Artëm E. Masunov

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Applicability of hybrid density functional theory methods to calculation of molecular hyperpolarizability

The donor/acceptor (D/A) substituted pi-conjugated organic molecules possess extremely fast nonlinear optical (NLO) response time that is purely electronic in origin. This makes them promising candidates for optoelectronic applications. In the present study, we utilized four hybrid density functionals (B3LYP, B97-2, PBE0, BMK), Hartree-Fock, and second order Moller-Plesset correlation energy correction, truncated at second-order (MP2) methods with different basis sets to estimate molecular first hyperpolarizability (beta) of D/A-substituted benzenes and stilbenes (D=OMe, OH, NMe(2), NH(2); A=NO(2), CN). The results of density functional theory (DFT) calculations are compared to those of MP2 method and to the experimental data. We addressed the following questions: (1) the accurate techniques to compare calculated results to each other and to experiment, (2) the choice of the basis set, (3) the effect of molecular planarity, and (4) the choice of the method. Comparison of the absolute values of hyperpolarizabilities obtained computationally and experimentally is complicated by the ambiguities in conventions and reference values used by different experimental groups. A much more tangible way is to compare the ratios of betas for two (or more) given molecules of interest that were calculated at the same level of theory and measured at the same laboratory using the same conventions and reference values. Coincidentally, it is the relative hyperpolarizabilities rather than absolute ones that are of importance in the rational molecular design of effective NLO materials. This design includes prediction of the most promising candidates from particular homologous series, which are to be synthesized and used for further investigation. In order to accomplish this goal, semiquantitative level of accuracy is usually sufficient. Augmentation of the basis set with polarization and diffuse functions changes beta by 20%; however, further extension of the basis set does not have significant effect. Thus, we recommend 6-31+G(*) basis set. We also show that the use of planar geometry constraints for the molecules, which can somewhat deviate from planarity in the gas phase, leads to sufficient accuracy (with an error less than 10%) of predicted values. For all the molecules studied, MP2 values are in better agreement with experiment, while DFT hybrid methods overestimate beta values. BMK functional gives the best agreement with experiment, with systematic overestimation close to the factor of 1.4. We propose to use the scaled BMK results for prediction of molecular hyperpolarizability at semiquantitative level of accuracy.

Dopant-mediated oxygen vacancy tuning in ceria nanoparticles

Ceria nanoparticles with 20 and 40 at.% RE (RE = Y, Sm, Gd, and Yb) dopants were synthesized through a microemulsion method. Independently of the dopant nature and concentration, nearly monodispersed nanoparticles of size 3-5 nm were observed in high resolution transmission electron microscopic analysis. The ceria lattice either expands or contracts depending on the dopant cation ionic radii, as indicated by x-ray diffraction studies. X-ray photoelectron and Raman spectroscopic studies were used to quantify the cerium oxidation state and oxygen vacancy concentration. The results show the tunability of the oxygen vacancy and Ce(3+) concentrations based on the dopant properties. First principles simulations using the free energy density functional theory method support the observed experimental trends. The reported results establish a relationship between the oxygen vacancies and oxidation states in doped ceria required for tailoring properties in catalytic and biomedical applications.

Contributions to the binding free energy of ligands to avidin and streptavidin

The free energy of binding of a ligand to a macromolecule is here formally decomposed into the (effective) energy of interaction, reorganization energy of the ligand and the macromolecule, conformational entropy change of the ligand and the macromolecule, and translational and rotational entropy loss of the ligand. Molecular dynamics simulations with implicit solvation are used to evaluate these contributions in the binding of biotin, biotin analogs, and two peptides to avidin and streptavidin. We find that the largest contribution opposing binding is the protein reorganization energy, which is calculated to be from 10 to 30 kcal/mol for the ligands considered here. The ligand reorganization energy is also significant for flexible ligands. The translational/rotational entropy is 4.5–6 kcal/mol at 1 M standard state and room temperature. The calculated binding free energies are in the correct range, but the large statistical uncertainty in the protein reorganization energy precludes precise predictions. For some complexes, the simulations show multiple binding modes, different from the one observed in the crystal structure. This finding is probably due to deficiencies in the force field but may also reflect considerable ligand flexibility. Proteins 2002;47:194–208.

Phosphate ester hydrolysis of biologically relevant molecules by cerium oxide nanoparticles

In an effort to characterize the interaction of cerium oxide nanoparticles (CNPs) in biological systems, we explored the reactivity of CNPs with the phosphate ester bonds of p-nitrophenylphosphate (pNPP), ATP, o-phospho-l-tyrosine, and DNA. The activity of the bond cleavage for pNPP at pH 7 is calculated to be 0.860 ± 0.010 nmol p-nitrophenol/min/μg CNPs. Interestingly, when CNPs bind to plasmid DNA, no cleavage products are detected. While cerium(IV) complexes generally exhibit the ability to break phosphorus-oxygen bonds, the reactions we report appear to be dependent on the availability of cerium(III) sites, not cerium(IV) sites. We investigated the dephosphorylation mechanism from the first principles and find the reaction proceeds through inversion of the phosphate group similar to an S(N)2 mechanism. The ability of CNPs to interact with phosphate ester bonds of biologically relevant molecules has important implications for their use as potential therapeutics.

Quantum chemistry of quantum dots: Effects of ligands and oxidation

We report Gaussian basis set density functional theory (DFT) calculations of the structure and spectra of several colloidal quantum dots (QDs) with a (CdSe)(n) core (n=6,15,17), that are either passivated by trimethylphosphine oxide ligands, or unpassivated and oxidized. From the ground state geometry optimization results we conclude that trimethylphosphine oxide ligands preserve the wurtzite structure of the QDs. Evaporation of the ligands may lead to surface reconstruction. We found that the number of two-coordinated atoms on the nanoparticles surface is the critical parameter defining the optical absorption properties. For (CdSe)(15) wurtzite-derived QD this number is maximal among all considered QDs and the optical absorption spectrum is strongly redshifted compared to QDs with threefold coordinated surface atoms. According to the time-dependent DFT results, surface reconstruction is accompanied by a significant decrease in the linear absorption. Oxidation of QDs destroys the perfection of the QD surface, increases the number of two-coordinated atoms and results in the appearance of an infrared absorption peak close to 700 nm. The vacant orbitals responsible for this near infrared transition have strong Se-O antibonding character. Conclusions of this study may be used in optimization of engineered nanoparticles for photodetectors and photovoltaic devices.

Supramolecular step in design of nonlinear optical materials: Effect of π…π stacking aggregation on hyperpolarizability

Theoretical estimation of nonlinear optical (NLO) properties is an important step in systematic search for optoelectronic materials. Density functional theory methods are often used to predict first molecular hyperpolarizability for compounds in advance of their synthesis. However, design of molecular NLO materials require an estimation of the bulk properties, which are often approximated as additive superposition of molecular tensors. It is therefore important to evaluate the accuracy of this additive approximation and estimate the extent by which intermolecular interactions influence the first molecular hyperpolarizability β. Here we focused on the stacking aggregates, including up to 12 model molecules (pNA and ANS) and observed enhancement and suppression of molecular hyperpolarizability relative to the additive sum. We found that degree of nonadditivity depends on relative orientation of the molecular dipole moments and does not correlate with intermolecular interaction energy. Frenkel exciton model, based on dipole-dipole approximation can be used for qualitative prediction of intermolecular effects. We report on inaccuracy of this model for the molecules with long π-systems that are significantly shifted relative to each other, when dipole-dipole approximation becomes inaccurate. To obtain more detailed information on the effect of intermolecular interactions on β we proposed electrostatic approach which accounts for the mutual polarization of the molecules by each other. We measure the induced polarization of each molecule in the aggregate by the charge of its donor (or acceptor) group. The proposed approach demonstrates linear correlation β(FF) vs β(elm) (estimated by finite field theory and electrostatic model, respectively) and allows decomposition of the hyperpolarizability for a molecular aggregate into separate molecular contributions. We used this decomposition to analyze the reasons of deviation of aggregate β from additivity, as well as the cooperative effect of intermolecular interactions on hyperpolarizability for stacks of growing size. In cases of positive cooperativity (enhancement), we found 6-8 molecules to be necessary to reach the asymptotic limit. In more frequent cases of negative cooperativity two opposite factors play role. The first one consists of direct lowering of β due to repulsive dipole-dipole interactions. The second factor is originated in a decrease of molecular dipole moments, which in turn leads to a decrease of dipole-dipole repulsion, and therefore increases β. For strong intermolecular repulsive dipole-dipole interactions these effects nearly cancel each other. In such cases the trimers and even dimers are sufficient to reach the asymptotic limit of the infinite stacks. Based on the observed trends we estimated non-additive correction to β for well known NLO crystals NPAN and MNMA. In the case of NPAN, stacking effect on molecular hyperpolarizability represents the leading component of the crystal packing effect and improves the agreement between calculated and experimental data which is further improved when frequency dependence is taken in account.

Quantum chemistry of the minimal CdSe clusters

Colloidal quantum dots are semiconductor nanocrystals (NCs) which have stimulated a great deal of research and have attracted technical interest in recent years due to their chemical stability and the tunability of photophysical properties. While internal structure of large quantum dots is similar to bulk, their surface structure and passivating role of capping ligands (surfactants) are not fully understood to date. We apply ab initio wavefunction methods, density functional theory, and semiempirical approaches to study the passivation effects of substituted phosphine and amine ligands on the minimal cluster Cd(2)Se(2), which is also used to benchmark different computational methods versus high level ab initio techniques. Full geometry optimization of Cd(2)Se(2) at different theory levels and ligand coverage is used to understand the affinities of various ligands and the impact of ligands on cluster structure. Most possible bonding patterns between ligands and surface CdSe atoms are considered, including a ligand coordinated to Se atoms. The degree of passivation of Cd and Se atoms (one or two ligands attached to one atom) is also studied. The results suggest that B3LYP/LANL2DZ level of theory is appropriate for the system modeling, whereas frequently used semiempirical methods (such as AM1 and PM3) produce unphysical results. The use of hydrogen atom for modeling of the cluster passivating ligands is found to yield unphysical results as well. Hence, the surface termination of II-VI semiconductor NCs with hydrogen atoms often used in computational models should probably be avoided. Basis set superposition error, zero-point energy, and thermal corrections, as well as solvent effects simulated with polarized continuum model are found to produce minor variations on the ligand binding energies. The effects of Cd-Se complex structure on both the electronic band gap (highest occupied molecular orbital-lowest unoccupied molecular orbital energy difference) and ligand binding energies are systematically examined. The role played by positive charges on ligand binding is also explored. The calculated binding energies for various ligands L are found to decrease in the order OPMe(3)>OPH(3)>NH(2)Me>/=NH(3)>/=NMe(3)>PMe(3)>PH(3) for neutral clusters and OPMe(3)>OPH(3)>PMe(3)>/=NMe(3)>/=NH(2)Me>/=NH(3)>PH(3) and OPMe(3)>OPH(3)>NH(2)Me>/=NMe(3)>/=PMe(3)>/=NH(3)>PH(3) for single and double ligations of positively charged Cd(2)Se(2) (2+) cluster, respectively.

Theoretical study of the effects of solvent environment on photophysical properties and electronic structure of paracyclophane chromophores

We use first-principles quantum-chemical approaches to study absorption and emission properties of recently synthesized distyrylbenzene (DSB) derivative chromophores and their dimers (two DSB molecules linked through a [2.2]paracyclophane moiety). Several solvent models are applied to model experimentally observed shifts and radiative lifetimes in Stokes nonpolar organic solvents (toluene) and water. The molecular environment is simulated using the implicit solvation models, as well as explicit water molecules and counterions. Calculations show that neither implicit nor explicit solvent models are sufficient to reproduce experimental observations. The contact pair between the chromophore and counterion, on the other hand, is able to reproduce the experimental data when a partial screening effect of the solvent is taken into account. Based on our simulations we suggest two mechanisms for the excited-state lifetime increase in aqueous solutions. These findings may have a number of implications for organic light-emitting devices, electronic functionalities of soluble polymers and molecular fluorescent labels, and their possible applications as biosensors and charge/energy conduits in nanoassemblies.

Fluorene-based metal-ion sensing probe with high sensitivity to Zn2+ and efficient two-photon absorption.

The photophysical, photochemical, two-photon absorption (2PA) and metal ion sensing properties of a new fluorene derivative (E)-1-(7-(4-(benzo[d]thiazol-2-yl)styryl)-9,9-bis(2-(2-ethoxyethoxy)ethyl)-9H-fluoren-2-yl)-3-(2-(9,10,16,17,18,19,21,22,23,24-decahydro-6H dibenzo[h,s][1,4,7,11,14,17]trioxatriazacycloicosin-20(7H)-yl)ethyl)thiourea (1) were investigated in organic and aqueous media. High sensitivity and selectivity of 1 to Zn(2+) in tetrahydrofuran and a water/acetonitrile mixture were shown by both absorption and fluorescence titration. The observed complexation processes corresponded to 1:1 stoichiometry with the range of binding constants approximately (2-3) x 10(5) M(-1). The degenerate 2PA spectra of 1 and 1/Zn(2+) complex were obtained in the 640-900 nm spectral range with the maximum values of two-photon action cross section for ligand/metal complex approximately (90-130) GM, using a standard two-photon induced fluorescence methodology under femtosecond excitation. The nature of the 2PA bands was analyzed by quantum chemical methods and a specific dependence on metal ion binding processes was shown. Ratiometric fluorescence detection (420/650 nm) provided a good dynamic range (10(-4) to 10(-6) M) for detecting Zn(2+), which along with the good photostability and 2PA properties of probe 1 makes it a good candidate in two-photon fluorescence microscopy imaging and sensing of Zn ions.