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Detailed molecular simulations are carried out to investigate the effect of temperature on orientational order in cubane molecular crystal. Transition from an orientationally ordered to an orientionally disordered plastic crystalline phase is reported and the orientational melting is associated with an anomaly in specific heat at constant pressure (C(sub p)) and compressibility (k) and the coefficient of thermal expansion of the plastic crystalline phase is more than twice that of crystalline phase.

A report is presented on the molecular simulations of solid stilbene in the isothermal-isobaric ensemble with variable-shape simulation. The structure was characterized by means of lattice parameters and radial distribution functions.

Simulations of adamantane are reported by carefully combining ab initio empirical approaches to enable simulations with internal degrees of freedom on crystalline adamantane up to pressure of 26 GPa. Two sets of simulations are carried out as a function of pressure of 26 GPa to understand changes in the crystal structure as well as molecular structure.

Computer simulation of a stilbene molecular crystal as a fucntion of pressure up to 4 GPa is reported. Molecular structure and the crystal structure of stilbene are characterized by calculating the radial distribution function and dihedral angle distribution, features associated with pedal motion and cell parameters.

A study uses four different sets of intermolecular and intramolecular potentials to investigate p-terphenyl at 300 K and 1 atm pressure. Results are in excellent agreement with X-ray diffraction results, which also suggests the existence of a similar transition as a function of pressure in polyphenyls such as biphenyl and p-hexaphenyl.

The pressure dependence of the properties at room temperature in the solid phase of biphenyl is studied. Properties such as molecular conformation, radial distribution functions, lattice parameters, and volume are presented.

Motivated by the outstanding properties of bis(BF2) core complexes as fluorophore probes, we present a systematic computational study of their vibrationally resolved one- and two-photon absorption spectra in vacuum and in solution. Electronic and vibrational structure calculations were performed using the coupled cluster CC2 method and the Kohn-Sham formulation of density functional theory (DFT). A nonempirical estimation of the inhomogeneous broadening, accomplished using the polarizable embedding (PE) approaches combined with time-dependent DFT and CC2 methods, is used as a key ingredient of the computational protocol employed for simulations of the spectral features in solution. The inhomogeneous broadening is also determined based on the Marcus theory employing linear response and state-specific polarizable continuum model (PCM) methods. It is found that the polarizable embedding CC2 and the state-specific PCM are the most successful approaches for description of environmental broadening. For the 1¹Ag → 1¹Bu transition, the non-Condon effects can be safely neglected and a fair agreement between the simulated and experimental band shapes is found. In contrast, the shape of the vibrationally resolved band corresponding to the two-photon allowed 1¹Ag → 2¹Ag transition is largely dominated by non-Condon effects. A generalized few-level model was also employed to analyze the mechanism of the electronic two-photon 1¹Ag → 2¹Ag excitation. It was found that the most important optical channel involves the 1¹Bu excited state. Ramifications of the findings for general band shape modeling are briefly discussed. [ABSTRACT FROM AUTHOR]

Understandingthe working mechanism and establishing structure–propertyrelationships for optical probes is an essential step to develop designprinciples for novel molecular probes. Here we study optical propertiesof a small-sized dielectric probe, namely, 4-carbamido pyridiniumcyclopentadienylide (CPYC) in benzene and in water solvents usinga sequential approach. In particular, the structure modeling has beencarried out using a Car–Parrinello hybrid QM/MM molecular dynamicsapproach, while the excitation energies were computed using time dependentdensity functional theory. To incorporate the solvent effect eithera polarizable continuum model or a semicontinuum description was employed.The molecular dipole moment of CPYC in water is more than two timeslarger than in benzene solvent. The positive and negative chargestend to accumulate on pyridinium and cyclopentadienylide rings, respectively,with increasing solvent polarity. Significant solvent-induced geometricalchanges have been reported in CPYC and this contributes to a significantred shift in spectra. Even though the absorption maxima for CPYC inbenzene and water solvents were underestimated, the solvatochromicshift has been reproduced in good agreement with experiments. We alsoreport that CPYC can be used as a two photon probe. [ABSTRACT FROM AUTHOR]

Dipolaraggregation is in many cases detrimental for the functioning of opticalmaterials. In this study we investigate self-aggregation and opticalabsorption of stilbazolium merocyanine (SM) in chloroform solutionby performing classical Molecular Dynamics (MD) simulations underambient conditions. The reversal solvatochromic shift, the large bathochromicshift, and the structured absorption band presented by SM in chloroformsolution are all aspects of its optical absorption behavior for whichthe existence of self-aggregation is yet not completely understood.Moreover, the spectroscopic properties of SM oligomers and their occurrencein solvent of low polarity remain a relevant topic that deserves tobe investigated. Our analysis of the aggregation behavior of SM inchloroform verified that the majority of the chromophores are involvedin the formation of oligomers in solution, where the whole dimer andpart of the trimer populations present a stable π-stacking structure.The optical properties of the monomers and oligomers in solution wereevaluated by means of a discrete polarizable embedding quantum mechanical/molecularmechanical (PE-QM/MM) response scheme where the quantum part is describedat the level of density functional theory. The visible absorptionspectrum of SM in chloroform is simulated using time average valuesobtained for the monomeric and oligomeric forms of SM from the PE-QM/MMcalculations performed on uncorrelated configurations extracted fromthe classical MD simulations. This study shows that the self-aggregationof SM in chloroform may exist, but it is not essential for reproducingthe reversal solvatochromic shift in chloroform and that the processdoes not contribute to enhance the bathochromic shift nor explainthe structure observed in its absorption band. Moreover, it is verifiedthat since the electronic transitions of the monomer and oligomersare close together, changes in the interplane separation between themonomeric units of the stacked oligomers substantially affect thespectral resolution of their contribution to the optical absorptionspectrum. [ABSTRACT FROM AUTHOR]

Solvent effects on the one- and two-photon absorption(1PA and2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studiedusing a discrete polarizable embedding (PE) response theory. The schemecomprises a quantum region containing the chromophore and an atomicallygranulated classical region for the solvent accounting for full interactionswithin and between the two regions. Either classical molecular dynamics(MD) or hybrid Car–Parrinello (CP) quantum/classical (QM/MM)molecular dynamics simulations are employed to describe the solvationof DO3 in DMSO, allowing for an analysis of the effect of the intermolecularshort-range repulsion, long-range attraction, and electrostatic interactionson the conformational changes of the chromophore and also the effectof the solute–solvent polarization. PE linear response calculationsare performed to verify the character, solvatochromic shift, and overlapof the two lowest energy transitions responsible for the linear absorptionspectrum of DO3 in DMSO in the visible spectral region. Results ofthe PE linear and quadratic response calculations, performed usinguncorrelated solute–solvent configurations sampled from eitherthe classical or hybrid CP QM/MM MD simulations, are used to estimatethe width of the line shape function of the two electronic lowestenergy excited states, which allow a prediction of the 2PA cross-sectionswithout the use of empirical parameters. Appropriate exchange-correlationfunctionals have been employed in order to describe the charge-transferprocess following the electronic transitions of the chromophore insolution. [ABSTRACT FROM AUTHOR]

We have studied the structures and absorption spectra of merocyanine, the photoresponsive isomer of the spiropyran (SP) −merocyanine (MC) pair, in chloroform and in water solvents using a combined hybrid QM/MM Car−Parrinello molecular dynamics (CP-QM/MM) and ZINDO approach. We report remarkable differences in the molecular structure and charge distribution of MC between the two solvents; the molecular structure of MC remains in neutral form in chloroform while it becomes charge-separated, zwitterionic, in water. The dipole moment of MC in water is about 50% larger than in chloroform, while the value for SP in water is in between, suggesting that the solvent is more influential than the conformation itself in deciding the dipole moment for the merocyanine−spiropyran pair. The calculations could reproduce the experimentally reported blue shift in the absorption spectra of MC when going from the nonpolar to the polar solvent, though the actual value of the absorption maximum is overestimated in chloroform solvent. We find that the CP-QM/MM approach is appropriate for structure modeling of solvatochromic and thermochromic molecules as this approach is able to capture the solvent and thermal-induced structural changes within the solute important for an accurate assessment of the properties. [ABSTRACT FROM AUTHOR]

In this work, we examine, by means of computational methods, the mechanism of Zn(2+) sensing by a bipyridine-centered, D-π-A-π-D-type ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q.; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular probe with enhanced two-photon response upon Zn(2+) binding for in vitro and in vivo bioimaging. Chem. Sci. 2014, 5, 3469-3474], after coordination to zinc ions the probe exhibits a large enhancement of the two-photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of the unbound (cation-free) and bound probe were calculated, including the influence of solute-solvent interactions, implicitly using a polarizable continuum model and explicitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the signal, structure-property relationships were also taken into account. Results of our simulations demonstrate that the one-photon absorption bands for both the unbound and bound forms correspond to the bright π → π* transition to the first excited state, which, on the other hand, exhibits negligible two-photon activity. On the basis of the results of the quadratic response calculations, we put forward a notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differences in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few-state model including the ground, first, and second excited states. The analysis of the optical channel suggests that the large two-photon response is due to the coordination-induced increase of the transition moment from the first to the second excited state.

Motivated by the outstanding properties of bis(BF2) core complexes as fluorophore probes, we present a systematic computational study of their vibrationally resolved one- and two-photon absorption spectra in vacuum and in solution. Electronic and vibrational structure calculations were performed using the coupled cluster CC2 method and the Kohn-Sham formulation of density functional theory (DFT). A nonempirical estimation of the inhomogeneous broadening, accomplished using the polarizable embedding (PE) approaches combined with time-dependent DFT and CC2 methods, is used as a key ingredient of the computational protocol employed for simulations of the spectral features in solution. The inhomogeneous broadening is also determined based on the Marcus theory employing linear response and state-specific polarizable continuum model (PCM) methods. It is found that the polarizable embedding CC2 and the state-specific PCM are the most successful approaches for description of environmental broadening. For the 1(1)A(g) → 1(1)B(u) transition, the non-Condon effects can be safely neglected and a fair agreement between the simulated and experimental band shapes is found. In contrast, the shape of the vibrationally resolved band corresponding to the two-photon allowed 1(1)A(g) → 2(1)A(g) transition is largely dominated by non-Condon effects. A generalized few-level model was also employed to analyze the mechanism of the electronic two-photon 1(1)A(g) → 2(1)A(g) excitation. It was found that the most important optical channel involves the 1(1)B(u) excited state. Ramifications of the findings for general band shape modeling are briefly discussed.

Detecting deposits of amyloid β fibrils in the brain is of paramount importance for an early diagnosis of Alzheimer's disease. A number of PET tracers have been developed for amyloid imaging, but many suffer from poor specificity and large signal to background ratio. Design of tracers with specificity and improved binding affinity requires knowledge about various potential binding sites in the amyloid β fibril available for the tracers and the nature of the local microenvironment of these sites. In this study we investigate the local structure of fibrils using two important probes, namely, thioflavin T (a fluorescent probe) and AZD2184 (a PET tracer). The target structures for amyloid-β(1-42) fibril are based on reported NMR solution models. By explicitly considering the effect of fibril flexibility on the available binding sites for all these models, the binding affinity of these probes has been investigated. The binding profiles of AZD2184 and thioflavin T were studied by molecular docking and molecular dynamics simulation methods. The two compounds were found to bind at the same sites of the fibril: three of which are within the fibril, and one is on the two sides of the Met35 residue on the surface. The binding affinity of AZD2184 and thioflavin T is found to be higher at the core sites than on the surface due to more contact residues. The binding affinity of AZD2184 is much higher than that of thioflavin T at every site due to electrostatic interaction and spatial restriction, which is in good agreement with experimental observation. However, the structural change of thioflavin T is much more significant than that of AZD2184, which is the chemical basis for its usage as a fluorescent probe. The ramifications of these results for the design and optimization of PET radioligands and fluorescent probes are briefly discussed.

We report on the nonlinear optical properties measurements and quantum-chemical calculations of a well-known photochromic system consisting of spiropyran and the merocyanine photoproduct. The study of nonlinear absorption and refraction properties of the molecules dissolved in chloroform were performed with the Z-scan technique, using femtosecond pulses in a wide range of wavelengths. Maxima in the two-photon absorption spectrum at 700 and 1050 nm were found for the merocyanine form, and the corresponding two-photon absorption cross section is 80 GM and 20 GM, respectively. The latter feature does not vanish completely in the nonlinear spectrum of the spiropyran form, possibly because of the existence of some photoconversion caused by the laser beam during the measurements. A nonlinear absorption peak at 900 nm is found in the spiropyran form with an effective cross section of about 20 GM; it is likely due to three-photon absorption or to absorption by some intermediate species. The experimental data are supported by calculations performed with the use of a hybrid quantum mechanics-molecular mechanics approach.

We present the results of wide spectral range Z-scan measurements of the two-photon absorption (2PA) spectrum of the Hoechst 33342 dye. The strongest 2PA of the dye in aqueous solution is found at 575 nm, and the associated two-photon absorption cross section is 245 GM. A weak but clearly visible 2PA band at ∼850 nm is also observed, a feature that could not be anticipated from the one-photon absorption spectrum. On the basis of the results of hybrid quantum mechanics/molecular mechanics calculations, we put forward a notion that the long-wavelength feature observed in the two-photon absorption spectrum of Hoechst 33342 is due to the formation of dye aggregates.

A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.

We have investigated the ambient temperature structure of 1-methyl-8-oxyquinolinium betaine (MOQB) in water solvent and compared to its gas-phase structure. We have employed Car-Parrinello molecular dynamics (CPMD) simulations within hybrid quantum mechanics-molecular mechanics (QM/MM) framework to study MOQB in water while CPMD technique has been used for the gas phase. We report significant solvent-induced geometrical changes in MOQB. The dipole moment of MOQB in water is 2 times larger than the gas-phase value. The average absorption spectra calculated from gas-phase configurations using Coulomb attenuated-B3LYP (CAMB3LYP) level of theory is comparable with experimental spectra reported in benzene (λ(max) = 590 nm), a nonpolar solvent. We have also computed the absorption spectra of MOQB in water solvent using continuum and semicontinuum solvent models. Based on this, we have calculated contributions from solvent-induced geometrical changes, hydrogen bonding, and intermolecular charge transfer to the solvatochromic shift and absorption spectra of MOQB in water. Absorption spectra calculations for MOQB in water with a semicontinuum approach for solvents using CAMB3LYP level of theory excellently reproduce the experimental spectra in water, where the theoretical λ(max) is 433 nm and the experimental λ(max) is around 440 nm.

Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been carried out with a variable shape simulation cell. The low-temperature crystalline phase and the room-temperature plastic crystalline phases have been studied employing the modified Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low-temperature ordered tetragonal phase of adamantane. The high-pressure ordered phase appears to be characterized by a slightly larger shift of the first peak toward a lower value of r in C-C, C-H, and H-H radial distribution functions as compared to the low-temperature tetragonal phase. The coexistence curve between the crystalline and plastic crystalline phase has been obtained approximately up to a pressure of 4 GPa.