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ABSTRACT: In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (β(t)) were calculated for a set of benzene, styrene, biphenyl and stilbene derivatives using HF, MP2 and DFT (31 different functionals) levels and over 71 distinct basis sets. In addition, we propose two new basis sets, NLO-V and aNLO-V, for NLO properties calculations. As the main outcomes it is shown that long-range corrected DFT functionals such as M062X, ωB97, cam-B3LYP, LC-BLYP and LC-ωPBE work satisfactorily for NLO properties when appropriate basis sets such as those proposed here (NLO-V or aNLO-V) are used. For most molecules with β ranging from 0 to 190 esu, the average absolute deviation was 13.2 esu for NLO-V basis sets, compared to 27.2 esu for the standard 6-31 G(2d) basis set. Therefore, we conclude that the new basis sets proposed here (NLO-V and aNLO-V), together with the cam-B3LYP functional, make an affordable calculation scheme to predict NLO properties of large organic molecules.
Journal of Molecular Modeling 11/2012; · 1.80 Impact Factor
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Organometallics 11/2012; 31(23):8063. · 3.96 Impact Factor
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ABSTRACT: Density functional theory (DFT) calculations of (1) H NMR chemical shifts for l-quebrachitol isomers were performed using the B3LYP functional employing the 6-31G(d,p) and 6-311 + G(2d,p) basis sets. The effect of the solvent on the B3LYP-calculated NMR spectrum was accounted for using the polarizable continuum model. Comparison is made with experimental (1) H NMR spectroscopic data, which shed light on the average uncertainty present in DFT calculations of chemical shifts and showed that the best match between experimental and theoretical B3LYP (1) H NMR profiles is a good strategy to assign the molecular structure present in the sample handled in the experimental measurements. Among four plausible O-methyl-inositol isomers, the l-quebrachitol 2a structure was unambiguously assigned based only on the comparative analysis of experimental and theoretical (1) H NMR chemical shift data. The B3LYP infrared (IR) spectrum was also calculated for the four isomers and compared with the experimental data, with analysis of the theoretical IR profiles corroborating assignment of the 2a structure. Therefore, it is confirmed in this study that a combined experimental/DFT spectroscopic investigation is a powerful tool in structural/conformational analysis studies.
Magnetic Resonance in Chemistry 08/2012; 50(9):608-14. · 1.44 Impact Factor
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ABSTRACT: In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis-diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all-electron basis sets (ABS). In addition, a modified all-electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6-31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol(-1) , which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol(-1) . For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol(-1) , respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree-Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6-31+G(d) or B3PW91/mDZP/6-31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP-DNA complex), the lower levels B3LYP/LANL2DZ/6-31+G(d) and B3LYP/SBKJC-VDZ/6-31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol(-1) , respectively, which is only 13% higher than the actual value. © 2012 Wiley Periodicals, Inc.
Journal of Computational Chemistry 07/2012; 33(29):2292-302. · 4.58 Impact Factor
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ABSTRACT: This study has focus on inclusion compounds formed by native cyclodextrins (CD) and dinuclear platinum(II) complex (bisPt), investigated by density functional theory and hybrid our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) approaches. The main goal here is to get insights on the molecular features governing the stability of bisPt@CD inclusion complexes, accounting for cavity size, host–guest orientation, and stoichiometry. The results indicate that the beta-CD is the most attractive host to form inclusion complex with bisPt, with DG found negative for the six orientations tested (A–F), ranging from 3.69 to 20.08 kcal/mol (ONIOM values). Besides the favorable size/shape relationship for bisPt@b-CD complex, the higher stability is also due the hydrogen bonds between the bisPt amine groups and the beta-CD oxygen atoms.
International Journal of Quantum Chemistry 07/2012; 112. · 1.36 Impact Factor
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ABSTRACT: In the present work, a Box–Behnken 34 design was applied to study inclusion complexes consisting of a saturated triglyceride with twelve carbons in each of the
three side chains (TLG—trilaurylglyceride) and α-cyclodextrin (α-CD) in different TLG:α-CD stoichiometries: 1:1 (TLG@1.α-CD),
1:2 (TLG@2.α-CD) and 1:3 (TLG@3.α-CD). Four intrinsic variables commonly used to set up the heating protocol in the classical
molecular-dynamics (MD) simulation were monitored: the heating ramp (W), the equilibrium time (E), the time step (S) and the
dielectric constant of the medium (C). Based on the obtained responses, the most appropriate heating protocol and general
aspects concerning the MD simulation of the host–guest supramolecular systems are discussed.
KeywordsMolecular dynamics–Triglycerides–α-Cyclodextrin–Box–Behnken design
Journal of Inclusion Phenomena 05/2012; 71(1):103-111. · 1.89 Impact Factor
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ABSTRACT: The hydrated α-cyclodextrin (α-CD) clusters resulting from the following process: nα-CD+n(H2O)6→α-CDn·6nH2O, with n=1, 2, 3, 4, have been investigated using semiempirical (PM3), ab initio Hartree-Fock and Density Functional Theory (BLYP
functional) levels of theory. The largest structure containing 576 atoms and 5,760 contracted basis functions (6-31G(d,p)
basis set) poses as a considerable hard task for quantum chemical calculations. As the number of basis function increases
rapidly with the cluster size, an alternative procedure to make the calculations feasible is certainly welcome, in order to
perform BLYP calculations with an adequate basis set. Through the aid of a computer program that we developed, it became of
practical use the selection of atom by atom basis sets, using the common chemical sense, enabling quantum mechanical calculations
to be performed for very large molecular interacting systems (inclusion complexes), at an affordable computational cost. In
this article we show how an appropriate selection of basis functions, leaving the CHn groups with a minimal basis set and the oxygen atoms (and OH groups) with a better quality basis set, lower considerably
the computational cost with no significant loss in the calculated interaction energies. A regular pattern is observed for
α-CD hydrated monomer, dimer, trimer and tetramer, therefore adding support to the use of this procedure when studying larger
hydrogen bonded clusters where electron correlation effects are important. We show that the procedure reported here enables
DFT calculations for hydrated cyclodextrin using basis set up to the 6-311++G(3df,3pd) triple zeta quality .
Journal of Inclusion Phenomena 04/2012; 59(3):265-277. · 1.89 Impact Factor
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ABSTRACT: Chemically modified tetracyclines (CMTs) have shown promising activity as matrix metalloproteinase (MMP) inhibitors acting
as zinc-binding groups. The first step in the design of new and effective drugs is the molecular description of the mechanism
of action in chemical and biological environments. In the present study, the structure and stability of [Zn(LH
n
)(H2O)2]2−x
(n=0, 1, 2 and x=−2, −1, 0) and [Zn(L)(His)3], where L represents five distinct, structurally related CMTs, are discussed. In addition to the effect of the ligand on
Zn(II) coordination, the role of the solvent and pH was also determined. The results suggested that O1–Oam (labeled as site
II in the present paper) of CMT-1, CMT-4 and CMT-7 was the most stable site in the gas phase and aqueous solution. However,
for CMT-3 and CMT-8, coordination at the O11–O12 moiety (site VI) was preferred. This coordination site is an essential binding
mode of CMTs with active zinc in the MMP catalytic site; therefore, our results support the singular behavior of CMT-3 and
CMT-8 as promising MMP inhibitors.
KeywordsTetracycline–DFT calculations–Matrix metalloproteinase–Chemically modified tetracycline
Theoretical Chemistry Accounts 04/2012; 128(3):377-388. · 2.16 Impact Factor
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ABSTRACT: The size, shape and surface chemistry of nanoparticles play an important role in cellular interaction. Thus, the main objective of the present study was the determination of the β-cyclodextrin (β-CD) self-assembly thermodynamic parameters and its structure, aiming to use these assemblies as a possible controlled drug release system. Light scattering measurements led us to obtain the β-CD's critical aggregation concentration (cac) values, and consequently the thermodynamic parameters of the β-CD spontaneous self-assembly in aqueous solution: Δ(agg)G(o) = -16.31 kJ mol(-1), Δ(agg)H(o) = -26.48 kJ mol(-1) and TΔ(agg)S(o) = -10.53 kJ mol(-1) at 298.15 K. Size distribution of the self-assembled nanoparticles below and above cac was 1.5 nm and 60-120 nm, respectively. The number of β-CD molecules per cluster and the second virial coefficient were identified through Debye's plot and molecular dynamic simulations proposed the three-fold assembly for this system below cac. Ampicillin (AMP) was used as a drug model in order to investigate the key role of the guest molecule in the self-assembly process and the β-CD:AMP supramolecular system was studied in solution, aiming to determine the structure of the supramolecular aggregate. Results obtained in solution indicated that the β-CD's cac was not affected by adding AMP. Moreover, different complex stoichiometries were identified by nuclear magnetic resonance and isothermal titration calorimetry experiments.
Physical Chemistry Chemical Physics 02/2012; 14(6):1934-44. · 3.57 Impact Factor
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ABSTRACT: In the present work, the structures and relative energies of 108 linked α-cyclodextrin dimers have been evaluated at a quantum mechanics level of theory. Contrary to hydrogen-bonded associations, the covalently bound tail-to-tail (TT) arrangement has been identified as the most favorable, regardless of the number of cross-linking groups and their spatial topologies. On the basis of the study of α-cyclodextrin tetramers, the outcomes have been extended to small molecular oligomers, suggesting the relative number of TT arrangements as the primary feature to the stability of larger covalently bound α-cyclodextrin associations. Despite the TT stability, long molecular tubes possessing only such association cannot exist because many TT associations imply the existence of many HH associations. In this context, it can be stated that relative energy stability associated with spatial requirements accounts for the small HT population experimentally expected in molecular tubes.
The Journal of Physical Chemistry C 01/2012; 116:18958. · 4.80 Impact Factor
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ABSTRACT: In the present work, a Box–Behnken 3^4 design was applied to study inclusion complexes consisting of a
saturated triglyceride with twelve carbons in each of the three side chains (TLG—trilaurylglyceride) and a-cyclodextrin (a-CD) in different TLG:a-CD stoichiometries: 1:1 (TLG@1.a-CD), 1:2 (TLG@2.a-CD) and 1:3 (TLG@3.a-CD). Four intrinsic variables commonly used to set up the heating protocol in the classical molecular-dynamics (MD) simulation were monitored: the heating ramp (W), the equilibrium time (E), the time step (S) and the dielectric constant of the medium (C). Based on the obtained responses, the most appropriate heating protocol and general aspects concerning the MD simulation of the host–guest supramolecular systems are discussed.
Journal of inclusion phenomena and macrocyclic chemistry 12/2011; 71:103-111. · 1.17 Impact Factor
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ABSTRACT: In the present study, the inclusion processes of β-carotene, astaxanthin, lycopene, and norbixin (NOR) into the β-cyclodextrin (β-CD) cavity were investigated by means of Raman spectroscopy and quantum mechanics calculations. The Raman ν(1) band assigned to C═C stretching was sensitive to the host-guest interaction and in general undergoes a blue shift (3-13 cm(-1)) after inclusion takes place, which is the consequence of the localization of single and double bonds. This is supported by the molecular modeling prediction, which inclusion complexes show the ν(1) band blue shifted by 1-8 cm(-1). The calculated complexation energies was small for most of derivatives and was found to be -11.1 kcal mol(-1) for inclusion of AST and +0.27 kcal mol(-1) for NOR. The stability order was qualitatively correlated to topological parameters accounting for the opening angle of the chain. This means that after inclusion the guest molecules assume a slightly more extended conformation, which enhances the host-guest contact, improving the interaction energy. The results discussed here clearly demonstrate the matrix effect on the carotenes' spectroscopic profile and should contribute to fully characterize the raw samples.
The Journal of Physical Chemistry A 08/2011; 115(30):8511-9. · 2.95 Impact Factor
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ABSTRACT: In the present study, the inclusion processes of β-carotene, astaxanthin, lycopene, and norbixin (NOR) into the β-cyclodextrin (β-CD) cavity were investigated by means of Raman spectroscopy and quantum mechanics calculations. The Raman ν(1) band assigned to C═C stretching was sensitive to the host-guest interaction and in general undergoes a blue shift (3-13 cm(-1)) after inclusion takes place, which is the consequence of the localization of single and double bonds. This is supported by the molecular modeling prediction, which inclusion complexes show the ν(1) band blue shifted by 1-8 cm(-1). The calculated complexation energies was small for most of derivatives and was found to be -11.1 kcal mol(-1) for inclusion of AST and +0.27 kcal mol(-1) for NOR. The stability order was qualitatively correlated to topological parameters accounting for the opening angle of the chain. This means that after inclusion the guest molecules assume a slightly more extended conformation, which enhances the host-guest contact, improving the interaction energy. The results discussed here clearly demonstrate the matrix effect on the carotenes' spectroscopic profile and should contribute to fully characterize the raw samples.
The Journal of Physical Chemistry A 07/2011; 115(30):8511-8519. · 2.95 Impact Factor
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ABSTRACT: The inclusion compound formed between cross-linked a-cyclodextrin dimer and substituted oligothiophene, was investigated using density functional theory (DFT). Energy gap, spectroscopy (IR, UV–vis, 13 C NMR, and 1 H NMR) and first hyperpolarizability data were analyzed for the free species and inclusion compound, pp-PT@(aCD–aCD). The semiconducting property of the included pp-PT was not substantially affected on inclusion, with the energy gap increasing by only 10% after interaction with aCD–aCD. On the other hand, the nonlinear op-tical (NLO) response was significantly decreased, with the first hyperpolarizability, b, predicted to be just more than 60% lower for the [2]rotaxane than for free pp-PT, but still having consid-erable magnitude. This was explained by the two-state model based on the charge-transfer contribution to the electronic transitions. The sensitivity of electronic spectra might also be useful for the inclusion complex characterization. The IR spec-trum was slightly sensitive to the host–guest interaction and the calculated 13 C NMR and 1 H NMR chemical shifts for the pp-PT guest showed appreciable variations of 5–10 and 1–1.5 ppm, respectively, and so can be used for the characterization of inclusion compounds. We concluded that the formation of inclusion complexes with CDs, seems indeed very promising and the use of encapsulating conducting material should be experimentally pursued.
Journal of Polymer Science Part B Polymer Physics 05/2011; 49:1101-1111. · 1.53 Impact Factor
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ABSTRACT: A conformational and vibrational analysis of cis-diamminedichloropalladium(ii) (cDDPd) is reported. Several theoretical methods (from Hartree-Fock to Møller-Plesset and Density Functional Theory) combined with different all-electron basis-sets are evaluated, in view of determining the best suited strategy for accurately representing this molecule. This choice is based on the best compromise between accuracy and computational requirements. Different scaling models were tested for obtaining the best scaling schemes of the vibrational modes to be used in this type of inorganic systems. The structural parameters and vibrational results predicted by the calculations are compared with the corresponding experimental data, namely X-ray structure and vibrational spectra. Finally, a complete assignment of the cDDPd vibrational spectra is presented.
Physical Chemistry Chemical Physics 11/2010; 12(42):14309-21. · 3.57 Impact Factor
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ABSTRACT: Two synthetic epoxide derivatives, important intermediates in organic synthesis, were obtained from L-quebrachitol, and their conformations were proposed based on spectroscopic analysis. Density functional theory (DFT) calculations of infrared and NMR spectra were shown to be reliable enough for organic chemistry applications. The observed structures were determined with the aid of the DFT spectroscopic data, stressing the relevance and utility of combined experimental/theoretical studies and also the usefulness of the (13)C NMR B3LYP/6-31G(d,p) calculations.
Organic Letters 11/2010; 12(23):5458-61. · 5.86 Impact Factor
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ABSTRACT: This work presents the crystal structure and the investigation under a supramolecular perspective of a squaric acid derivative obtained from the replacement of the hydroxyl groups by anilines. The squaraine obtained (1,2-dianilinesquaraine) crystallizes in the Pbcn space group, in a unit cell with a = 26.5911(8) Å, b = 6.1445(10) Å, and c = 7.5515(5) Å. The bond lengths in the oxocarbon ring, squarate-N and C−O bonds present the character of double bonds. Also the difference between the longer and shorter C-C bond in the four-membered ring (ΔCC) is 0.0667 Å, showing a good degree of equalization of these bond lengths. The phenyl rings are slightly distorted in relation to the squarate ring, and the angle measured between the best plane fitted in each ring is 37.2(9)°. Each molecule is connected to the other through a hydrogen bond involving the N-H···O moieties, where the donor···acceptor distance is 2.826(1) Å, forming ribbons in a unidimensional arrangement C(5)R22(10) along the b axis. These structures are mutually connected by π-stacking interactions extending the supramolecular structure in a two-dimensional fashion. Besides, an interesting crossed structure can be easily identified in the formed sheets that are built through the C-H/π interactions. DFT calculations at the B3LYP/6-311++G(d,p) level of theory show an approximately planar molecular structure for the isolated molecule. However, when a dimer model built from hydrogen bonds is considered, the optimized structure presents considerable torsion between the phenyl and squarate rings, as observed in the experimental data. The electronic spectrum shows a strong absorption band at 341 nm that is red-shifted compared to the squarate maximum absorption (290 nm), indicating a more effective electronic delocalization. The most characteristic vibrational modes of the oxocarbon species were used as spectroscopic probe to understand how the substituent groups affect the oxocarbon moiety and, consequently, the vibrational spectra. The analysis shows that the modes associated with the C-Cox bonds are the most affected. Also the character of the double bond of squarate-N and the single bond for the phenyl-N are easily identified. In a general form, the calculated vibrational modes of the dimer model were in better accordance with the experimental data, mainly when the mode has a contribution from the acceptor molecule in the intermolecular interaction.
The Journal of Physical Chemistry A 09/2010; 114(37):10097-109. · 2.95 Impact Factor
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ABSTRACT: article, we have investigated the dicopper(II) model complex [Cu 2 (-OH)(C 21 H 33 ON 6)] 2 (Complex-A) under a computational perspective, using the DFT method, since this approach has been very useful in the treatment of bimetallic copper systems. The structural and spectroscopic study of Complex-A as well as the structural analysis of the BDNPP/Complex-A (Complex-B) adduct have been carried out. The calculated parameters for Complex-A are in good accordance with the experimental X-ray data. Some remarkable points can be observed from the calculated UV–vis relative excitations. The Complex-B computed structure verifies its identity as a key intermediate species in the BDNPP hydrolysis mechanism. The Cu II Cu II calculated distance in Complex-B (3.026 Å) is shorter than the calculated for Complex-A (3.080 Å); one copper atom is bonded to the oxygen of phosphate [Cu (2)O64 –P] at 2.511 Å. These arguments clearly suggest a monodentate interaction and lead to a new mechanism involving terminal substrate coordination and subsequent intramolecular nucleophilic attack by a bridging hydroxide. Such a hypothesis is completely new in terms of homobimetallic copper systems, and may have important implications regarding the chemistry of several biological dinuclear catalytic sites.
International Journal of Quantum Chemistry 01/2010; 110:1432-1442. · 1.36 Impact Factor
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ABSTRACT: Spectroscopic techniques, including Raman, IR, UV/vis, and NMR were used to characterize the samples of the azo dye Ponceau 4R (also known as E124, New Coccine; Cochineal Red; C.I. no. 16255; Food Red No. 102), which is 1,3-naphthalenedisulfonic acid, 7-hydroxy-8-[(4-sulfo-1-naphthalenyl) azo] trisodium salt in aqueous solution and solid state. In addition, first principle calculations were carried out for the azo (OH) and hydrazo (NH) tautomers in order to assist in the assignment of the experimental data. The two intense bands observed in the UV/vis spectrum, centered at 332 and 507 nm, can be compared to the calculated values at 296 and 474 nm for azo and 315 and 500 nm for hydrazo isomer, with the latter in closer agreement to the experiment. The Raman spectrum is quite sensitive to tautomeric equilibrium; in solid state and aqueous solution, three bands were observed around 1574, 1515, and 1364 cm(-1), assigned to mixed modes including deltaNH + betaCH + nuCC, deltaNH + nuC horizontal lineO + nuC horizontal lineN + betaCH and nuCC vibrations, respectively. These assignments are predicted only for the NH species centered at 1606, 1554, and 1375 cm(-1). The calculated Raman spectrum for the azo (OH) tautomer showed two strong bands at 1468 (nuN = N + deltaOH) and 1324 cm(-1) (nuCC + nuC-N), which were not obtained experimentally. The (13)C NMR spectrum showed a very characteristic peak at 192 ppm assigned to the carbon bound to oxygen in the naphthol ring; the predicted values were 165 ppm for OH and 187 for NH isomer, supporting once again the predominance of NH species in solution. Therefore, all of the experimental and theoretical results strongly suggest the food dye Ponceau 4R or E124 has a major contribution of the hydrazo structure instead of the azo form as the most abundant in condensate phase.
The Journal of Physical Chemistry A 10/2009; 114(1):526-34. · 2.95 Impact Factor
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ABSTRACT: Empty linear associations accounting for three alpha-CD units and their corresponding pseudorotaxanes have been studied by means of long length molecular dynamics (MD) simulations in a vacuum and in aqueous solution. Results from MD for empty sequences lead to a quite stable arrangement formed by three mutually perpendicular cyclodextrin (CD) units named here as 3P. In such a spatial arrangement, the van der Waals term in the force field is pronounced, accounting for almost 40% of the association energy, which ensures the noticeable stability of the 3P association even in aqueous media. In addition, it can be stated that only the presence of the oligomer forces the CD units to acquire an almost linear association. Mutually perpendicular-based arrangements are the most favorable spatial disposition in aqueous media. We believe this work is the first step toward a more ambitious study including very large CD sequences, aiming to understand the association process in aqueous solution at a molecular level.
The Journal of Physical Chemistry B 08/2009; 113(29):9762-9. · 3.70 Impact Factor
