Investigation of the electronic structure of the TCNQ-TTF system. I. TCNQ and TTF monomers and dimers in the all-valence-electron approximation

Closed-shell and DODS CNDO/2 calculations have been performed for neutral and charged TCNQ and TTF monomers and different dimers. For the sake of comparison the calculation have also performed for the corresponding TCNE molecules.The most important result obtained indicates a large splitting of the lowest unfilled level of TCNQ in going from the monomer to the stacked (TCNQ)₂ dimer. The same holds true for the HOMO level of the (TTF)₂ dimer. This indicates that one should expect a broad conduction band for the neutral poly (TCNQ) chain and a broad valence band for the neutral poly (TTF) chain. In order to test the quality of the CNDO/2 approximation scheme a comparison is attempted with existing experimental findings as well as with some MINDO results and available theoretical predictions within different approximation schemes.     

双卟啉化合物的构象平衡及π-π作用研究

制备并表征了一系列以柔韧烷氧化相连的自由双卟啉及其锌配合物,以＾１Ｈ－ＮＭＲ考察了烷氧链长度及锌离子对双卟啉构象平衡的影响。结果表明,双卟啉存在开放式及闭合式构象平衡,随烷氧链的增长,构象平衡由开放式向闭合式移动,当链上碳原子数为４时最有利于双卟啉形成闭合式构象。     

Study of NH stretching vibrations in small ammonia clusters by infrared spectroscopy in He droplets and ab initio calculations

Infrared spectra of the NH stretching vibrations of (NH3)n clusters (n = 2-4) have been obtained using the helium droplet isolation technique and first principles electronic structure anharmonic calculations. The measured spectra exhibit well-resolved bands, which have been assigned to the nu1, nu3, and 2nu4 modes of the ammonia fragments in the clusters. The formation of a hydrogen bond in ammonia dimers leads to an increase of the infrared intensity by about a factor of 4. In the larger clusters the infrared intensity per hydrogen bond is close to that found in dimers and approaches the value in the NH3 crystal. The intensity of the 2nu4 overtone band in the trimer and tetramer increases by a factor of 10 relative to that in the monomer and dimer, and is comparable to the intensity of the nu1 and nu3 fundamental bands in larger clusters. This indicates the onset of the strong anharmonic coupling of the 2nu4 and nu1 modes in larger clusters. The experimental assignments are compared to the ones obtained from first principles electronic structure anharmonic calculations for the dimer and trimer clusters. The anharmonic calculations were performed at the M?ller-Plesset (MP2) level of electronic structure theory and were based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structures. In general, there is excellent (<20 cm(-1)) agreement between the experimentally measured band origins for the N-H stretching frequencies and the calculated anharmonic vibrational frequencies. However, the calculations were found to overestimate the infrared intensities in clusters by about a factor of 4.     

Dimerization of the keto tautomer of acetohydroxamic acid-infrared matrix isolation and theoretical study

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO...HON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO...HN hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular NH...O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies (DeltaE(ZPE)(CP)I, II=-7.02, -6.34 kcal mol-1) being less stable than calculated structures III and IV (DeltaE(ZPE)(CP)III, IV=-9.50, -8.87 kcal mol-1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO...HON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA)2 dimers in the studied matrixes indicates that the formation of (AHA)2 is kinetically and not thermodynamically controlled.     

DFT study of conjugational electronic structures of aminoalkyl end-capped oligothiophenes up to octamers

The molecular geometries and electronic properties of a series of bis(aminoalkyl) end-capped oligothiophenes (BRnTs) were investigated by means of the density functional theory (DFT). The calculations were performed on dimers up to octamers in the neutral and ionic species using the B3LYP/6-31G(d,p) level of theory. The results obtained show that the conjugated systems in the p- and n-doped oligomers had more aromaticity, with expanded and planar chains. The calculated energy gap values between the frontier molecular orbitals for the end-capped oligomers were larger than those for the unsubstituted oligomers, in which with increase in the oligomer chain length, the conduction band gap decreased. The calculated first excitation energies of BRnTs at the TD-B3LYP/6-31G(d,p) level indicated that both doped oligomers (p- and n-type) had lower excitation energies than the neutral states, and that they displayed red shifts in their absorption spectra. Moreover, the results obtained for the natural bond orbital (NBO) analysis showed that closing the end-side oligothiophene chains with the aminoalkyl groups eased the hole or electron transfer, owning to better charge delocalization through the backbone structures of BRnTs.     

Heterogeneous proton-bound dimers with a high dipole moment monomer: how could we experimentally observe these anomalous ionic hydrogen bonds?

Electronic structure calculations (CBS-QB3 and G3MP2) have been used to predict a suitable method to experimentally observe the anomalous structure which is predicted to exist in a proton-bound dimer with a high dipole moment monomer. The enthalpy associated with forming the proton-bound dimer from its protonated and neutral monomers is shown to be linearly related to the difference in proton affinities which has been observed experimentally. However, unlike previous experimental studies, the linear correlation is not predicted to depend strongly, if at all, on whether the basic sites are C=O, C=N, or O(H) n-donor bases. Thermochemical measurements, then, are probably not the best method to distinguish between the structures of heterogeneous proton-bound dimers. It has been shown that a suitable method to experimentally observe the anomalous structure of proton-bound dimers containing a high dipole moment monomer (or very polar monomer) is by spectroscopic measurement. The O-H+-O asymmetric stretch is probably not the best infrared band to try to correlate with structure. The best band to observe is one which is in a region of the spectrum not masked by other absorptions and is also sensitive to the proximity of the binding proton. For example, it is shown that the methanol-free O-H stretch is very sensitive to the O-H+ bond distance for a series of heterogeneous proton-bound dimers containing methanol. It is predicted that the free O-H stretch of the methanol/acetonitrile proton-bound dimer is more closely related to the O-H stretch in protonated methanol than the O-H stretch in neutral methanol. Observations of these bands should confirm that the proton is closer to methanol in the methanol/acetonitrile proton-bound dimer despite acetonitrile having a higher proton affinity.     

Residual Dipolar-Coupling-Based Conformational Comparison of Noncovalent Ubiquitin Homodimer with Covalently Linked Diubiquitin

Although the conformation of the polymer chain of Ubiquitin (Ub) mainly depends on the type of isopeptide linkage connecting two Ub molecules, the non-covalent (noncovalent) interaction between two Ub molecules within the chain could also tune their conformational preference. Here, we studied the conformation of noncovalently formed Ub dimers in solution using residual dipolar couplings (RDCs). Comparing the RDC derived alignment tensor of the noncovalently formed dimer with the two most abundant (K11 and K48) covalent linked Ub dimers revealed that the conformation of K11 linked and noncovalent Ub dimers were similar. Between the various NMR and crystal structures of K11 linked Ub dimers, RDC tensor analysis showed that the structure of K11 linked dimer crystalized at neutral pH is similar to noncovalent dimer. Analogous to the experimental study, the comparison of predicted order matrix of various covalent Ub dimers with that of the experimentally determined order matrix of noncovalent Ub dimer also suggests that the conformation of K11 linked dimers crystalized at neutral pH is similar to the noncovalent dimer.     

Structures of aliphatic amino acid proton-bound dimers by infrared multiple photon dissociation spectroscopy in the 700-2,000 cm(-1) region

Structural aspects of proton-bound dimers composed of amino acids with aliphatic side chains are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. Features in the IRMPD spectra in the 700-2,000 cm-1 range are due primarily to C=O stretching, NH2 bending, and COH bending. It was possible to distinguish between isomeric structures by comparing the experimental IRMPD spectra and those predicted using B3LYP/6-31+G(d,p). It was possible, based on the calculations and IRMPD spectra, to assign the experimental spectrum of the glycine proton-bound dimer to a structure which was slightly different from that assigned by previous spectroscopic investigations and in agreement with recent thermochemical studies. Since all proton-bound dimers studied here, composed of the different amino acids, have very similar spectra, it is expected that they also have very similar lowest-energy structures including the mixed alanine/glycine proton-bound dimer. In fact, the spectra are so similar that it would be very challenging to distinguish, for example, the glycine proton-bound dimer from the alanine or valine proton-bound dimers in the 700-2,000 cm-1 range. According to the calculated IR spectra it is shown that in the approximately 2,000-3,200 cm-1 range differentiating between different structures as well as different proton-bound dimers may be possible. This is due mainly to differences in the asymmetric stretch of the binding proton which is predicted to occur in this region.     

Magnitude and orientation dependence of intermolecular interaction of perfluoropropane dimer studied by high-level ab initio calculations: comparison with propane dimer

Intermolecular interaction energies of 12 orientations of C(3)F(8) dimers were calculated with electron correlation correction by the second-order M?ller-Plesset perturbation method. The antiparallel C(2h) dimer has the largest interaction energy (-1.45 kcal/mol). Electron correlation correction increases the attraction considerably. Electrostatic energy is not large. Dispersion is mainly responsible for the attraction. Orientation dependence of the interaction energy of the C(3)F(8) dimer is substantially smaller than that of the C(3)H(8) dimer. The calculated interaction energy of the C(3)F(8) dimer at the potential minimum is 78% of that of the C(3)H(8) dimer (-1.85 kcal/mol), whereas the interaction energies of the CF(4) and C(2)F(6) dimers are larger than those of the CH(4) and C(2)H(6) dimers. The intermolecular separation in the C(3)F(8) dimer at the potential minimum is substantially larger than that in the C(3)H(8) dimer. The larger intermolecular separation due to the steric repulsion between fluorine atoms is the cause of the smaller interaction energy of the C(3)F(8) dimer at the potential minimum. The calculated intermolecular interaction energy potentials of the C(3)F(8) dimers using an all atom model OPLS-AA (OPLS all atom model) force field and a united atom model force field were compared with the ab initio calculations. Although the two force fields well reproduces the experimental vapor and liquid properties of perfluoroalkenes, the comparison shows that the united atom model underestimates the potential depth and orientation dependence of the interaction energy. The potentials obtained by the OPLS-AA force field are close to those obtained by the ab initio calculations.     

Comparison of quantum mechanical and experimental gas-phase basicities of amines and alcohols

A comparison was made between the experimental and B3LYP relative gas-phase basicities and proton affinities of a series of 9 amine, 3 alcohol, and 3 alkanolamine molecules. While agreement is good for most of the species studied, it is poor for the alkanolamines and 1,2-ethanediol. A series of calculations were undertaken at the B3LYP and MP2 levels using various basis sets to see if the uncertainties in the calculations can account for the discrepancies. The results suggest that this is unlikely and that the theoretical values are likely to be reasonably accurate. Calculations are also presented for the dimer formation energies of alkanolamine molecules, diamine molecules, and 1,2-ethanediol. These calculations suggest that all of these species can form proton-bound dimers. The alkanolamines and 1,2-ethanediol also appear to have relatively high formation energies for neutral dimers.     

Quantum chemical semiempirical approach to the structural and thermodynamic characteristics of fluoroalkanols at the air/water interface

In the framework of quantum chemical PM3 approximation, the geometrical structure and thermodynamic functions characteristics of the formation of monomers (n = 1-14, 34), dimers (n = 1-14, 34), and trimers and tetramers (n = 1-8) of fluoroalkanols with the composition C(n)F(2)(n+1)CH(2)CH(2)OH are calculated. It is shown that, in contrast to the fatty alcohols, which have a flat zigzag structure, the fluoroalkanol monomers are helical with an average backbone torsion angle equal to 162 degrees. For the minimum-energy structure of dimers, the self-organization of the molecules in a dimer was observed; that leads to an opposite alternation of the torsion angles corresponding to the matching atoms in the two molecules that form the dimer. This results in the fact that the most stable conformation of the dimer is the double helix. The lead (39.5 A) and diameter (7.3 A) of the double helix are determined from the calculations of C(34)F(69)CH(2)CH(2)OH dimers. Enthalpy, entropy, and Gibbs energy of the clusterization are shown to be linearly dependent on the length of the fluorinated chain. From the analysis of these thermodynamic quantities, it is concluded that dimerization of fluoroalkanols at the air/water interface takes place if the hydrocarbon link number exceeds 6, whereas for ordinary alcohols this characteristic number is 11. These calculated values agree with experimental data. The additive scheme for the evaluation of the clusterization free energies for arbitrary clusters is developed and applied to obtain the estimate of the Gibbs clusterization energy for infinitely large clusters.     

Thermodynamics and kinetics of glyoxal dimer formation: a computational study

Density functional theory (B3LYP//6-311+G) calculations including Poisson-Boltzmann implicit solvent were used to study the hydration of glyoxal and subsequent formation of dimeric species in solution. Our calculations show that the dioxolane ring dimer is the thermodynamic sink among all monomers and dimers with varying degrees of hydration. Although fully hydrated species are thermodynamically favored over their less hydrated counterparts, we find that a preliminary dehydration step precedes dimerization and ring closure. Ring closure of the open dimer monohydrate to the dioxolane ring dimer is kinetically favored over both hydration to the open dimer dihydrate and ring closure to form the dioxane ring dimer. The kinetic barriers for different geometric approaches for dimerization suggest an explanation why oligomerization stops after the formation of a dioxolane ring trimer as observed experimentally.     

Formamide dimers: a computational and matrix isolation study

The dimerization of formamide (FMA) has been investigated by matrix isolation spectroscopy, static ab initio calculations, and ab initio molecular dynamics (AIMD) simulations. Comparison of the experimental matrix IR spectra with the ab initio calculations reveals that two types of dimers A and C are predominantly formed, with two and one strong NH...O hydrogen bonds, respectively. This is in accordance with previously published experiments. In addition, there is also experimental evidence for the formation of the thermally labile dimer B after deposition of high concentrations of FMA in solid xenon. The AIMD simulations of the aggregation process show that in all cases dimer C is initially formed, but rearrangement to the more stable doubly hydrogen-bonded structures A or B occurs for a fraction of collisions on the sub-picosecond time scale.     

In situ localization and structural analysis of the malaria pigment hemozoin

Raman microspectroscopy was applied for an in situ localization of the malaria pigment hemozoin in Plasmodium falciparum-infected erythrocytes. The Raman spectra (lambdaexc=633 nm) of hemozoin show very intense signals with a very good signal-to-noise ratio. These in situ Raman signals of hemozoin were compared to Raman spectra of extracted hemozoin, of the synthetic analogue beta-hematin, and of hematin and hemin. beta-Hematin was synthesized according to the acid-catalyzed dehydration of hematin and the anhydrous dehydrohalogenation of hemin which lead to good crystals with lengths of about 5-30 microm. The Raman spectra (lambdaexc=1064 nm) of hemozoin and beta-hematin show almost identical behaviors, while some low wavenumber modes might be used to distinguish between the morphology of differently synthesized beta-hematin samples. The intensity pattern of the resonance Raman spectra (lambdaexc=568 nm) of hemozoin and beta-hematin differ significantly from those of hematin and hemin. The most striking difference is an additional band at 1655 cm(-1) which was only observed in the spectra of hemozoin and beta-hematin and cannot be seen in the spectra of hematin and hemin. Raman spectra of the beta-hematin dimer were calculated ab initio (DFT) for the first time and used for an assignment of the experimentally derived Raman bands. The calculated atomic displacements provide valuable insight into the most important molecular vibrations of the hemozoin dimer. With help from these DFT calculations, it was possible to assign the Raman band at 1655 cm(-1) to a mode located at the propionic acid side chain, which links the hemozoin dimers to each other. The Raman band at 1568 cm(-1), which has been shown to be influenced by an attachment of the antimalarial drug chloroquine in an earlier study, could be assigned to a C=C stretching mode spread across one of the porphyrin rings and is therefore expected to be influenced by a pi-pi-stacking to the drug.     

Binding Energies of Proton-Bound Dimers of Imidazole and n-Acetylalanine Methyl Ester Obtained by Blackbody Infrared Radiative Dissociation

The dissociation kinetics of protonated n-acetyl-L-alanine methyl ester dimer (AcAlaME(d)), imidazole dimer, and their cross dimer were measured using blackbody infrared radiative dissociation (BIRD). Master equation modeling of these data was used to extract threshold dissociation energies (E(o)) for the dimers. Values of 1.18 +/- 0.06, 1.11 +/- 0.04, and 1.12 +/- 0.08 eV were obtained for AcAlaME(d), imidazole dimer, and the cross dimer, respectively. Assuming that the reverse activation barrier for dissociation of the ion-molecule complex is negligible, the value of E(o) can be compared to the dissociation enthalpy (DeltaH(d) degrees ) from HPMS data. The E(o) values obtained for the imidazole dimer and the cross dimer are in agreement with HPMS values; the value for AcAlaME(d) is somewhat lower. Radiative rate constants used in the master equation modeling were determined using transition dipole moments calculated at the semiempirical (AM1) level for all dimers and compared to ab initio (RHF/3-21G*) calculations where possible. To reproduce the experimentally measured dissociation rates using master equation modeling, it was necessary to multiply semiempirical transition dipole moments by a factor between 2 and 3. Values for transition dipole moments from the ab initio calculations could be used for two of the dimers but appear to be too low for AcAlaME(d). These results demonstrate that BIRD, in combination with master equation modeling, can be used to determine threshold dissociation energies for intermediate size ions that are in neither the truncated Boltzmann nor the rapid energy exchange limit.     

Ligand rotation in [Ar(R)N]3M-N2-M'[N(R)Ar]3(M, M' = MoIII, NbIII; R = iPr and tBu) dimers

Earlier calculations on the model N2-bridged dimer (micro-N2)-{Mo[NH2]3}2 revealed that ligand rotation away from a trigonal arrangement around the metal centres was energetically favourable resulting in a reversal of the singlet and triplet energies such that the singlet state was stabilized 13 kJ mol(-1) below the D(3d) triplet structure. These calculations, however, ignored the steric bulk of the amide ligands N(R)Ar (R =iPr and tBu, Ar = 3,5-C6H3Me2) which may prevent or limit the extent of ligand rotation. In order to investigate the consequences of steric crowding, density functional calculations using QM/MM techniques have been performed on the Mo(III)Mo(III) and Mo(III)Nb(III) intermediate dimer complexes (mu-N(2))-{Mo[N(R)Ar]3}2 and [Ar(R)N]3Mo-(mu-N2)-Nb[N(R)Ar]3 formed when three-coordinate Mo[N(R)Ar]3 and Nb[N(R)Ar]3 react with dinitrogen. The calculations indicate that ligand rotation away from a trigonal arrangement is energetically favourable for all of the ligands investigated and that the distortion is largely electronic in origin. However, the steric constraints of the bulky amide groups do play a role in determining the final orientation of the ligands, in particular, whether the ligands are rotated at one or both metal centres of the dimer. Analogous to the model system, QM/MM calculations predict a singlet ground state for the (mu-N2)-{Mo[N(R)Ar]3}2 dimers, a result which is seemingly at odds with the experimental triplet ground state found for the related (mu-N2)-{Mo[N(tBu)Ph]3}2 system. However, QM/MM calculations on the (mu-N2)-{Mo[N(tBu)Ph]3}2 dimer reveal that the singlet-triplet gap is nearly 20 kJ mol(-1) smaller and therefore this complex is expected to exhibit very different magnetic behaviour to the (mu-N2)-{Mo[N(R)Ar]3}2 system.     

The synthesis of covalently linked tetraarylporphyrin dimers

A new and general synthesis of porphyrin dimers is described. The synthesis involves the reaction of dibromoalkanes with phenolic porphyrins, such as 5(4-hydroxyphenyl)-10,15,20-tritolylporphyrin, to form σ-bromoalkyl porphyrin ethers. The latter compounds are then reacted with a second phenolic porphyrin to give porphyrin dimers. A mixed metalloporphyrin dimer has been prepared which contains both V(IV) and Cu(II). The compounds have been examined spectroscopically. The free-base porphyrin dimers show a splitting of the intense Soret band. This is interpreted as indicative of weak singlet energy transfer between the covalently linked porphyrins.     

Theoretical study of peptide model dimers. Homo versus heterochiral complexes

The study of possible chiral recognition of a series of peptide models (For-Gly-NH₂, For-Ala-NH₂ and four of their fluoro substituted derivatives) has been carried out by means of DFT calculations. Homo (L,L) and heterochiral (L,D) dimers formed by hydrogen bond (HB) complexation have been considered. Initially, the conformational preferences of the monomers have been calculated and used to generate all the possible homo and heterochiral dimers. The energetic results show that in most cases, the β monomers are the most stable while in the dimers, the γ–γ complexes show the strongest interaction energies. In three of the four chiral cases studied, a heterochiral dimer is the most stable one. In addition, the electron density and nuclear shielding of the complexes have been studied.     

Electronic Properties of Vinylene-Linked Heterocyclic Conducting Polymers: Predictive Design and Rational Guidance from DFT Calculations

The band structure and electronic properties in a series of vinylene-linked heterocyclic conducting polymers are investigated using density functional theory (DFT). In order to accurately calculate electronic band gaps, we utilize hybrid functionals with fully periodic boundary conditions to understand the effect of chemical functionalization on the electronic structure of these materials. The use of predictive first-principles calculations coupled with simple chemical arguments highlights the critical role that aromaticity plays in obtaining a low band gap polymer. Contrary to some approaches which erroneously attempt to lower the band gap by increasing the aromaticity of the polymer backbone, we show that being aromatic (or quinoidal) in itself does not ensure a low band gap. Rather, an iterative approach which destabilizes the ground state of the parent polymer toward the aromatic ? quinoidal level crossing on the potential energy surface is a more effective way of lowering the band gap in these conjugated systems. Our results highlight the use of predictive calculations guided by rational chemical intuition for designing low band gap polymers in photovoltaic materials.     

Effect of dimer formation via hydrogen bonding on static and dynamic nonlinear optical characteristics of chromophores

The effect of head-to-tail azochromophore dimer formation on the values of static and dynamic first hyperpolarizability is studied on the basis of calculations performed at M06-2X/aug-cc-pVDZ and ωB97X-D/aug-cc-pVDZ computational levels; the results are compared with those obtained at second-order Moller-Plesset pertubation theory (MP2)/aug-cc-pVDZ. Azochromophores DO3 and AAB-DCV , participating in the dimer formation, contain nitro- or dicyanovinylene acceptor moieties. The structure of the studied dimers is obtained at the B3LYP-D3/6-31++G (d,p) level with basis set superposition error (BSSE) correction. Dynamic first hyperpolarizabilities are calculated at radiation frequencies of 0.65 eV, 0.918 eV and 1.165 eV. The essential effect of dimer formation is demonstrated: it results in almost a 3.5 times increase of the first hyperpolarizability. In the series D1 - D2 - D3 , β(2ω) values at 0.65 eV increase in a way similar to the static case: β(2ω) for D2 and D3 are 1.5 and 1.8 times higher than that for D1 . The notable resonance enhancement of β(2ω) for the studied hydrogen-bonded dimers is demonstrated at radiation frequency of 1.165 eV.