Iterative method for finding the low‐energy conformations based on the concept of molecular volumes

The recently proposed overlapping spheres (OS) method (Raos, N. Croat Chem Acta 1999, 72, 727) finds low‐energy conformations by minimizing the repulsion potential dependent on the free molecular volume inside the sphere with radius R_v. The sphere is situated at the geometrical center of the molecule or at the center of a molecular segment. The method was checked on branched alkanes and cyclic molecules (1,4‐diethylcyclohexane and copper(II) monochelates with N‐alkylated amino acids), yielding in all cases stable conformations with usually lower conformational energy than the “seed” conformations. The simple rules for segmentation of a molecule, based mostly on the topological considerations, were derived from the results of successfull optimizations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1353–1360, 2000     

Intercalation of Proflavine in ssDNA Aptamers: Effect on Binding of the Specific Target Chloramphenicol

The structural modification of ssDNA‐based aptamers upon specific binding of its target molecule leads to changes of the charge‐transfer resistance (R_ct) of a negatively‐charged free‐diffusing redox probe. The aptamer adopts a structure due to self‐hybridization which is stabilized using profalvine as intercalator. The pre‐organized aptamer structure is used to detect chloramphenicol (CAP) requiring a substantial change of the aptamer structure indicated by a CAP concentration dependent increase in the R_ct values. Pre‐incubation of the aptamer‐modified electrode with an intercalator allows for the modulation of the aptamer/target interaction and hence for a modulation of the CAP‐dependent variation of the R_ct values.     

Theoretical electronic studies of aluminum monobromide and aluminum monoiodide

By using CASSCF/MRCI methods, theoretical molecular calculations have been performed for 12 electronic states for AlBr molecule and 12 electronic states for AlI molecule in the representation ^2s+1Λ (neglecting spin‐orbit effects). Calculated potential energy curves are displayed. Spectroscopic constants including the harmonic vibrational wave number ω_e, the electronic energy T_e referred to the ground state and the equilibrium internuclear distance R_e are predicted for these singlet and triplet electronic states for both AlBr and AlI molecules. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Diamagnetic Raman Optical Activity of Chlorine,Bromine, and Iodine Gases

Magnetic Raman optical activity of gases provides unique information about their electric and magnetic properties. Magnetic Raman optical activity has recently been observed in a paramagnetic gas (Angew. Chem. Int. Ed. 2012 , 51, 11058; Angew. Chem. 2012 , 124, 11220). In diamagnetic molecules, it has been considered too weak to be measurable. However, in chlorine, bromine and iodine vapors, we could detect a significant signal as well. Zeeman splitting of electronic ground‐state energy levels cannot rationalize the observed circular intensity difference (CID) values of about 10⁻⁴. These are explicable by participation of paramagnetic excited electronic states. Then a simple model including one electronic excited state provides reasonable spectral intensities. The results suggest that this kind of scattering by diamagnetic molecules is a general event observable under resonance conditions. The phenomenon sheds new light on the role of excited states in the Raman scattering, and may be used to probe molecular geometry and electronic structure.     

Diamagnetic Raman Optical Activity of Chlorine,Bromine, and Iodine Gases

Magnetic Raman optical activity of gases provides unique information about their electric and magnetic properties. Magnetic Raman optical activity has recently been observed in a paramagnetic gas (Angew. Chem. Int. Ed. 2012 , 51, 11058; Angew. Chem. 2012 , 124, 11220). In diamagnetic molecules, it has been considered too weak to be measurable. However, in chlorine, bromine and iodine vapors, we could detect a significant signal as well. Zeeman splitting of electronic ground‐state energy levels cannot rationalize the observed circular intensity difference (CID) values of about 10^?4. These are explicable by participation of paramagnetic excited electronic states. Then a simple model including one electronic excited state provides reasonable spectral intensities. The results suggest that this kind of scattering by diamagnetic molecules is a general event observable under resonance conditions. The phenomenon sheds new light on the role of excited states in the Raman scattering, and may be used to probe molecular geometry and electronic structure.     

Prediction of a Neutral Noble Gas Compound in the Triplet State

Discovery of the HArF molecule associated with H?Ar covalent bonding [Nature, 2000 , 406, 874–876] has revolutionized the field of noble gas chemistry. In general, this class of noble gas compound involving conventional chemical bonds exists as closed‐shell species in a singlet electronic state. For the first time, in a bid to predict neutral noble gas chemical compounds in their triplet electronic state, we have carried out a systematic investigation of xenon inserted FN and FP species by using quantum chemical calculations with density functional theory and various post‐Hartree–Fock‐based correlated methods, including the multireference configuration interaction technique. The FXeP and FXeN species are predicted to be stable by all the computational methods employed in the present work, such as density functional theory (DFT), second‐order Møller–Plesset perturbation theory (MP2), coupled‐cluster theory (CCSD(T)), and multireference configuration interaction (MRCI). For the purpose of comparison we have also included the Kr‐inserted compounds of FN and FP species. Geometrical parameters, dissociation energies, transition‐state barrier heights, atomic charge distributions, vibrational frequency data, and atoms‐in‐molecules properties clearly indicate that it is possible to experimentally realize the most stable state of FXeP and FXeN molecules, which is triplet in nature, through the matrix isolation technique under cryogenic conditions.     

Effective potential energy curves of H2 molecule evolving in a strong time‐dependent magnetic field

Evolution of hydrogen molecule, starting initially from its field‐free ground state, in a time‐dependent (TD) magnetic field of order 10¹¹ G is presented in a parallel internuclear axis and magnetic field‐axis configuration. Effective potential energy curves (EPECs), in terms of exchange and correlation energy, of the hydrogen molecule as a function of TD magnetic‐field strength, are analyzed through TD density functional computations based on a quantum fluid dynamics approach. The numerical computations are performed for internuclear separation R ranging from 0.1 to 14.0 a.u. The EPECs exhibit field‐dependent significant potential‐well minima both at large internuclear separations and at short internuclear separations with a considerable increase in the exchange and correlation energy of the hydrogen molecule. The results, when compared with the time‐independent (TI) studies involving static TI magnetic fields, reveal TD behavior of field‐dependent crossovers between different spin‐states of hydrogen molecule as indicated by the TI investigations in static magnetic fields. Besides this, present work reveals interesting dynamics in the TD total‐electronic charge‐density distribution of the hydrogen molecule. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A hybrid ab initio/free electron computational model for conjugated dye molecules: Simple cyanines and oxonols

Justifications developed for the application the free electron model to the π‐orbitals of conjugated molecules suggest that the optical properties of these molecules would be well described by a one‐dimensional free electron model with a potential chosen to reproduce the energy level spacing of the ground state occupied π‐orbitals. Such a hybrid ab initio/free electron modeling approach, where the free electron potential parameters are optimized on a molecule‐by‐molecule basis, is developed, and applied to a series of simple cyanine and oxonol dyes. The ensuing predictions for λ_max, oscillator strengths, and redox properties compare well to available experimental information. Two important strengths of this approach are that no explicit calculations of the excited electronic state are required, and that the ab initio determination of the occupied π‐orbital level spacing considers all the electrons (π and σ) of the entire molecule in a specified geometry, environment, etc. This second characteristic gives the ability to efficiently model modifications of the optical properties of conjugated molecules resulting from chemical and/or physical modifications occuring within and remote to the conjugated region of the molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 943–953, 2000     

Steric and electronic evaluations of P(o‐tol)R2, where R is phenyl or cyclohexyl: crystal structures of SeP(o‐tol)R2

The crystal structures of SeP(o‐tol)R₂, where o‐tol is ortho‐tolyl (2‐methylphenyl) and R is Ph (phenyl), namely (2‐methylphenyl)diphenylphosphane selenide, C₁₉H₁₇PSe, or Cy (cyclohexyl), namely dicyclohexyl(2‐methylphenyl)phosphane selenide, C₁₉H₂₉PSe, were determined to aid in the evaluation of the steric and electronic behaviour of these analogous phosphane compounds. The compounds crystallized in similar monoclinic crystal systems, but are differentiated in their unit cells by a doubling of the number of independent molecules for R = Cy (Z′ = 2) and the choice of glide plane by convention. The preferred orientation for the o‐tolyl substituent obtained from the X‐ray structural analysis is gauche for R = Ph and anti for R = Cy (using the Se—P—C_ipso—C_ortho torsion angles as reference). Density functional theory (DFT) calculations showed both conformations to be equally probable and indicate that the preferred solid‐state conformer is probably due to the minimization of repulsion energies, resulting in a packing arrangement primarily featuring weak C—H…Se interactions and additional C—H…π interactions in the R = Ph structure. A detailed electronic and steric analysis was conducted on both phosphanes using Se—P bond lengths, multinuclear NMR ¹J_Se–P coupling constants, theoretical topological evaluation and crystallographic and solid‐angle calculations, and compared to selected literature examples. The results indicate that the use of the o‐tolyl substituent increases both the electron‐donating capability and the steric size, but is also dependent on whether the o‐tolyl group adopts a gauche or anti conformation. The single‐crystal geometrical data are unable to detect electronic differences between these two structures due to the somewhat large displacement parameters observed for the Se atom in the R = Cy structure.     

Enantioselective Guest Effect on the Spin State of a Chiral Coordination Framework

The diversity of spin crossover (SCO) complexes that, on the one hand, display variable temperature, abruptness and hysteresis of the spin transition, and on the other hand, are spin‐sensitive to the various guest molecules, makes these materials unique for the detection of different organic and inorganic compounds. We have developed a homochiral SCO coordination polymer with a spin transition sensitive to the inclusion of the guest 2‐butanol, and these solvates with (R)‐ and (S)‐alcohols demonstrate different SCO behaviours depending on the chirality of the organic analyte. A stereoselective response to the guest inclusion is detected as a shift in the temperature of the transition both from dia‐ to para‐ and from para‐ to diamagnetic states in heating and cooling modes respectively. Furthermore, the Mössbauer spectroscopy directly visualizes how the metallic centres in a chiral coordination framework differently sense the interaction with guests of different chiralities.     

Step‐Mediated Anisotropic Adsorption and Condensation of tert‐Butylamine on Cu(111)

Scanning tunneling microscopy (STM) combined with density functional theory (DFT) calculations were applied in studying the anisotropic adsorption and condensation of tert‐butylamine (t‐BA) molecules in the vicinity of the steps on the Cu(111) surface. The preferential adsorption at the upper step edges and uneven distribution of t‐BA in the vicinity of the steps illustrate the asymmetric electronic structure of the surface steps. Our observation demonstrates that the adsorption and diffusion of a polar molecule would be significantly mediated by steps on metal surfaces due to the molecule–step interaction and the intermolecular interactions.     

Conformation Diversity of a Fused‐Ring Pyrazine Derivative on Au(111) and Highly Ordered Pyrolytic Graphite

Heterocyclic aromatic compounds have attracted considerable attention because of their high carrier mobility that can be exploited in organic field‐effect transistors. This contribution presents a comparative study of the packing structure of 3,6‐didodecyl‐12‐(3,6‐didodecylphenanthro[9,10‐b]phenazin‐13‐yl)phenanthro[9,10‐b]phenazine (DP), an N‐heterocyclic aromatic compound, on Au(111) and highly ordered pyrolytic graphite (HOPG). High‐resolution scanning tunneling microscopy (STM) combined with atomistic simulations provide a picture of the interface of this organic semiconductor on an electrode that can have an impact on the field‐effect transistor (FET) performance. DP molecules adsorb with different conformational isomers (R/S: trans isomers; C: cis isomer) on HOPG and Au(111) substrates. All three isomers are found in the long‐range disordered lamella domains on Au(111). In contrast, only the R/S trans isomers self‐assemble into stable chiral domains on the HOPG surface. The substrate‐dependent adsorption configuration selectivity is supported by theoretical calculations. The van der Waals interaction between the molecules and the substrate dominates the adsorption binding energy of the DP molecules on the solid surface. The results provide molecular evidence of the interface structures of organic semiconductors on electrode surfaces.     

On the electronic structure of Li2 (X 1\documentclass{article}\pagestyle{empty}\begin{document}$\Sigma^{+}_{\mathrm{g}}$\end{document}) and its changes with internuclear distance

A compact, yet accurate, and strictly virial‐compliant ab initio electronic wavefunction for ground‐state Li₂ is exploited for a study of the molecule's electronic structure and electron density. Symmetry‐breaking problems that emerge at the single‐configuration level are solved in a multiconfigurational spin‐coupled approach that enables simultaneous optimization of angularly correlated “resonating” configurations. Particular emphasis is placed on the accurate determination of the electron density's bifurcation points and of the quadrupole moment as a function of internuclear distance R. Tentative connections are drawn between the R dependence of the electron density's topological structure and quadrupole moment and that of the electronic wavefunction. Computation of the latter constitutes the first application to systems other than isolated atoms of the optimized basis set generalized multiconfiguration spin‐coupled method, which entails use of nonorthogonal orbitals and Slater‐type basis functions with variationally optimized exponential parameters. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 378–397, 2000     

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975). Acta Cryst. B 31 , 1454–1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol –OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)‐21‐acetyloxy‐6,9,17,19‐tetrahydroxy‐23‐methoxy‐2,4,12,16,18,20,22‐heptamethyl‐8‐[(E)‐N‐(4‐methylpiperazin‐4‐ium‐1‐yl)formimidoyl]‐1,11‐dioxo‐1,2‐dihydro‐2,7‐(epoxypentadeca[1,11,13]trienimino)naphtho[2,1‐b]furan‐5‐olate pentahydrate, C₄₃H₅₈N₄O₁₂·5H₂O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O—H...O and N—H...N hydrogen bonds. Four of the symmetry‐independent water molecules are arranged via hydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interact via O—H...O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.     

Chiral‐Substrate‐Assisted Stereoselective Epoxidation Catalyzed by H2O2‐Dependent Cytochrome P450SPα

The stereoselective epoxidation of styrene was catalyzed by H₂O₂‐dependent cytochrome P450_SPα in the presence of carboxylic acids as decoy molecules. The stereoselectivity of styrene oxide could be altered by the nature of the decoy molecules. In particular, the chirality at the α‐positions of the decoy molecules induced a clear difference in the chirality of the product: (R)‐ibuprofen enhanced the formation of (S)‐styrene oxide, whereas (S)‐ibuprofen preferentially afforded (R)‐styrene oxide. The crystal structure of an (R)‐ibuprofen‐bound cytochrome P450_SPα (resolution 1.9 Å) revealed that the carboxylate group of (R)‐ibuprofen served as an acid–base catalyst to initiate the epoxidation. A docking simulation of the binding of styrene in the active site of the (R)‐ibuprofen‐bound form suggested that the orientation of the vinyl group of styrene in the active site agreed with the formation of (S)‐styrene oxide.     

Three‐dimensional hydrogen‐bonded structures in the guanidinium salts of the monocyclic dicarboxylic acids rac‐trans‐cyclohexane‐1,2‐dicarboxylic acid (2:1, anhydrous), isophthalic acid (1:1, monohydrate) and terephthalic acid (2:1, trihydrate)

The structures of bis(guanidinium) rac‐trans‐cyclohexane‐1,2‐dicarboxylate, 2CH₆N₃⁺·C₈H₁₀O₄²⁻, (I), guanidinium 3‐carboxybenzoate monohydrate, CH₆N₃⁺·C₈H₅O₄⁻·H₂O, (II), and bis(guanidinium) benzene‐1,4‐dicarboxylate trihydrate, 2CH₆N₃⁺·C₈H₄O₄²⁻·3H₂O, (III), all reveal three‐dimensional hydrogen‐bonded framework structures. In anhydrous (I), both guanidinium cations form classic cyclic R₂²(8) N—H...O,O′_carboxylate and asymmetric cyclic R₂¹(6) hydrogen‐bonding interactions, while one cation forms an unusual enlarged cyclic interaction with O‐atom acceptors of separate ortho‐related carboxylate groups [graph set R₂²(11)]. Cations and anions also associate across inversion centres, giving cyclic R₄²(8) motifs. In the 1:1 guanidinium salt, (II), the cation forms two separate cyclic R₂¹(6) interactions, one with a carboxyl O‐atom acceptor and the other with the solvent water molecule. The structure is unusual in that both carboxyl groups form short interanion O...H...O contacts, one across a crystallographic inversion centre [O...O = 2.483 (2) Å] and the other about a twofold axis of rotation [O...O = 2.462 (2) Å], representing shared sites on these elements for the single acid H atom. The water molecule links the cation–anion ribbon structures into a three‐dimensional framework. In (III), the repeating molecular unit comprises a benzene‐1,4‐dicarboxylate dianion which lies across a crystallographic inversion centre, two guanidinium cations and two solvent water molecules (each set related by twofold rotational symmetry), and a single water molecule which lies on a twofold axis. Each guanidinium cation forms three types of cyclic interaction with the dianions: one R₂¹(6), the others R₃²(8) and R₃³(10) (both of these involving the water molecules), giving a three‐dimensional structure through bridges down the b‐cell direction. The water molecule at the general site also forms an unusual cyclic R₂²(4) homodimeric association across an inversion centre [O...O = 2.875 (2) Å]. The work described here provides further examples of the common cyclic guanidinium–carboxylate hydrogen‐bonding associations, as well as featuring other less common cyclic motifs.     

Assessment and acceleration of binding energy calculations for protein–ligand complexes by the fragment molecular orbital method

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics‐based force fields, although they cannot fully describe protein–ligand interactions. A noteworthy computational method in development involves large‐scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large‐scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange‐correlation functionals, and solvation effects) on the binding energies of the FK506‐binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2‐MP2/6‐31G(d), is suitable for evaluating the protein–ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure–activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein–ligand interaction distance. Our acceleration scheme, which uses FMO2‐HF/STO‐3G:MP2/6‐31G(d) at R_int = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy. © 2015 Wiley Periodicals, Inc.     

(R)‐12‐Hydroxystearic Acid Hydrazides as Very Efficient Gelators: Diffusion,Partial Thixotropy,and Self‐Healing in Self‐Standing Gels

The gelation properties of derivatives of N‐alkylated (R)‐12‐hydroxystearic acid hydrazide (n‐HSAH, n=0, 2, 6, 10; n is the length of an n‐alkyl chain on the terminal nitrogen atom) in a wide variety of liquids is reported. The n‐HSAH compounds were derived from a naturally occurring alkanoic acid, (R)‐12‐hydroxystearic acid (R‐12HSA), and although they differ from the analogous N‐alkyl (R)‐12‐hydroxystearamides (n‐HSAA) only by the presence of one N?H group, their behavior as gelators is very different. For example, the parent molecule (0‐HSAH) is a supergelator in ethylene glycol, in which it forms self‐standing gels that are self‐healing, partially thixotropic, moldable, and load‐bearing; gels of 0‐HSAA are not self‐standing. 0‐HSAH is structurally the simplest molecular gelator of which we are aware that is capable of forming both self‐standing and partially thixotropic gels. Also, diffusion of the cationic dye erythrosine B and the anionic dye methylene blue in 0‐HSAH/ethylene glycol gel blocks is much slower than the self‐diffusion of ethylene glycol. Polarizing optical microscopy, X‐ray diffraction, and FTIR studies revealed that the self‐assembled fibrillar networks (SAFINs) of the gels are crystalline, and that 0‐HSAH molecules may be arranged in a triclinic subcell with bilayer stacking. The SAFINs are stabilized by strong hydrogen‐bonding interactions between the hydrazide groups of adjacent molecules and a perpendicular hydrogen‐bonding network between the pendent hydroxyl groups of 0‐HSAH. The other n‐HSAH (n=2, 6, 10) molecules appear to be arranged in orthorhombic subcells with monolayers and strong hydrogen‐bonding interactions between the hydrazide group of one gelator molecule and the hydroxyl group of a neighboring one. These results show how small structural modifications of structurally simple gelator molecules can be exploited to form gels with novel properties that can lead potentially to valuable applications, such as in drug delivery.