory. The transition states and minimum-energy pathways connecting the reactants (ptC isomers) and the products have been found via intrinsic reaction coordinate calculations at the B3LYP/6-311+G(d,p) level of theory. The high-energy ptC isomers (ptC2 and ptC3) lead to the formation of 2, while the low-energy ptC isomer, ptC1, rearranges to a bicyclic carbene, bicyclo[4.1.0]hepta-4,6-diene-2-yne-7-ylidene (6). In the latter, we note that both the reactant and the product are yet to be identified in the laboratory. Relative energies, activation energies, reaction energies, and nucleus independent chemical shift values have been calculated to access the thermodynamic and kinetic stabilities and the aromatic nature of these peculiar molecules. Rotational and centrifugal distortion constants have also been estimated for all ptC isomers, which may assist the efforts of microwave spectroscopists.

Energetic and spectroscopic properties of the low-lying C7H2 isomers: a high-level ab initio perspective.

We use high-level ab initio CCSD(T) and CCSDT(Q) methods to investigate the energetic and spectroscopic properties of nine low-lying isomers of C7H2, which lie within 1 eV. Among these, heptatriynylidene (1), 1-(buta-1,3-diynyl)cyclopropenylidene (2) and heptahexaenylidene (9) have been detected experimentally. The other six isomers, 1,2-(diethynyl)cyclopropenylidene (3), bicyclo[4.1.0]hepta-1,2,4,5-tetraene-7-ylidene (4), cyclohepta-1,2,3,4-tetraen-6-yne (5), bicyclo[4.1.0]hepta-4,6-diene-2-yne-7-ylidene (6), bicyclo[4.1.0]hepta-1,5-diene-3-yne-7-ylidene (7) and 1-(buta-1,3-diynyl)propadienylidene (8), remain hypothetical to date. Except for 1, all of the isomers are associated with a non-zero dipole moment (µ≠ 0). Although Fourier-transform microwave spectroscopy had detected 2 and 9, our study reveals that six hypothetical isomers (3-8) are thermodynamically sandwiched between the experimentally known and astronomically relevant isomers 2 and 9. The structural parameters, dipole moments, rotational and centrifugal distortion constants, harmonic vibrational frequencies, and infra-red intensities presented here may be useful for the laboratory detection of these previously unidentified isomers (3-8) and also all others (2-9) in astronomical sources.

Matrix-Isolated Infrared Absorption Spectrum of CH2IOO Radical.

The peroxyiodomethyl radical, CH2IOO, was generated in cryogenic matrices using tandem supersonic nozzles. One hyperthermal nozzle decomposes diiodomethane (CH2I2) to generate intense beams of CH2I radicals, while the second nozzle continuously deposits O2/argon (Ar) on the matrix at 10 K. The CH2I and O2 in the Ar matrix react to produce the target peroxy radical (CH2IOO). The absorption spectra of the products are monitored with a Fourier transform infrared spectrometer. Eight of the 12 fundamental infrared bands for CH2IOO were observed in an argon matrix at 5 K. The experimental frequencies (cm(-1)) are ν3 = 1407.3, ν4 = 1230.4, ν5 = 1223.2, ν6 = 1085.3, ν7 = 919.9, ν8 = 839.9, ν9 = 567.5, and ν10 = 496.2. Additional confirmation for the vibrational assignment comes from a study of the CH2I(18)O(18)O isotopic species. The six observed frequencies (cm(-1)) for CH2I(18)O(18)O are ν3 = 1407.8, ν4 = 1228.0, ν6 = 1030.8, ν7 = 899.6, ν8 = 836.0, and ν10 = 494.6. Unlike CH2I(16)O(16)O, the ν5 and ν9 bands were not observed for CH2I(18)O(18)O. To guide the experimental analysis, ab initio calculations of the infrared spectrum based on second-order vibrational perturbation theory were performed using force fields computed with relativistic coupled-cluster methods. The experimental frequencies are shown to be in good agreement with the computed fundamental frequencies except for ν9 (for CH2IOO) and ν10 (for CH2I(18)O(18)O). Our findings were compared with the study by Lee and Lee conducted in a para-H2 matrix. The fundamental frequencies are in good agreement (within 6 cm(-1)) except for the two low-frequency modes, ν9 (for CH2IOO) and ν10 (for CH2I(18)O(18)O) likely due to different matrix shifts for para-H2 and Ar matrices. In addition, our calculations are in somewhat better agreement with the experiment values than the calculations by Lee and Lee. Our study also shows that reaction CH2I + O2 produces the peroxy radical CH2IOO in cold matrices (10 K) instead of Criegee intermediate CH2OO, which is generated in gas phase (300 K and low pressure); the same finding was also reported by Lee and Lee.

Electronic transitions of C6H4+ isomers: neon matrix and theoretical studies.

Three open-chain isomers of C6H4(+) and two cyclic ones were detected following mass-selective trapping in 6 K neon matrixes. The open-chain cations 5-hexene-1,3-diyne (CH2═CH-CC-CC-H)(+) and cis- (cis-HCC-CH═CH-CCH)(+) and trans-3-hexene-1,5-diyne (trans-HCC-CH═CH-CCH)(+), possess two absorption systems commencing at 609 and 373, 622 and 385, and 585 and 373 nm, respectively. They are assigned to the 1 (2)A" and 2 (2)A" ← X (2)A", 1(2)A2 and 2 (2)A2 ← X (2)B1, and 1 (2)Bg and 2 (2)B(g) ← X (2)A(u) electronic transitions of these cations. Two overlapping systems are detected at around 420 nm and tentatively assigned to the 1 (2)A" ← X (2)A" electronic transitions of propargyl cyclopropene and 2 (2)B1 ← X (2)A2 of o-benzyne cation structures. The assignment of the electronic transitions is based on theoretical vertical excitation energies calculated with CASPT2 and EOMEE-CCSDT methods for 12 isomers of C6H4(+). These have been carried out at the geometries optimized using several ab initio methods. Adiabatic excitation energies were calculated for the five identified isomers of C6H4(+).

An in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad.

Coronavirus disease 19 (COVID19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, several countries are at risk of the pandemic caused by this virus. In the absence of any vaccine or virus-specific antiviral treatments, the need is to fast track search for potential drug candidates to combat the virus. Though there are known drugs that are being repurposed to fight against the SARS-CoV-2, there is a requirement for the virus-specific drugs at the earliest. One of the main drug targets of SARS-CoV-2 is an essential non-structural protein, 3CL protease, critical for the life cycle of the virus. We have used molecular docking studies to screen a chemically diverse set of small molecules to identify potential drug candidates to target this protein. Of the 22,630 molecules from varied small molecule libraries, based on the binding affinities and physicochemical properties, we finalized 30 molecules to be potential drug candidates. Eight of these molecules bind in a manner allowing for the scope of a nearly orthogonal backside nucleophilic attack on their suitably placed electrophilic carbonyl groups by the thiol group of cysteine residue 145, while remaining inside a 4 Ǻ distance range. It is interesting since carbonyl groups are known to be attacked in a similar fashion by external nucleophiles and can be relevant when considering these molecules as potential mechanism-based irreversible inhibitors of the 3CLPro. Further, ADMET analysis and Molecular dynamics simulations and available bioactive assays led to the identification of three molecules with high potential to be explored as drug candidates/lead molecules to target 3CLPro of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Carbonyl diazide, OC(N3)2: synthesis, purification, and IR spectrum.

Carbonyl diazide (1), OC(N(3))(2), is prepared by reaction of triphosgene and tetra-n-butylammonium azide in a solution of diethyl ether or dimethyl ether. The advantage of this synthetic method, relative to other procedures, is that the use of triphosgene, OC(OCCl(3))(2), mitigates the need to use highly poisonous reagents such as phosgene, OCCl(2), or chlorofluorocarbonyl, OC(Cl)F. The identity and purity of OC(N(3))(2) are established by gas-phase IR spectroscopy, which reveals the presence of both syn-syn and anti-syn conformers. Computed anharmonic vibrational frequencies and infrared intensities of carbonyl diazide (1) display excellent agreement with experiment, and reveal the presence of strong Fermi resonances.