Cascading Effect of Large Molecular Motion in Crystals: A Topotactic Polymorphic Transition Paves the Way to Topochemical Polymerization.

A topochemical polymerization governed by a topotactic polymorphic transition is reported. A monomer functionalized with azide and an internal alkyne crystallized as an unreactive polymorph with two molecules in the asymmetric unit. The molecules are aligned in a head-to-head fashion, thereby avoiding the azide-alkyne proximity for the topochemical azide-alkyne cycloaddition (TAAC) reaction. However, upon heating, one of the two conformers underwent a drastic 180° rotation, leading to a single-crystal-to-single-crystal (SCSC) polymorphic transition to a reactive form, wherein the molecules are head-to-tail arranged, ensuring azide-alkyne proximity. The new polymorph underwent TAAC reaction to form a trisubstituted 1,2,3-triazole-linked polymer. These results, showing unexpected topochemical reactivity of a crystal due to the intermediacy of an SCSC polymorphic transition from an unreactive form to a reactive form, highlight that predicting topochemical reactivity by relying on the static crystal structure can be misleading.

A2B- and A3-Type Boron(III)Subchlorins Derived from meso-Diethoxycarbonyltripyrrane: Synthesis and Photophysical Exploration.

The first direct fabrication of A2B- and A3-type B(III)subchlorins from meso-ethoxycarbonyl-substituted tripyrrane has been realized by condensation with appropriate acid chlorides (benzoyl chloride, butyryl chloride, and ethyl chlorooxoacetate). The aliphatic acid chloride-based annulation reaction is new to subporphyrinoid chemistry. The phenyl (6a)- or n-propyl (6b)-substituted derivatives could be oxidized to the corresponding B(III)subporphyrins upon refluxing with DDQ, whereas the triethoxycarbonyl moiety (6c) was found to be resistant to oxidation and exhibits the most red-shifted absorption (587 nm) and emission (604 nm). The study indicates that absorption and emission behaviors of the B(III)subchlorin can be tuned by the introduction of electron-rich or electron-deficient substituents at the meso-position. B(III)subchlorins 6a and 6c generate singlet oxygen efficiently (44 and 40%, respectively) and, thus, may find application as potential photosensitizers in photodynamic therapy (PDT).

Meso-Free Boron(III)subchlorin and Its µ-Oxo Dimer with Interacting Chromophores.

Meso-free B(III)subchlorin 1 has been realized exclusively for the first time from meso-ethoxycarbonyl-substituted tripyrrane along with the first subchlorin dimer 2 as its µ-oxo analogue via a facile one-pot approach. The subchlorin is highly stable toward oxidation; hence, it was not contaminated with the corresponding subporphyrin analogue 3. The subchlorin (56%) and its dimer (30%) exhibit singlet oxygen generation ability for the first time. The B-O-B dimer displays strong exciton coupling between the two macrocycles.

Synthetic access to calix[3]pyrroles via meso-expansion: hosts with diverse guest chemistry.

Calix[3]pyrroles were synthesized for the first time. These macrocycles display versatile guest binding ability based on the bridges connecting the two α-positions of the tripyrrane moiety e.g. with an ethene bridge they showed colorimetric sensing of fluoride and cyanide ions, whereas with a phenylene spacer they exhibited fluorometric sensing of fluoride ions only, and the macrocycle with an ethylene unit acted as a host towards the water molecule with unique penta-coordinated oxygen in the solid state.

Experimental and theoretical investigation of intramolecular cooperativity in cyclic benzene trimer motif.

A series of new symmetrical tripodal molecules 1a-4b with a central benzene scaffold substituted with methyl/ethyl groups and three benzimidazolyl units having a bithiophene/biphenyl/5-alkylthiophene motif at the 2-position via a -CH2- unit were synthesized and characterized by elemental analysis, HR-MS, and NMR spectroscopy. NMR spectral data reveal that all molecules adopt a cyclic benzene trimer (CBT) using three benzimidazolyl units. Intramolecular cooperative edge-to-face C-H⋯π interactions stabilize the CBT motif in solution and are strong in ethyl substituted molecules (1b-4b) compared to methyl substituted (1a-4a) ones. However, the strength of the CBT unit in the tripodal molecule is independent of the length of the substituent at the 2-position of the benzimidazolyl unit. The relative 1H NMR chemical shift calculated at the MPW1PW91/6-311+G(d,p) level of theory corroborates the experimental values, and the calculations predict the distribution of the structures into syn isomers. The relative change in the NMR chemical shift is justified by the relative change in the magnitude of the (3,+3) critical point (CP) in the molecular electrostatic potential (MESP) topography. Also, a linear correlation of the intramolecular C-H⋯π interactions evaluated at M062X/6-311+G(d,p) with the relative NMR chemical shift suggest the latter as a measure of intramolecular cooperativity.

Fragment-Based Approaches for Supramolecular Interaction Energies: Applications to Foldamers and Their Complexes with Anions.

We explore the application of our multilayer Molecules-in-Molecules (MIM) fragment-based method for the study of the energies in supramolecular systems, viz. foldamers and their anion bound complexes. The performance of five different density functional theory (DFT) methods in conjunction with the fragmentation-based method is evaluated against the unfragmented energies for a test set of 5 foldamers (82 to 170 atoms). A systematic protocol has been developed to account for the π···π interactions in such systems in addition to the traditional fragmentation of the system along the backbone comprised of covalently bonded dimer (or trimer) units. We find a significant improvement in the performance of the method on going from a one-layer MIM1 model (errors >10 kcal/mol) to a two-layer MIM2 model (errors 0-2 kcal/mol), due to the incorporation of long-range interactions in the latter approach. Furthermore, we extend the applicability of MIM2 models to determine accurate binding energies of macromolecular receptor-anion complexes. For three different anion bound macrocycles, our MIM2 protocol provides total energies within 1.5 kcal/mol of the unfragmented energies for most of the DFT methods. The corresponding anion binding energies are calculated within 0.5 kcal/mol of the unfragmented binding energies due to systematic error cancellation between the macrocycle and the macrocycle-anion complex. Finally, we have calibrated the absolute accuracy in the calculated binding energies by comparison with unfragmented DLPNO-CCSD(T) calculations on three macromolecule-chloride anion complexes. The most accurate results are obtained using a MIM2 model using DLPNO-CCSD(T) calculations on trimer units as the high level and DFT-D3 (e.g., M06-2X-D3) as the low level of theory, yielding sub kcal/mol errors in the anion binding energies. Our protocol can be an accurate method to calculate anion binding energies for very large supramolecular systems.

Iodo-Cycloisomerization of Aryl(indol-3-yl)methane-Tethered Propargyl Alcohols to 3-Iodocarbazoles via Selective 1,2-Alkyl Migration.

Herein, we disclose the first report on iodo-cycloisomerization of 1-(indol-3-yl)-1-arylbut-3-yn-2-ols to form 3-iodocarbazoles. The synthesis proceeds through a cascade 5-endo-spirocyclization, followed by selective 1,2-alkyl migration. This method governs the green synthesis principles such as open-flask reaction, AcOEt as the solvent, rt reaction with short time, use of iodine, and broad substrate scope with atom and step economy.

Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.

We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0.01 ppm for 1H chemical shifts and 0.07 ppm for 13C chemical shifts. In addition, the performance of MIM-NMR has been assessed on two large peptides: the helical portion of ubiquitin ( 1UBQ ) containing 12 residues where the X-ray structure is known, and E6-binding protein of papilloma virus ( 1RIJ ) containing 23 residues where the structure has been derived from solution-phase NMR analysis. The solvation environment is incorporated in these MIM-NMR calculations, either through an explicit, implicit, or a combination of both solvation models. Using an explicit treatment of the solvent molecules within the first solvation sphere (3 Å) and an implicit solvation model for the rest of the interactions, the 1H and 13C chemical shifts of ubiquitin show excellent agreement with experiment (mean absolute deviation of 0.31 ppm for 1H and 1.72 ppm for 13C), while the larger E6-binding protein yields a mean absolute deviation of 0.34 ppm for 1H chemical shifts. The proposed MIM-NMR method is computationally cost-effective and provides a substantial speedup relative to conventional full calculations, the largest density functional NMR calculation included in this work involving more than 600 atoms and over 10,000 basis functions. The MIM-NMR solvation protocols developed in this work may pave the way for very accurate de novo prediction of NMR chemical shifts of a range of large biomolecules in the future.

Molecules-in-molecules fragment-based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides.

The molecules-in-molecules (MIM) fragment-based method has recently been adapted to evaluate the chiroptical (vibrational circular dichroism [VCD] and Raman optical activity [ROA]) spectra of large molecules such as peptides. In the MIM-VCD and MIM-ROA methods, the relevant higher energy derivatives of the parent molecule are assembled from the corresponding derivatives of smaller fragment subsystems. In addition, the missing long-range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM-VCD and MIM-ROA fragment-based methods to explore the evolution of the chiroptical spectroscopic characteristics of 310 -helix, α-helix, ß-hairpin, γ-turn, and ß-extended conformers of gas phase polyalanine (chain length n = 6-14). The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size. For a better understanding the site-specific effects on the vibrational spectra, isotopic substitutions were also performed employing the MIM method. An increasing redshift with the number of isotopically labeled 13 C=O functional groups in the peptide molecule was seen. For larger polypeptides, we implemented the two-step-MIM model to circumvent the high computational expense associated with the evaluation of chiroptical spectra at a high level of theory using large basis sets. The chiroptical spectra of α-(alanine)20 polypeptide obtained using the two-step-MIM model, including continuum solvation effects, show good agreement with the full calculations and experiment. This benchmark study suggests that the MIM-fragment approach can assist in predicting and interpreting chiroptical spectra of large polypeptides.

Evaluation of Energy Gradients and Infrared Vibrational Spectra through Molecules-in-Molecules Fragment-Based Approach.

Molecules-in-Molecules (MIM) is a general hybrid fragment-based extrapolation approach for calculating accurate total energies of large molecules, similar in spirit to the popular ONIOM methodology. In this work, the MIM model is extended for the precise evaluation of the energy gradients and infrared (IR) vibrational spectra of large molecules. The overlapping subsystems in this work are constructed from nonoverlapping fragments using a number-based scheme, and the dangling bonds are saturated with link-hydrogen atoms. Independent fragment calculations are performed to evaluate the energies and its gradients. Subsequently, the link-atom energy gradient components are projected back onto the corresponding host and supporting atoms, through the Jacobian projection method, as in the ONIOM approach. After geometry optimization, the Jacobian link-atom projection method is also employed for the precise evaluation of the force constants and dipole derivatives of the full molecule. The performance of the MIM model is benchmarked on 25 small-to-large peptides, with inevitable weak long-range intramolecular interactions. Upon accounting these long-range interactions through a second layer, at an inexpensive low-level of theory (MIM2), the energy accuracy improve by 80%, compared to MIM with one layer (MIM1). The MIM2 IR frequencies and intensities have an ∼75% improvement, compared to the corresponding values at the MIM1 level of theory. A similar improvement is also observed for anion, cation, and radical systems constructed from the neutral benchmark molecules. The accuracy and performance of the benchmark systems validate the MIM model for exploring the vibrational infrared spectra of large molecules.

Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

We present the first implementation of the vibrational circular dichroism (VCD) spectrum of large molecules through the Molecules-in-Molecules (MIM) fragment-based method. An efficient projection of the relevant higher energy derivatives from smaller fragments to the parent molecule enables the extension of the MIM method for the evaluation of VCD spectra (MIM-VCD). The overlapping primary subsystems in this work are constructed from interacting fragments using a number-based scheme and the dangling bonds are saturated with link hydrogen atoms. Independent fragment calculations are performed to evaluate the energies, Hessian matrix, atomic polar tensor (APT), and the atomic axial tensor (AAT). Subsequently, the link atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, as in the ONIOM approach. In the two-layer model, the long-range interactions between fragments are accounted for using a less computationally intensive lower level of theory. The performance of the MIM model is calibrated on the d- and l-enantiomers of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and VCD intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-VCD method is employed to predict the VCD spectra of perhydrotriphenylene and cryptophane-A, yielding spectra in agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-VCD model for exploring vibrational circular dichroism spectra of large molecules.

Construction of high-dimensional neural network potentials using environment-dependent atom pairs.

An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.

An ab initio investigation on (CO2)n and CO2(Ar)m clusters: geometries and IR spectra.

An ab initio investigation on CO(2) homoclusters is done at MPWB1K6-31++G(2d) level of theory. Electrostatic guidelines are found to be useful for generating initial structures of (CO(2))(n) clusters. The ab initio minimum energy geometries of (CO(2))(n) with n=2-8 are T shaped, cyclic, trigonal pyramidal, tetragonal pyramidal, tetragonal bipyramidal, pentagonal bipyramidal, and pentagonal bipyramid with one CO(2) molecule attached to it. A test calculation on (CO(2))(20) cluster is also reported. The geometric parameters of the energetically most favored (CO(2))(n) clusters match quite well their experimental counterparts (wherever available) as well as those derived from molecular dynamics studies. The effect of clustering is quantified through the asymmetric C-O stretching frequency shift relative to the single CO(2) molecule. (CO(2))(n) clusters show an increasing blueshift from 1.8 to 9.6 cm(-1) on increasing number of CO(2) molecules from n=2 to 8. The energetics and geometries of CO(2)(Ar)(m) clusters have also been explored at the same level of theory. The geometries for m=1-6 show a predominant T type of the argon-CO(2) molecule interaction. Higher clusters with m=7-12 show that the argon atoms cluster around the oxygen atom after the saturation of the central carbon atom. The CO(2)(Ar)(m) clusters exhibit an increasing redshift in the C-O asymmetric stretch relative to CO(2) molecule of 0.7-5.6 cm(-1) with increasing number of argon atoms through m=1-8.

Effect of matrix on IR frequencies of acetylene and acetylene-methanol complex: infrared matrix isolation and ab initio study.

Effect of nitrogen and argon matrices on the C-H asymmetric stretching and bending infrared frequencies of the acetylene molecule, C(2)H(2), has been studied by matrix isolation experiments as well as by calculations at MP2 level of theory. The complexes of C(2)H(2) in nitrogen and argon matrices, viz., C(2)H(2)(N(2))(m) (with m=2-8) and C(2)H(2)(Ar)(n) (with n=2-10) are theoretically explored. The computed acetylenic C-H asymmetric stretch in C(2)H(2)-nitrogen complexes shows a redshift of 3.0 to 11.9 cm(-1) compared with the frequencies of the free acetylene molecule, and a corresponding blueshift of 7.4 to 26.2 cm(-1) when C(2)H(2) is complexed with argon atoms. The trends in the computed shifts are in good agreement with the experiments. The molecular electrostatic potential minimum of C(2)H(2) becomes more negative when complexed with nitrogen than on complexation with argon. This observation implies a greater basic character for C(2)H(2) in the nitrogen matrix, favoring the formation of H-pi(C(2)H(2)-MeOH) complex as compared to that in the Ar matrix. Experimentally the preferential formation of H-pi(C(2)H(2)-MeOH) complex in the N(2) matrix has indeed been observed.