Resonance Raman studies of beta-substituted porphyrin systems with unusual electronic absorption properties.

Zn(II) and Cu(II) porphyrins with beta-conjugated barbiturate functional groups have low-energy electronic transitions which are unusual in that there are two strong bands in the Soret region. Resonance excitation of the two bands shows that each has features characteristic of both the porphyrin and barbiturate groups, with some perturbation to these features caused by the interaction of the two chromophores. The resonance Raman (RR) spectrum (lambda(exc)=413.1 nm) of the 412 nm band shows two bands at 1722 and 1743 cm(-1) attributable to C==O stretches in the substituent. Changes in frequency of porphyrin core modes due to the differing metal centres are reproduced by density functional theory calculations. The Q band RR spectra show modes with anomalous polarization which may be attributed to A(2g) modes, however no overtone or combination bands are observed.     

Spectroscopic and theoretical studies on solid 1,2-ethylenediamine dihydrochloride salt.

A structural study of [H3N(CH2)2NH3)]2+.2Cl-, the smallest element of the homologous series of the alpha,omega-diamine dihydrochlorides, was carried out by means of Raman and FTIR spectroscopy coupled to ab initio molecular orbital (MO) calculations. As a primary concern, an adequate molecular model for the representation of these solid amine salts was chosen. Thus, several models, varying in the number and position of the counterions as well as in the number of diamine units, were considered. It was found that the best molecular system (i.e., that yielding the best compromise between accuracy and computational requirements) consists of one ethylenediamine cation surrounded by six chloride ions in an arrangement based on the crystal structure reported in the literature for [H3N(CH2)2NH3)]2+.2Cl-. This conclusion will hopefully allow for a better understanding of the conformational preferences, in the solid state, of these biologically relevant linear polyamines.     

Helical arrays of pendant fullerenes on optically active poly(phenylacetylene)s

Novel, optically active, stereoregular poly(phenylacetylene)s bearing the bulky fullerene as the pendant were synthesized by copolymerization of an achiral phenylacetylene bearing a [60]fullerene unit with optically active phenylacetylene components in the presence of a rhodium catalyst. The C60-bound phenylacetylene was prepared by treatment of C60 with N-(4-ethynylbenzyl)glycine in a Prato reaction. The obtained copolymers exhibited induced circular dichroism (ICD) in solution both in the main-chain region and in the achiral fullerene chromophoric region, although their ICD intensities were highly dependent on the structures of the optically active phenylacetylenes and the solution temperature. These results indicate that the optically active copolymers form one-handed helical structures and that the pendant achiral fullerene groups are arranged in helical arrays with a predominant screw sense along the polymer backbone. The structures and morphology of the copolymers on solid substrates were also investigated by atomic force microscopy.     

Density Functional Study of Tetraphenylporphyrin Long-Range Exciton Coupling

The performance of time-dependent density functional theory (TDDFT) for calculations of long-range exciton circular dichroism (CD) is investigated. Tetraphenylporphyrin (TPP) is used as a representative of a class of strongly absorbing chromophores for which exciton CD with chromophore separations of 50 Å and even beyond has been observed experimentally. A dimer model for TPP is set up to reproduce long-range exciton CD previously observed for a brevetoxin derivative. The calculated CD intensity is consistent with TPP separations of over 40 Å. It is found that a hybrid functional with fully long-range corrected range-separated exchange performs best for full TDDFT calculations of the dimer. The range-separation parameter is optimally tuned for TPP, resulting in a good quality TPP absorption spectrum and small DFT delocalization error (measured by the curvature of the energy calculated as a function of fractional electron numbers). Calculated TDDFT data for the absorption spectra of TPP are also used as input for a ‘matrix method’ (MM) model of the exciton CD. For long-range exciton CD, comparison of MM spectra with full TDDFT CD spectra for the dimer shows that the matrix method is capable of producing very accurate results. A MM spectrum obtained from TPP absorption data calculated with the nonhybrid Becke88–Perdew86 (BP) functional is shown to match the experimental brevetoxin spectrum ‘best’, but for the wrong reasons.     

Spectroscopic and theoretical study of vibrational spectra of hydrogen‐bonded tropolone

Theoretical simulation of the bandshape and fine structure of the ν_s stretching band is presented for tropolone‐H and tropolone‐D taking into account an adiabatic coupling between the high‐frequency O–H(D) stretching and the low‐frequency intra‐ and intermolecular OO stretching modes, and linear and quadratic distortions of the potential energies for the low‐frequency vibrations in the excited state of the O–H(D) stretching vibration. In order to determine the low‐frequency vibrations, the experimental spectra of the polycrystalline tropolone in the far‐infrared and the low‐frequency Raman range have been recorded for the first time. The experimental frequencies in the low‐frequency region are compared with the results of the HF/6‐31G** and Becke3LYP/6‐31G** calculations carried out for the tropolone dimer. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 275–282, 1999     

A novel type of optically active helical polymers: Synthesis and characterization of poly(N‐propargylureas)

This article presents two novel artificial helical polymers, substituted polyacetylenes with urea groups in side chains. Poly( 4 ) and poly( 5 ) can be obtained in high yields (≥97%) and with moderate molecular weights (11,000–14,000). Poly( 4 ) contains chiral centers in side chains, and poly( 5 ) is an achiral polymer. Both of the two polymers adopted helical structures under certain conditions. More interestingly, poly( 4 ) exhibited large specific optical rotations, resulting from the predominant one‐handed screw sense. The helical conformation in poly( 5 ) was stable against heat, while poly( 4 ) underwent conformational transition from helix to random coil upon increasing temperature from 0 to 55 °C. Solvents had considerable influence on the stability of the helical conformation in poly( 4 ). The screw sense adopted by the helices was also largely affected by the nature of the solvent. Poly( 4 ‐co‐ 5 )s formed helical conformation and showed large optical rotations, following the Sergeants and Soldiers rule. By comparing the present two polymers (with one ? N? H groups) with the three polymers previously reported (with two ? N? H groups in side chains), the nature of the hydrogen bonds formed between the neighboring urea groups played big roles in the formation of stable helical conformation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4112–4121, 2008     

An Ab initio theoretical investigation on the geometrical and electronic structures of BAun−/0 (n = 1–4) clusters

An ab initio theoretical investigation on the geometrical and electronic structures and photoelectron spectroscopies (PES) of BAu_n^?/0 (n = 1–4) auroboranes has been performed in this work. Density functional theory and coupled cluster method (CCSD(T)) calculations indicate that BAu (n = 1–4) clusters with n‐Au terminals possess similar geometrical structures and bonding patterns with the corresponding boron hydrides BH. The PES spectra of BAu (n = 1–4) anions have been simulated computationally to facilitate their future experimental characterizations. In this series, the T_d BAu anion appears to be unique and particularly interesting: it possesses a perfect tetrahedral geometry and has the highest vertical electron detachment energy (VDE = 3.69 eV), largest HOMO‐LUMO gap (ΔE_gap = 3.0 eV), and the highest first excitation energy (E_ex = 2.18 eV). The possibility to use the tetrahedral BAu unit as the building block of Li⁺[BAu₄]^? ion‐pair and other [BAu₄]^?‐containing inorganic solids is discussed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides

Secondary structures for AcAla_nNH₂ (n=2–4) peptides have been analyzed by means of ab initio MP2, CCSD(T), and DFT‐B3PW91 methods using large basis sets and including implicit hydration effects and thermal corrections. In addition to the classical “pure” right‐handed 3₁₀‐ and α‐helices, left‐handed polyproline II, inverse γ‐turn, and fully extended conformations, a large number of “mixed” structures obtained by combining characteristic φ/ψ angles of each residue in every way have been found. All mixed structures are energetically accessible and can be present at significant levels in aqueous solution. Furthermore, they represent the way through which hierarchical unfolding of 3₁₀‐ and α‐helices or nonhierarchical polyproline II to fully extended transitions occur. Computational results are in qualitative agreement with the large amount of experimental data for simpler polyalanines and provide significant insight into their thermodynamic properties and how these can be modulated by interactions with solvent.     

Mechanism of cysteine oxidation by a hydroxyl radical: a theoretical study.

Cysteine oxidation by HO(.) was studied at a high level of ab initio theory in both gas phase and aqueous solution. Potential energy surface scans in the gas phase performed for the model system methanethiol+HO(.) indicate that the reactants can form two intermediate states: a sulfur-oxygen adduct and a hydrogen bound reactant complex. However these states appear to play a minor role in the reaction mechanism as long as they are fast dissociating states. Thus the main reaction channel predicted at the QCISD(T)/6-311+G(2df,2pd) level of theory is the direct hydrogen atom abstraction. The reaction mechanism is not perturbed by solvation which was found to induce only small variations in the Gibbs free energy of different reactant configurations. The larger size reactant system cysteine+HO* was treated by the integrated molecular orbital+molecular orbital (IMOMO) hybrid method mixing the QCISD(T)/6-311+G(2df,2pd) and the UMP2/6-311+G(d,p) levels of theory. The calculated potential energy, enthalpy, and Gibbs free energy barriers are slightly different from those of methanethiol. The method gave a rate constant for cysteine oxidation in aqueous solution, k=2.4 x 10(9) mol(-1) dm(3) s(-1), which is in good agreement with the experimental rate constant. Further analysis showed that the reaction is not very sensitive to hydrogen bonding and electrical polarity of the molecular environment.     

On the DFT Ground State of Crystalline Bromine and Iodine

We report on an erroneous ground state within common density functional theory (DFT) methods for the solid elements bromine and iodine. Phonon computations at the GGA level for both molecular crystals yield imaginary vibrational modes, erroneously indicating dynamic instability—that fact alone could easily pass as a computational artefact, but these imaginary modes lead to energetically more favorable and dynamically stable structures, made up of infinite monoatomic chains. In contrast, meta‐GGA and hybrid functionals yield the correct energetic order for bromine, while for iodine, most global hybrids do not improve the GGA result significantly. The qualitatively correct answer, in both cases, is given by the long‐range corrected hybrid LC‐ωPBE, the Minnesota functionals M06L and M06, and by periodic Hartree–Fock and MP2 theory. This poor performance of economic DFT functionals should be kept in mind, for example, during global structure optimizations of systems with significant contributions from halogen bonds.     

Structural, kinetic, and theoretical studies on models of the zinc-containing phosphodiesterase active center: medium-dependent reaction mechanisms

Dinuclear zinc(II) complexes [Zn(2)(bpmp)(mu-OH)](ClO(4))(2) (1) and [Zn(2)(bpmp)(H(2)O)(2)](ClO(4))(3) (2) (H-BPMP=2,6-bis[bis(2-pyridylmethyl)aminomethyl]-4-methylphenol) have been synthesized, structurally characterized, and pH-driven changes in metal coordination observed. The transesterification reaction of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) in the presence of the two complexes was studied both in a water/DMSO (70:30) mixture and in DMSO. Complex 2 was not reactive whereas for 1 considerable rate enhancement of the spontaneous hydrolysis reaction was observed. A detailed mechanistic investigation by kinetic studies, spectroscopic measurements ((1)H, (31)P NMR spectroscopy), and ESI-MS analysis in conjunction with ab initio calculations was performed on 1. Based on these results, two medium-dependent mechanisms are presented and an unusual bridging phosphate intermediate is proposed for the process in DMSO.     

Formation of phosphaethyne dimers: a mechanistic study

High-level ab initio (CCSD(T), CBS-QB3 and CASSCF, CASPT2, MR-ACPF, MR-ACPF-2) and density functional theory (B3LYP) calculations were carried out to study the dimerization of phosphaacetylene or phosphaethyne (HCP). Seventeen low energy closed-shell and five open-shell phosphaacetylene dimers were found on the potential energy surface. Two head-to-head, one head-to-tail and three other dimerization reaction pathways were determined, all with high activation barriers, suggesting that closed-shell minima are usually kinetically stable. An open-shell head-to-head reaction pathway has also been found with moderate initial barrier (95.0 kJ mol(-1)) leading to 1,2- and 1,3-diphosphacyclobutadiene, suggesting that polymerization of HCP and oligomerization of its derivatives have open-shell mechanism. Formation of 1,2-diphosphacyclobutadiene is both thermodynamically and kinetically favored over 1,3-diphosphacyclobutadiene. A head-to-head reaction involving LiBr as a catalyst was also studied. It has been pointed out that LiBr catalyze the closed-shell mechanism. All the four possible reaction channels of this reaction yield 1,4-diphosphatriafulvene with a fairly low activation Gibbs-free energy (44.8 kJ mol(-1)), suggesting that this compound could be synthesized. This finding fully supports the experimental results.     

Beta Sheets with a Twist: The Conformation of Helical Polyisocyanopeptides Determined by Using Vibrational Circular Dichroism

Detailed information on the architecture of polyisocyanopeptides based on vibrational circular dichroism (VCD) spectroscopy in combination with DFT calculations is presented. It is demonstrated that the screw sense of the helical polyisocyanides can be determined directly from the C?N‐stretch vibrational region of the VCD spectrum. Analysis of the VCD signals associated with the amide I and amide II modes provides detailed information on the peptide side‐chain arrangement in the polymer and indicates the presence of a helical β‐sheet architecture, in which the dihedral angles are slightly different to those of natural β‐sheet helices.     

Theoretical determination of the vibrational Raman optical activity signatures of helical polypropylene chains.

Raman and vibrational Raman optical activity (VROA) spectra of helical conformers of polypropylene chains are simulated using ab initio methods to unravel the relationships between the vibrational signatures and the primary and secondary structures of the chains. For a polypropylene chain containing three units, conformational effects are shown to lead to more acute signatures for VROA than for Raman spectra. In addition to regular polypropylene chains, which can display right and left helicities with the same probability, chirality and therefore helicity are enforced by substituting one chain end with a phenyl group. The simulations predict that the threefold helical structures, which correspond to (TG)(N) conformations of the backbone, have a specific VROA backward signature in the form of an intense couplet around 1100 cm(-1). This couplet is associated with collective wagging and twisting motions, while most of its intensity comes from the anisotropic invariants combining normal coordinate derivatives of the electric dipole-electric dipole polarizability and of the electric dipole-magnetic dipole polarizability. A similar signature has already been found in model helical polyethylene chains, whereas it is very weak in forward VROA.     

The nature of halogen...halogen synthons: crystallographic and theoretical studies

A study of the halogen...halogen contacts in organic compounds using ab initio calculations and the results of previously reported crystallographic studies show that these interactions are controlled by electrostatics. These contacts can be represented by the geometric parameters of the C--X1...X2--C moieties (where theta1=C--X1...X2 and theta2=X1...X2--C; ri=X1...X2 distance). The distributions of the contacts within the sum of van der Waals radii (rvdW) versus thetai (theta1=theta2) show a maximum at theta approximately 150 degrees for X=Cl, Br, and I. This maximum is not seen in the distribution of F...F contacts. These results are in good agreement with our ab initio calculations. The theoretical results show that the position of the maximum depends on three factors: 1) The type of halogen atom, 2) the hybridization of the ipso carbon atom, and 3) the nature of the other atoms that are bonded to the ipso carbon atom apart from the halogen atom. Calculations show that the strength of these contacts decreases in the following order: I...I>Br...Br>Cl...Cl. Their relative strengths decrease as a function of the hybridization of the ipso carbon atom in the following order: sp2>sp>sp3. Attaching an electronegative atom to the carbon atom strengthens the halogen...halogen contacts. An electrostatic model is proposed based on two assumptions: 1) The presence of a positive electrostatic end cap on the halogen atom (except for fluorine) and 2) the electronic charge is anisotropically distributed around the halogen atom.     

Spectroscopic Determination of the Electronic Structure of a Uranium Single-Ion Magnet

Early actinide ions have large spin-orbit couplings and crystal field interactions, leading to large anisotropies. The success in using actinides as single-molecule magnets has so far been modest, underlining the need for rational strategies. Indeed, the electronic structure of actinide single-molecule magnets and its relation to their magnetic properties remains largely unexplored. A uranium(III) single-molecule magnet, [U^III{SiMe₂NPh}₃-tacn)(OPPh₃)] (tacn=1,4,7-triazacyclononane), has been investigated by means of a combination of magnetic, spectroscopic and theoretical methods to elucidate the origin of its static and dynamic magnetic properties.     

Amphiphilic organic ion pairs in solution: a theoretical study.

The macroscopic manifestation of hydrophobic interactions for amphiphilic organic ion pairs (tetraalkylammonium-anion) has been shown experimentally by measuring their association constants and their affinity with the organic phase. Beyond a certain size, there is a direct relation between association constants and chain lengths in tetraalkylammonium ions. We propose to cast a bridge between these results and geometrical properties considered at the level of a single ion pair by means of quantum chemistry calculations performed on model systems: trimethylalkylammonium-pentyl sulfate instead of tetraalkylammonium-dodecyl sulfate. Two limiting cases are considered: head-to-head configurations, which yield an optimal electrostatic interaction between polar heads, and parallel configurations with a balance between electrostatic and hydrophobic interactions. All properties (geometries, complexation energies, and atomic charges) were obtained at the MP2 level of calculation, with water described by a continuum model (CPCM). Dispersion forces link hydrocarbon chains of tetraalkylammonium ions and pentyl sulfate, thus yielding (for the largest ion pairs) parallel configurations favored with respect to head-to-head geometries by solute-solvent electrostatic interactions. Given the small experimental association energies, we probe the accuracy limit of the MP2 and CPCM methods. However, clear trends are obtained as a function of chain length, which agree with the experimental observations. The calculated monotonic stabilization of ion pairs when the hydrocarbon chain increases in length is discussed in terms of electrostatic interactions (between ions and between ion pairs and water), dispersion forces, and cavitation energies.