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  • 1. Ai, Yuejie
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ji, Yongfei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Song, Wei-Guo
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hydrophobicity and Hydrophilicity Balance Determines Shape Selectivity of Suzuki Coupling Reactions Inside Pd@meso-SiO2 Nanoreactor2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 19, p. 10244-10251Article in journal (Refereed)
    Abstract [en]

    Molecular sorting and catalysis directed by shape selectivity have been extensively applied in porous extended frameworks for a low-carbon, predictable, renewable component of modern industry. A comprehensive understanding of the underlying recognition mechanism toward different shapes is unfortunately still missing, owing to the lack of structural and dynamic information under operating conditions. We demonstrate here that such difficulties can be overcome by state-of-the-art molecular dynamics simulations which provide atomistic details that are not accessible experimentally, as exemplified by our interpretation for the experimentally observed aggregation induced shape selectivity for Suzuki C-C coupling reaction catalyzed by Pd particles in mesoporous silica. It is found that both aggregation ability and aggregating pattern of the reactants play the decisive role in controlling the shape selectivity, which are in turn determined by the balance between the hydrophobicity and hydrophilicity of the reactants, or in other words, by the balance between the noncovalent hydrogen bonding interaction and van der Waals forces. A general rule that allows prediction of the shape selectivity of a reactant has been proposed and verified against experiments. We show that molecular modeling is a powerful tool for rational design of new mesoporous systems and for the control of catalytic reactions that are important for the petrochemical industry.

  • 2. Bai, Linyi
    et al.
    Zhu, Liangliang
    Ang, Chung Yen
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wu, Shaojue
    Zeng, Yongfei
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Iron( III)-Quantity-Dependent Aggregation-Dispersion Conversion of Functionalized Gold Nanoparticles2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 14, p. 4032-4037Article in journal (Refereed)
    Abstract [en]

    Developing gold nanoparticles (AuNPs) with well-designed functionality is highly desirable for boosting the performance and versatility of inorganic-organic hybrid materials. In an attempt to achieve ion recognition with specific signal expressions, we present here 4-piperazinyl-1,8-naphthalimide-functionalized AuNPs for the realization of quantitative recognition of Fe-III ions with dual (colorimetric and fluorescent) output. The research takes advantage of 1)quantity-controlled chelation-mode transformation of the piperazinyl moiety on the AuNPs towards Fe-III, thereby resulting in an aggregation-dispersion conversion of the AuNPs in solution, and 2)photoinduced electron transfer of a naphthaimide fluorophore on the AuNPs, thus leading to reversible absorption and emission changes. The functional AuNPs are also responsive to pH variations. This strategy for realizing the aggregation-dispersion conversion of AuNPs with returnable signal output might exhibit application potential for advanced nanoscale chemosensors.

  • 3. Bu, L.
    et al.
    Chen, J.
    Wei, X.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Y.
    An AIE and ICT based NIR florescent probe for cysteine and homocysteine2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 136, p. 724-731Article in journal (Refereed)
    Abstract [en]

    A combination of aggregation-induced emission and intramolecular charge transfer was achieved by using a triphenylamine analogue and a dicyanovinyl moiety as the electron donating and accepting units, respectively. Hence, we designed and synthesized a probe with a D-π-A framework as a near-infrared fluorescence turn-on probe for biothiols (cysteine and homocysteine). Owing to the remarkable intramolecular charge transfer effect as well as intramolecular rotations associated with the donor moiety, the probe exhibits extremely weak fluorescence, which becomes a good starting point for developing fluorescence “turn-on” probes. Upon reaction with cysteine or homocysteine utilizing the dicyanovinyl moiety, the intramolecular charge transfer character was weakened, and the reacting products were observed to aggregate in aqueous solutions, resulting in the aggregation-induced emission effect with red fluorescence at 651 and 656 nm, respectively. Hence, the probe could be used as a fluorescence “turn-on” sensor for cysteine and homocysteine, with the sensing time of less than 4 min and the detection limits of 8.4 μM and 5.7 μM towards cysteine and homocysteine, respectively. The probe could distinguish cysteine and homocysteine from glutathione. The sensing mechanism was systematically investigated by employing high resolution mass spectrometry, 1H NMR and density functional theory calculations as well as checking the solvent viscosity dependent fluorescence, and thus the nucleophilic addition products, the intramolecular charge transfer character, and the aggregation-induced emission behaviour were clearly elucidated. It is noteworthy that the low cytotoxicity, the intrinsic aggregation-induced emission nature and near-infrared emissions enable the application of the probe in living cell imaging. © 2016 Elsevier Ltd

  • 4. Cai, Shengyun
    et al.
    Hu, Xiaohao
    Tian, Guojian
    Zhou, Haitao
    Chen, Wei
    Huang, Jinhai
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Su, Jianhua
    Photo-stable substituted dihydroindolo[2,3-b]carbazole-based organic dyes: tuning the photovoltaic properties by optimizing the pi structure for panchromatic DSSCs2014In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 70, no 43, p. 8122-8128Article in journal (Refereed)
    Abstract [en]

    Three dihydroindolo[2,3-b]carbazole (DDC) donor based organic dyes (DDC6-DDC8) with long conjugated systems were successfully synthesized and characterized by optical, electrochemical, computational analysis, and photovoltaic methods. It was found that the elongated pi system as well as the high molar extinction coefficients (4.2-5.3 M-1 cm(-1)) sufficiently reinforced the light harvesting ability with the IPCE response of one dye DDC8 extended to 850 nm, which resulted in large J(sc) of these dyes based devices (high as 16.41 mA cm(-2)). The attached alkyl chains suppress the dark current to some extent, resulting the DDC6 and DDC7 devices in high V-oc, while DDC8 displayed low V-oc, because BTD in DDC8 could attract the iodine ion, which could accelerate the charge recombination. Among the three dyes, DDC7 displayed the best performance with an eta value 6.53% under 4 mu m thick scattering layer (condition 1+1), which was boosted to 7.49% under 8 mu m thick scattering layer (condition 1+2). The photo-stability measurements indicated that all the three dyes are fairly photo-stable.

  • 5. Chen, Bin
    et al.
    Ding, Yubin
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, Weihong
    Hill, Jonathan P.
    Ariga, Katsuhiko
    Xie, Yongshu
    Steric hindrance-enforced distortion as a general strategy for the design of fluorescence "turn-on" cyanide probes2013In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 49, no 86, p. 10136-10138Article in journal (Refereed)
    Abstract [en]

    For the rational design of fluorescence "turn-on" cyanide probes, a general strategy is developed by introducing a dicyanovinyl group at the sterically demanding position of a large pi framework.

  • 6. Chen, Bin
    et al.
    Sun, Xi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    TICT based fluorescence "turn-on" hydrazine probes2014In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 199, p. 93-100Article in journal (Refereed)
    Abstract [en]

    Fluorescence "turn-on" probes PC3 and C3 with weak background emissions were developed for hydrazine sensing. The aldehyde and dicyanovinyl groups were used as the recognition units for PD and C3, respectively. Because of low reactivity of the aldehyde group, the fluorescence of PC3 was enhanced by only ca. 93 folds upon addition of a large amount of 1646 eq. hydrazine. In contrast, 0 exhibited fluorescence enhancement by ca. 239 folds upon addition of only 1.3 eq. hydrazine, and thus it showed high sensitivity towards hydrazine, with the detection limit of 7 ppb. In aqueous systems, it also works well with improved selectivity for hydrazine over CN-. The weak fluorescence of PC3 and 0 can be ascribed to twisted intramolecular charge transfer (TICT) processes by the combination of the bulky diphenylamino and 9-anthryl units, which were well demonstrated by theoretical calculations, viscosity dependent fluorescence, and fluorescence decay behaviour. Addition of hydrazine induced the disappearance of the TICT deactivation pathway, resulting in the observed fluorescence enhancement. It can be concluded that the combination of the bulky diphenylamino and 9-anthryl units is an effective approach for developing fluorescence turn-on hydrazine probes based on the TICT mechanism.

  • 7. Chen, Bin
    et al.
    Yu, Gang
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ding, Yubin
    Wang, Cheng
    Liu, Zhiwei
    Xie, Yongshu
    Full-colour luminescent compounds based on anthracene and 2,2 '-dipyridylamine2013In: Journal of Materials Chemistry C, ISSN 2050-7526, Vol. 1, no 44, p. 7409-7417Article in journal (Refereed)
    Abstract [en]

    Starting from two simple units of anthracene and 2,2'-dipyridylamine, a series of new luminescent compounds 1-8 were designed and synthesized by a combined strategy of changing the connection mode between the two units, extending the conjugation size, and introducing an additional electron donor. Photophysical properties of 1-8 were investigated and discussed on the basis of solvatochromic behaviour, theoretical calculations, crystal structure, and optimized structures. Interestingly, the emission wavelengths of these compounds could be successfully tuned from violet to red both in solutions and the solid-state, and prominent positive solvatochromism was observed for the compounds with a D-p-A framework. Consider compound 7 as an example, it shows peaks at 526 nm and 627 nm in cyclohexane and DMSO, respectively. Meanwhile, the quantum yield was decreased from 0.80 in cyclohexane to 0.12 in DMSO. The introduction of bulky groups was demonstrated to be effective for suppressing the aggregation effect and thus improving the solid state emission quantum yield. These results indicate that the combined structure modulation strategy offers a powerful tool for tuning the emission behaviour. To demonstrate the possibility of practical applications, 2 was employed as the emitting material for the fabrication of deep-blue organic light-emitting diodes (OLEDs), which showed a maximum external quantum efficiency of 2.2%. The CIE coordinates of (0.15, 0.08) are indicative of excellent blue color purity.

  • 8. Chen, Long
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ying, Weijiang
    Zhang, Xiaoyu
    Guo, Fuling
    Li, Jing
    Hua, Jianli
    5,6-Bis(octyloxy)benzo[c][1,2,5]thiadiazole-Bridged Dyes for Dye-Sensitized Solar Cells with High Open-Circuit Voltage Performance2013In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 9, p. 1770-1780Article in journal (Refereed)
    Abstract [en]

    Three new metal-free dyes with a 5,6-bis(octyloxy) benzo[c][1,2,5] thiadiazole core (DOBT-I-III) have been designed and synthesized for use as DSSCs. Their absorption properties and electrochemical and photovoltaic performances have been investigated systematically. The DSSCs based on DOBT-I-III show high open-circuit voltages (V-oc) of 829, 818, and 784 mV, respectively. Of the three dyes, DOBT-III, which contains a thiophene-bridging linker, exhibits the best photovoltaic performance: a short-circuit photocurrent density (J(sc)) of 12.74 mA cm(-2) and a fill factor (FF) of 0.73, which corresponds to an overall conversion efficiency of 7.29% under standard global AM 1.5 solar conditions.

  • 9. Chen, S.
    et al.
    Li, W.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, W. -H
    Aggregation-controlled photochromism based on a dithienylethene derivative with aggregation-induced emission2017In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 5, no 10, p. 2717-2722Article in journal (Refereed)
    Abstract [en]

    We report novel aggregation-induced emission (AIE) characteristics involving aggregation-controlled photochromism properties of a dithienylethene derivative, BTE-EQ, where two quinolinemalononitrile (EQ) units are covalently attached to a dithienylethene core. The typical AIE effect of BTE-EQ has been found to originate from the AIE character of the EQ units with respect to the reference compound BTE, which does not contain an EQ unit. The photochromism study, together with density functional theory calculations, reveals that the photochromic activity of BTE-EQ can be reversibly switched off and on by controlling the aggregation state during the AIE process, which provides a novel route to controlling the photochromism of diarylethenes.

  • 10. Chen, S.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Song, L.
    A fluorescent photochromic diarylethene based on naphthalic anhydride with strong solvatochromism2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 47, p. 29854-29859Article in journal (Refereed)
    Abstract [en]

    A novel "push-pull" diarylethene molecule consisting of an electron withdrawing ethene bridge (1,8-naphthalic anhydride) and two moderate electron donating side chains (2,5-dimethylthiophene) has been designed and synthesized. The photochromism study, together with density functional theory calculations, revealed that the molecule exhibits reversible fluorescence switching capacity upon photo-isomerization and remarkable solvatochromism with red shift of the fluorescence maximum by more than 150 nm owing to intramolecular charge transfer.

  • 11. Chen, Shangjun
    et al.
    Li, Wenlong
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, Wei-Hong
    Substitution effect on the photochromic properties of benzo[b]thiophene-1,1-dioxide based diarylethenes2015In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, no 106, p. 87626-87634Article in journal (Refereed)
    Abstract [en]

    Benzo[b]thiophene-1,1-dioxide based diarylethenes (DAEs), BTT-1 to BTT-4, containing methyl, phenyl, formyl and triphenylamine groups at the 5,5'-position of the thiophene rings have been developed for gaining an insight into the substituent effect on the absorption and photochromic properties. Electron-donating substituents, such as phenyl and triphenylamine groups, are found to be effective at shifting the absorption band to a longer wavelength and decreasing the cyclization quantum yield. The electron-withdrawing formyl group can increase the cyclization quantum yield, but it reduces the thermal stability of the ring-closed isomer to some extent. BTT-4 bearing a triphenylamine group shows the poorest fatigue resistance among these four compounds, which is possibly due to the larger extended pi-conjugation length in the ring-closed isomer. BTT-2 bearing a phenyl unit undergoes typical photochromic reaction not only in solution, but also in PMMA thin film and in bulky crystals with excellent fatigue resistance and thermal stability.

  • 12. Chen, Wei
    et al.
    Zhang, Zhiyun
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Su, Jianhua
    Highly sensitive detection of low-level water content in organic solvents and cyanide in aqueous media using novel solvatochromic AIEE fluorophores2015In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, no 16, p. 12191-12201Article in journal (Refereed)
    Abstract [en]

    A great deal of effort has been devoted to develop easy-to-use fluorescent probes for detecting analytes due to their advantages in the field of chemo- and bio-sensing. Herein, two novel 2,2 '-biindenyl-based derivatives BDM and BDBM containing dicyanovinyl groups have been designed and synthesized, and are shown to possess the remarkable dual properties of solvatochromism and aggregation-induced emission enhancement (AIEE). Importantly, both of them are found to serve as fluorescent indicators for the qualitative and quantitative detection of low-level water in organic solvents. Meanwhile, both BDM and BDBM emit yellowish orange and orange fluorescence, respectively, in their aggregated states. Furthermore, with dicyanovinyl groups as the recognition sites, both compounds can act as colourimetric and fluorescent sensors for highly sensitive and selective detection of cyanide in aqueous media, and the apparent response signals can be observed by the naked eye even in the presence of various interference anions, promising practical applications for detecting cyanide in drinking water. Besides, optical spectroscopic techniques, NMR titration measurements, and density functional theory calculations are conducted to rationalize the sensing mechanisms of the two probes.

  • 13. Ding, Li
    et al.
    Zhang, Zhiyun
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Su, Jianhua
    Highly sensitive determination of low-level water content in organic solvents using novel solvatochromic dyes based on thioxanthone2013In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 49, no 66, p. 7319-7321Article in journal (Refereed)
    Abstract [en]

    Two thioxanthone-based fluorescent probes exhibited prominent solvatofluorochromism, and they were further found to be useful as fluorescence indicators for the qualitative and quantitative detection of low-level water content in various solvent media.

  • 14. Ding, Yubin
    et al.
    Li, Tong
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, Weihong
    Xie, Yongshu
    From nonconjugation to conjugation: novel meso-OH substituted dipyrromethanes as fluorescence turn-on Zn2+ probes2013In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 11, no 16, p. 2685-2692Article in journal (Refereed)
    Abstract [en]

    Most reported Zn2+ probes suffer from the interference of background fluorescence originated from the conjugated structures of commonly utilized fluorophores. In this work, three novel meso-hydroxyl group substituted dipyrromethanes DPMOH1-DPMOH3 were synthesized and found to be colourless and nonfluorescent due to the interruption of the conjugated p system by an sp(3) carbon between the two pyrrolic units. Interestingly, only the addition of Zn2+ to the solutions of DPMOH1-DPMOH3 promoted their oxidation to dipyrrin forms, and bright fluorescence "turn on" was observed due to the formation of corresponding dipyrrin complexes with the dipyrrin : zinc stoichiometry of 2 :1. Zn2+ detection mechanism was investigated by UV-Vis, fluorescence, H-1 NMR and HRMS analyses, which can be ascribed to the CHEF type fluorescence enhancement, resulting from good rigidity of the dipyrrin complexes. Hence, DPMOH1-DPMOH3 can be used as fluorescence turn-on Zn2+ probes with the advantage of no background fluorescence.

  • 15. Ding, Yubin
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hill, Jonathan P.
    Ariga, Katsuhiko
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Andreasson, Joakim
    Zhu, Weihong
    Tian, He
    Xie, Yongshu
    Acid/Base Switching of the Tautomerism and Conformation of a Dioxoporphyrin for Integrated Binary Subtraction2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 40, p. 12910-12916Article in journal (Refereed)
    Abstract [en]

    Compared with most of the reported logic devices based on the supramolecular approach, systems based on individual molecules can avoid challenging construction requirements. Herein, a novel dioxoporphyrin DPH22 was synthesized and two of its tautomers were characterized by single-crystal X-ray diffraction studies. Compound DPH22 exhibits multichannel controllable stepwise tautomerization, protonation, and deprotonation processes through interactions with H and F- ions. By using the addition of H+ and F- ions as inputs and UVNis absorption values at.1=412, 510, 562, and 603 nm as outputs, the controlled tautomerism of DPH22 has been successfully used for the construction of an integrated molecular level half-subtractor and comparator. In addition, this acid/base-switched tautomerism is reversible, thus endowing the system with ease of reset and recycling; consequently, there is no need to modulate complicated intermolecular interactions and electron-/chargetransfer processes.

  • 16. Ding, Yubin
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Tong
    Zhu, Weihong
    Xie, Yongshu
    alpha-Monoacylated and alpha,alpha '- and alpha,beta '-Diacylated Dipyrrins as Highly Sensitive Fluorescence "Turn-on" Zn2+ Probes2013In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 78, no 11, p. 5328-5338Article in journal (Refereed)
    Abstract [en]

    With the purpose of developing readily synthesized CHEF (chelation-enhanced fluorescence) type Zn2+ probes with relatively simple molecular structures and excellent sensing behavior, p-anisoyl chloride was used for the acylation of 5-(pentafluorophenyl)dipyrromethane. Interestingly, the alpha,beta'-diacylated product PS2 with a unique substitution mode was obtained in high yield in addition to the normal a-substituted mono- and diacylated products PSI and PS3. Further oxidation of PS1-PS3 afforded dipyrrins S1-S3. Crystal structure and H-1 NMR measurements of S2 demonstrate the existence of a pure tautomer, which is consistent with DFT calculations. S1-S3 show highly Zn2+ selective "turn-on" fluorescence based on a CHEF mechanism by the formation of 2:1 (probe:metal) Zn2+ complexes. The emission colors can be easily tuned from green to red by changing the dipyrrin substitution modes. Furthermore, these probes demonstrate fast responses and wide applicable pH ranges. Among them, S2 shows the highest Zn2+ sensitivity, with a detection limit of 4.4 x 10(-8) M.

  • 17. Hede, T.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Leck, C.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Model HULIS compounds in nanoaerosol clusters: investigations of surface tension and aggregate formation using molecular dynamics simulations2011In: Atmospheric Chemistry And Physics, ISSN 1680-7316, E-ISSN 1680-7324, Vol. 11, no 13, p. 6549-6557Article in journal (Refereed)
    Abstract [en]

    Cloud condensation nuclei act as cores for water vapour condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use molecular dynamics simulations to show that model humic-like substances (HULIS) in systems containing 10 000 water molecules mimic experimental data well referring to reduction of surface tension. The model HULIS compounds investigated in this study are cis-pinonic acid (CPA), pinic acid (PAD) and pinonaldehyde (PAL). The structural properties examined show the ability for the model HULIS compounds to aggregate inside the nanoaerosol clusters.

  • 18. Hede, Thomas
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Leck, Caroline
    Tu, Yaoquan
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    HULIS in Nanoaerosol Clusters; Investigations of Surface Tension and Aggregate Formation using Molecular Dynamics Simulations2011In: Atmospheric Chemistry and Physics Discussions, ISSN 1680-7367, E-ISSN 1680-7375Article in journal (Other academic)
    Abstract [en]

    Cloud condensation nuclei act as cores for water vapor condensation, and their composition and chemical properties may enhance or depress the ability for droplet growth. In this study we use molecular dynamics simulations to show that humic-like substances of larger systems (8.6 nm in diameter) mimic experimental data well referring to reduction of surface tension. The structural properties examined show the ability for the humic-like substances to aggregate inside the nanoaerosol clusters.

  • 19. Hong, Tao
    et al.
    Song, Heli
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Weibing
    Xie, Yongshu
    Syntheses of mono- and diacylated bipyrroles with rich substitution modes and development of a prodigiosin derivative as a fluorescent Zn(II) probe2014In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, no 12, p. 6133-6140Article in journal (Refereed)
    Abstract [en]

    The acylation of 2,20-bipyrrole with pentafluorobenzoyl chloride in the presence of AlCl3 afforded six acylated products with rich alpha-, beta-, beta(1)-, alpha,alpha'-, alpha,beta(')-, and alpha,beta(1)'-substitution modes for 1-6, respectively. Then, the alpha,alpha'-diacylated compound 4 was used to synthesize a prodigiosin derivative 9, which provides an alternative method for the syntheses of prodigiosin derivatives. Crystal structures of 1, 4 and 9 show interesting supramolecular dimers formed by multiple hydrogen bonds, O...pi interactions, as well as pi... pi interactions. Interestingly, 9 shows fluorescence turn-on probing behavior towards Zn2+ both in DMF and in DMF-HEPES, with high sensitivity and selectivity. The detection limit for Zn2+ in DMF was calculated to be 1.1 x 10(-8) M.

  • 20.
    Hua, Weijie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fronzoni, Giovanna
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Stener, Mauro
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fe L-Edge X-ray Absorption Spectra of Fe(II) Polypyridyl Spin Crossover Complexes from Time-Dependent Density Functional Theory2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 51, p. 14075-14085Article in journal (Refereed)
    Abstract [en]

    L-edge near-edge X-ray fine structure spectroscopy (NEXAFS) has become a powerful tool to study the electronic structure and dynamics of metallo-organic and biological compounds in solution. Here, we present a series of density functional theory calculations of Fe L-edge NEXAFS for spin crossover (SCO) complexes within the time-dependent framework. Several key factors that control the L-edge excitations have been carefully examined using an Fe(II) polypyridyl complex [Fe(tren(py)(3))](2+) (where tren(py)(3) = tris(2-pyridylmethyliminoethyl)amine) as a model system. It is found that the electronic spectra of the low-spin (LS, singlet), intermediate-spin (IS, triplet), and high-spin (HS, quintet) states have distinct profiles. The relative energy positions, but not the spectral profiles, of different spin states are sensitive to the choice of the functionals. The inclusion of the vibronic coupling leads to almost no visible change in the resulting NEXAFS spectra because it is governed only by low-frequency modes of less than 500 cm(-1). With the help of the molecular dynamics sampling in acetonitrile at 300 K, our calculations reveal that the thermal motion can lead to a noticeable broadening of the spectra. The main peak position is strongly associated with the length of the Fe-N bond.

  • 21. Jana, Avijit
    et al.
    Bai, Linyi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Morphology Tuning of Self-Assembled Perylene. Monoimide from Nanoparticles to Colloidosomes with Enhanced Excimeric NIR Emission for Bioimaging2016In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 8, no 3, p. 2336-2347Article in journal (Refereed)
    Abstract [en]

    Organic near-infrared (NIR) fluorescent probes have been recognized as an emerging class of materials exhibiting a great potential in advanced bioanalytical applications. However, synthesizing such organic probes that could simultaneously work in the NIR spectral range and have large Stokes shift, high stability in biological systems, and high photostability have been proven challenging. In this work, aggregation induced excimeric NIR emission in aqueous media was observed from a suitably substituted perylene monoimide (PeIm) dye. Controlled entrapment of the dye into pluronic F127 micellar system to preserve its monomeric green emission in aqueous media was also established. The aggregation process of the PeIm dye to form organic nanoparticles (NPs) was evaluated experimentally by the means of transmission electron microscope imaging as well as theoretically by the molecular dynamics simulation studies. Tuning the morphology along with the formation of colloidosomes by the controlled self-aggregation of PeIm NPs in aqueous suspension was demonstrated successfully. Finally, both excimeric and monomeric emissive PeIm NPs as well as PeIm colloidosomes were employed for the bioimaging in vitro.

  • 22. Jana, Avijit
    et al.
    Nguyen, Kim Truc
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, Pengcheng
    Tan, Nguan Soon
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Perylene-Derived Single-Component Organic Nanoparticles with Tunable Emission: Efficient Anticancer Drug Carriers with Real-Time Monitoring of Drug Release2014In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 8, no 6, p. 5939-5952Article in journal (Refereed)
    Abstract [en]

    An organic nanoparticle-based drug delivery system with high drug loading efficacy (similar to 79 wt %) was developed using a perylene-derived photoremovable protecting group, namely, perylene-3,4,9,10-tetrayltetramethanol (Pe(OH)(4)). The anticancer drug chlorambucil was protected by coupling with Pe(OH)(4) to form photocaged nanoparticles (Pe(OH)(4)). The photorelease mechanism of chlorambucil from the Pe(Cbl)(4) conjugate was investigated experimentally by high-resolution mass spectrometry and theoretically by density functional theory calculations. The Pe(Cbl)(4) nanoparticles perform four important roles: (i) a nanocarrier for drug delivery, (ii) a phototrigger for drug release, (iii) a fluorescent chromophore for cell imaging, and (iv) a photoswitchable fluorophore for real-time monitoring of drug release. Tunable emission of the perylene-derived nanoparticles was demonstrated by comparing the emission properties of the Pe(OH)(4) and Pe(Cbl)(4) nanoparticles with perylene-3-ylmethanol. These nanoparticles were subsequently employed in cell imaging for investigating their intracellular localization. Furthermore, the in vivo toxicity of the Pe(OH)(4) nanoparticles was investigated using the mouse model. Histological tissue analysis of five major organs, i.e., heart, kidney, spleen, liver, and lung, indicates that the nanoparticles did not show any obvious damage to these major organs under the experimental conditions. The current research presents a successful example of integrating multiple functions into single-component organic nanoparticles for drug delivery.

  • 23. Jiang, Tao
    et al.
    Li, Dongyu
    Hang, Yandi
    Gao, Yuting
    Zhang, Hequn
    Zhao, Xinyuan
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Bo
    Qian, Jun
    Hua, Jianli
    Tetraphenylethene end-capped diketopyrrolopyrrole fluorogens with AIE and large two-photon absorption cross-sections features and application in bioimaging2016In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 133, p. 201-213Article in journal (Refereed)
    Abstract [en]

    In this work, a series of new diketopyrrolopyrrole-based dyes have been synthesized by connecting tetraphenylethene to the diketopyrrolopyrrole core. All the four compounds exhibit good aggregation induced emission property with nonemissive in the solution but strong red fluorescence in the aggregate or solid state. Also, these new dyes exhibit large two-photon absorption cross sections (a), in which the a data measured by the open aperture Z-scan technique are determined to be 150, 300, 1140 and 1016 GM for four dyes, respectively. In addition, compound with stilbene and four tetraphenylethene units (DPP-TPE-3) was used as the luminogen and encapsulated into nanoparticles for cell imaging and two-photon excited fluorescence blood vessels imaging. The result indicates that it can be used as the effective fluorescence probe for bioimaging and has great potential for bioapplications. (C) 2016 Elsevier Ltd. All rights reserved.

  • 24.
    Kang, Yu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Tu, Yaoquan
    Wang, Qi
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    On the Mechanism of Protein Adsorption onto Hydroxylated and Nonhydroxylated TiO2 Surfaces2010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 34, p. 14496-14502Article in journal (Refereed)
    Abstract [en]

    Protein adsorption onto implant surfaces is of great importance for the regulation of implant bioactivity. Surface modification of implants is a promising way in the molecular design of biocompatible materials against nonspecific adsorption of proteins. On the basis of these fundamental facts, we focus in this work on the different behavior of protein adsorption on hydroxylated and nonhydroxylated rutile TiO2 (110) surfaces through molecular dynamics simulations. Our investigation indicates that the distribution of the water molecules at the interface induced by the surface modification plays an important role in the protein adsorption. The surface with modified hydroxyl groups was observed to have much greater affinity to the protein, as reflected by the larger protein-surface electrostatic interaction and by the larger amount of adsorbed residues. The highly ordered structure of the modified hydroxyl groups on the hydroxylated surface diminishes the possibility of hydrogen bond formation between the surface and the water molecules above it, which in turn makes it easier for the protein to move closer to the surface with hydroxyl modification.

  • 25. Kapilashrami, Mukes
    et al.
    Wang, Yung Jui
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Glans, Per-Anders
    Fang, Mei
    Riazanova, Anastasia V.
    Belova, Lyubov M.
    Rao, K. Venkat
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Luo, Yi
    Barbiellini, Bernardo
    Lin, Hsin
    Markiewicz, Robert
    Bansil, Arun
    Hussain, Zahid
    Guo, Jinghua
    Understanding the magnetic interaction between intrinsic defects and impurity ions in room-temperature ferromagnetic Mg1-xFexO thin films2016In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 28, no 15, article id 156002Article in journal (Refereed)
    Abstract [en]

    Understanding the nature and characteristics of the intrinsic defects and impurities in the dielectric barrier separating the ferromagnetic electrodes in a magnetic tunneling junction is of great importance for understanding the often observed 'barrier-breakdown' therein. In this connection, we present herein systematic experimental (SQUID and synchrotron-radiation-based x-ray absorption spectroscopy) and computational studies on the electronic and magnetic properties of Mg1-xFexO thin films. Our studies reveal: (i) defect aggregates comprised of basic and trimer units (Fe impurity coupled to 1 or 2 Mg vacancies) and (ii) existence of two competing magnetic orders, defect- and dopant-induced, with spin densities aligning anti-parallel if the trimer is present in the oxide matrix. These findings open up new avenues for designing tunneling barriers with high endurance and tunneling effect upon tuning the concentration/distribution of the two magnetic orders.

  • 26. Kong, Jiahui
    et al.
    Li, Qizhao
    Li, Minzhi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Xu
    Zhu, Weihua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Modulation of the structures and properties of bidipyrrin zinc complexes by introducing terminal alpha-methoxy groups2017In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 137, p. 430-436Article in journal (Refereed)
    Abstract [en]

    A bidipyrrin nickel complex was synthesized in a high yield by oxidatively coupling between the ligands in the corresponding 2:1 (L:M) type of dipyrrin nickel complex, and further demetallation afforded the free bidipyrrin ligand. Interestingly, when treating the bidipyrrin nickel complex or the free bidipyrrin with FeCl3 in CH2Cl2/MeOH, the symmetric di-alpha-methoxy bidipyrrin could be synthesized in a high yield, with two methoxy groups attached to the terminal pyrrolic alpha-positions. Moreover, the coordination of the unsubstituted and disubstituted bidipyrrins with Zn(OAc)(2),2H(2)O afforded two similar M2L2 type of bidipyrrin helical complexes with different ligand conformations and different Zn center dot center dot center dot Zn distances of 5.353 and 3.357 angstrom, respectively. The difference in the conformations may be related to the electrostatic repulsions between the methoxy substituents. These results indicate that the dyes based on helical bidipyrrin zinc complexes with tunable structures and photophysical properties may be developed simply by modulating the terminal alpha-substituents.

  • 27. Kong, Jiahui
    et al.
    Zhang, Qiong
    Savage, Mathew
    Li, Minzhi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yang, Sihai
    Liang, Xu
    Zhu, Weihua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Tetra- and Octapyrroles Synthesized from Confusion and Fusion Approaches2016In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 18, no 19, p. 5046-5049Article in journal (Refereed)
    Abstract [en]

    By oxidation of an alternately N-confused bilane in CH2Cl2, a C-N fused tetrapyrrin was synthesized that bears a 5.5.5-tricyclic ring generated from an intramolecular C-N linkage. When CH3CN was used as the reaction medium, a multiply C-N-fused octapyrrolic dimer was also obtained that contained two 5.5.5.7.5-pentacyclic moieties and a bipyrrole unit generated from the intramolecular C-N linkage and intermolecular C-C linkage, respectively. This could be coordinated with Ni(acac)(2) to afford a mixed-ligand complex.

  • 28. Li, Hong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zhan-Qi
    Qu, Da-Hui
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    A Switchable bis-Branched [1]Rotaxane featuring Dual-Mode Molecular Motions and Tunable Molecular Aggregation2014In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 6, no 21, p. 18921-18929Article in journal (Refereed)
    Abstract [en]

    A multifunctional bis-branched [1]rotaxane containing a perylene bisimide (PBI) core and two identical bistable[1]rotaxane arms terminated with ferrocene units was prepared and characterized by H-1 NMR, C-13 NMR, and 2D ROESY NMR spectroscopies and by HR-ESI spectrometry. The system is shown to possess several key features: (1) In acetone solution, external acid base stimuli can result in relative mechanical movements of its ring and thread, which can induce extension and contraction movements of the whole system accompanied by a rotational movement of the ferrocene units, thus realizing dual-mode molecular motions, and the optimized conformations at different states are obtained through molecular dynamics simulations employing the general Amber force field. (2) The introduction of PBI enables the system fluorescence encoding through distance-dependent photoinduced electron transfer process from the ferrocene units to the PBI fluorophore. (3) The addition of Zn2+ can increase the degree of aggregation of the system, while adding base hinders aggregation because of the movement of the macrocyde. The tunable aggregated nanostructural morphologies of [1]rotaxane were examined by scanning electron microscopy. These results can pave the way to achieve precise control of integrated and coupling nanomechanical motions at a single-molecule level and provide more insight into controlling the aggregate behavior of switchable mechanically interlocked molecules.

  • 29. Li, Hong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wu, Ying
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Qu, Da-Hui
    A Musclelike [2](2)Rotaxane: Synthesis, Performance, and Molecular Dynamics Simulations2014In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 79, no 15, p. 6996-7004Article in journal (Refereed)
    Abstract [en]

    A novel bistable symmetric [2](2)rotaxane was prepared by a threading-followed-by-stoppering strategy and characterized with H-1, C-13, and 2D ROESY NMR spectroscopy and HR-ESI spectrometry. The symmetric [2] (2)rotaxane system consists of an anthracene-based bis(crown ether) as macrocycles, and each of the two dibenzo[24]crown-8 (DB24C8) rings is threaded by the pendant substituents a symmetrically substituted central rotatable ferrocene subunit that possesses two distinguishable recognition sites for the DB24C8 ring: namely, a dibenzylammonium site and an N-methyltriazolium site. The uniform shuttling motion of the thread relative to the two DB24C8 rings in [2](2)rotaxane can be driven by external acid base stimuli, which was evidenced by H-1 and 2D ROESY NMR spectroscopy. Furthermore, molecular dynamics simulations of the [2](2)rotaxane were carried out both in protonated (stretched) and in neutral (contracted) forms. The calculated percentage change in molecular length of the [2](2)rotaxane between the two end-capping bis(methoxyl)phenyl groups is about 48% in the two different states (in acetone), which is much larger than the percentage change (similar to 27%) in human muscle. Moreover, in the two states, the C*-Cp-Cp-C* dihedral angles are computed as -177 degrees in the stretched state and -112 degrees in the contracted state, indicating a correlation between the translational and rotational motions of the [2](2)rotaxane.

  • 30. Li, Hong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Qu, Da-Hui
    Two Switchable Star-Shaped [1](n)Rotaxanes with Different Multibranched Cores2014In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 16, no 18, p. 4940-4943Article in journal (Refereed)
    Abstract [en]

    Two novel star-shaped [1](n)rotaxanes with three and four identical [1]rotaxane arms but different multibranched cores were designed, synthesized, and well-characterized. In the two systems, external base acid stimuli result in the uniform relative mechanical movement of the macrocydic rings and threads of their [1]rotaxane arms. The energy-minimized structures of the two rotaxanes in different states were obtained using molecular dynamics simulations in acetone solution, suggesting the construction of more sophisticated molecular machines mimicking the extension and contraction motions.

  • 31. Li, T.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, J.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ma, X.
    Tian, H.
    Photoresponsive Supramolecular Assemblies Based on a C3-Symmetric Benzene-1,3,5-tricarboxamide Anchored Diarylethene2016In: Advanced Optical Materials, ISSN 2195-1071Article in journal (Refereed)
    Abstract [en]

    A functional C3-symmetric benzene-1,3,5-tricarboxamide-anchored diarylethene molecule (C3-BTE) is synthesized, which evolves into ordered superstructures with tunable morphology properties both in different solvent and via alternative light stimuli. The formation of rod-like assemblies from C3-BTE is reported and the self-assembly property of C3-BTE can be realized through alternative light stimuli in nonpolar solvents such as toluene.

  • 32. Li, Wenlong
    et al.
    Cai, Yunsong
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    Zhu, Wei-Hong
    Sterically hindered diarylethenes with a benzobis(thiadiazole) bridge: photochemical and kinetic studies2015In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 3, no 33, p. 8665-8674Article in journal (Refereed)
    Abstract [en]

    Four rationally designed diarylethenes (DAEs) 1-4 with a benzobis(thiadiazole) bridge are specifically designed for gaining insights into steric effects on photochromic performances. It is shown that, upon increasing steric hindrance, the exchanging rate between two main conformers in the ring-open form gradually slows down, offering the opportunity for isolating photoactive anti-parallel conformers. Impressively, the separated anti-parallel conformer shows high cyclization quantum yields over the unresolved common DAEs. The typical donor-pi-acceptor (D-pi-A) feature in ring-open DAEs 1-4 endows their prominent fluorescence, which can be conveniently modulated by photocyclization. In the ring-closed form, the excess steric hindrance is found to seriously disrupt the thermal bistability, and particularly 3c fades quickly with a half-life of several hours at ambient temperature. In contrast, both 1c and 2c exhibit excellent stability, which originates from the stabilization effects of intramolecular hydrogen bonds. This work demonstrates the steric effects on the photochemical and kinetic behaviors of DAEs, providing a unique approach to develop photochromic DAEs with high photosensitivity.

  • 33. Li, Wenlong
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xie, Yongshu
    Wu, Yue
    Li, Mengqi
    Wu, Xin-Yan
    Zhu, Wei-Hong
    Tian, He
    Enantiospecific photoresponse of sterically hindered diarylethenes for chiroptical switches and photomemories2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 9186Article in journal (Refereed)
    Abstract [en]

    Light-driven transcription, replication and enzyme catalysis are critically dependent upon a delicate transfer between molecular and supramolecular chirality. Chemists have well realized the impressive stereospecificity over many thermally accessible cycloaddition with chiral catalysts, but making light work in the enantiomer control of diarylethene photocyclization has proved to be more challenging. Here, we report a unique sterically hindered diarylethene (BBTE) system with absolute enantiospecific photocyclization and cycloreversion. Moreover, we have fully separated all the five thermally stable isomers, consisting of one achiral parallel conformer, one pair of anti-parallel ring-open enantiomers, and another pair of ring-closed enantiomers, whose absolute chiral configurations are entirely elucidated by single X-ray crystallographic analyses. The photo-responsive feature exhibits a reversible, complete enantio-control transformation without racemism, offering an unrivaled unimolecular enantiospecific platform for potential applications as bistable chiroptical switches and all-photonic photomemories with optical rotation as non-destructive readout.

  • 34.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Applications of Molecular Dynamics in Atmospheric and Solution Chemistry2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial charges and the inter-atomic interactions are modeled by approximate potential functions that produce satisfactory results at an economical computational cost. The three-dimensional trajectory of a many-body system is generated by integrating Newton’s equations of motion, and subsequent statistical analysis on the trajectories provides microscopic insight into the physical properties of the system.

    The applications in this thesis of molecular dynamics simulations in solution chemistry comprise four aspects: the 113Cd nuclear magnetic resonance shielding constant of aqua Cd(II) ions, paramagnetic 19F nuclear magnetic resonance shift in fluorinated cysteine, solvation free energies and structures of metal ions, and protein adsorption onto TiO2. In the studies of nuclear magnetic resonance parameters, the relativistic effect of the 113Cd nucleus and the paramagnetic shift of 19F induced by triplet O2 are well reproduced by a combined molecular dynamics and density functional theory approach. The simulation of the aqua Cd(II) ion is also extended to several other monovalent, divalent and trivalent metal ions, where careful parameterization of the metal ions ensures the reproduction of experimental solvation structures and free energies. Molecular dynamics simulations also provided insight into the mechanism of protein adsorption onto the TiO2 surface by suggesting that the interfacial water molecules play an important role of mediating the adsorption and that the hydroxylated TiO2 surface has a large affinity to the proteins.

    The applications of molecular dynamics simulations in atmospheric chemistry are mainly focused on two types of organic components in aerosol droplets: humic-like compounds and amino acids. The humic-like substances, including cis-pinonic acid, pinic acid and pinonaldehyde, are surface-active organic compounds that are able to depress the surface tension of water droplets, as revealed by both experimental measurements and theoretical computations. These compounds either concentrate on the droplet surface or aggregate inside the droplet. Their effects on the surface tension can be modeled by the Langmuir-Szyszkowski equation. The amino acids are not strong surfactants and their influence on the surface tension is much smaller. Simulations show that the zwitterionic forms of serine, glycine and alanine have hydrophilic characteristics, while those of valine, methionine and phenylalanine are hydrophobic. The curvature dependence of the surface tension is also analyzed, and a slight improvement in the Köhler equation is obtained by introducing surface tension corrections for droplets containing glycine and serine.

    Through several examples it is shown that molecular dynamics simulations serve as a promising tool in the study of aqueous systems. Both solute-solvent interactions and interfaces can be treated properly by choosing suitable potential functions and parameters. Specifically, molecular dynamics simulations provide a microscopic picture that evolves with time, making it possible to follow the dynamic processes such as protein adsorption or atmospheric droplet formation. Moreover, molecular dynamics simulations treat a large number of molecules and give a statistical description of the system; therefore it is convenient to compare the simulated results with experimentally measured data. The simulations can provide hints for better design of experiments, while experimental data can be fed into the refinement of the simulation model. As an important complementary to experiments, molecular dynamics simulations will continue to play significant roles in the research fields of physics, chemistry, materials science, biology and medicine.

  • 35.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on electronic structure and x-ray spectroscopies of 2D materials2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Extraordinary chemical and physical properties have been discovered from the studies of two-dimensional (2D) materials, ever since the successful exfoliation of graphene, the first 2D material. Theoretical investigations of electronic structure and spectroscopies of these materials play a fundamental role in deep understanding the various properties. In particular, the band structure and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy can provide critical information near the Fermi level. In this thesis, we performed first-principles density functional theory calculations to study the electronic structure and NEXAFS spectra of four materials, including three 2D materials and one bulk material. The three 2D materials are atomically thin bismuth telluride, nitrogen and boron nitride doped graphenes. The bulk material is lithium intercalated graphite, an analogue of lithium doped graphene. Our studies provide important electronic property information of the studied materials, and are helpful for understanding their properties and developing potential applications.

  • 36.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, Vincenzo
    Li, Cui
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. CNR-ICCOM, Italy .
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 7, p. 3325-3339Article in journal (Refereed)
    Abstract [en]

    Motivated by the growing importance of organometallic nanostructured materials and nanoparticles as microscopic devices for diagnostic and sensing applications, and by the recent considerable development in the simulation of such materials, we here choose a prototype system para-nitroaniline (pNA) on gold nanoparticles to demonstrate effective strategies for designing metal nanoparticles with organic conjugates from fundamental principles. We investigated the motion, adsorption mode, and physical chemistry properties of gold-pNA particles, increasing in size, through classical molecular dynamics (MD) simulations in connection with quantum chemistry (QC) calculations. We apply the quantum mechanics-capacitance molecular mechanics method [Z. Rinkevicius et al. J. Chem. Theory Comput. 2014, 10, 989] for calculations of the properties of the conjugate nanoparticles, where time dependent density functional theory is used for the QM part and a capacitance-polarizability parametrization of the MM part, where induced dipoles and charges by metallic charge transfer are considered. Dispersion and short-range repulsion forces are included as well. The scheme is applied to one- and two-photon absorption of gold-pNA clusters increasing in size toward the nanometer scale. Charge imaging of the surface introduces red-shifts both because of altered excitation energy dependence and variation of the relative intensity of the inherent states making up for the total band profile. For the smaller nanoparticles the difference in the crystal facets are important for the spectral outcome which is also influenced by the surrounding MM environment.

  • 37.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Hede, T.
    Tu, Y.
    Leck, C.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Glycine in aerosol water droplets: a critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations2011In: Atmospheric Chemistry And Physics, ISSN 1680-7316, E-ISSN 1680-7324, Vol. 11, no 2, p. 519-527Article in journal (Refereed)
    Abstract [en]

    Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the Kohler theory which describes the nucleation and the equilibrium growth of cloud droplets, the surface tension of an aerosol droplet is one of the most important factors that determine the critical supersaturation of droplet activation. In this paper, with specific interest to remote marine aerosol, we predict the surface tension of aerosol droplets by performing molecular dynamics simulations on two model systems, the pure water droplets and glycine in water droplets. The curvature dependence of the surface tension is interpolated by a quadratic polynomial over the nano-sized droplets and the limiting case of a planar interface, so that the so-called Aitken mode particles which are critical for droplet formation could be covered and the Kohler equation could be improved by incorporating surface tension corrections.

  • 38.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hede, Thomas
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cloud droplet activation mechanisms of amino acid aerosol particles: insight from molecular dynamics simulations2013In: Tellus. Series B, Chemical and physical meteorology, ISSN 0280-6509, E-ISSN 1600-0889, Vol. 65, p. 65-Article in journal (Refereed)
    Abstract [en]

    Atmospheric amino acids constitute a large fraction of water-soluble organic nitrogen compounds in aerosol particles, and have been confirmed as effective cloud condensation nuclei (CCN) materials in laboratory experiments. We present a molecular dynamics (MD) study of six amino acids with different structures and chemical properties that are relevant to the remote marine atmospheric aerosol-cloud system, with the aim of investigating the detailed mechanism of their induced changes in surface activity and surface tension, which are important properties for cloud drop activation. Distributions and orientations of the amino acid molecules are studied; these L-amino acids are serine (SER), glycine (GLY), alanine (ALA), valine (VAL), methionine (MET) and phenylalanine (PHE) and are categorised as hydrophilic and amphiphilic according to their affinities to water. The results suggest that the presence of surface-concentrated amphiphilic amino acid molecules give rise to enhanced Lennard-Jones repulsion, which in turn results in decreased surface tension of a planar interface and an increased surface tension of the spherical interface of droplets with diameters below 10 nm. The observed surface tension perturbation for the different amino acids under study not only serves as benchmark for future studies of more complex systems, but also shows that amphiphilic amino acids are surface active. The MD simulations used in this study reproduce experimental results of surface tension measurements for planar interfaces and the method is therefore applicable for spherical interfaces of nano-size for which experimental measurements are not possible to conduct.

  • 39.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hede, Thomas
    Tu, Yaoquan
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Molecular Dynamics Study on the Surface Tension of Atmospheric Water Droplets Containing Amino AcidsManuscript (preprint) (Other academic)
    Abstract [en]

    Atmospheric amino acids constitute an important fraction of the water-soluble organic nitrogen compounds in both marine and continental aerosols, and have been confirmed as effective cloud condensation nuclei materials in laboratory tests. We here present molecular dynamics study of six types of amino acids in atmospheric water droplets, in order to investigate molecular distributions, orientations and induced changes in surface tension, and to evaluate their indirect effects on optical properties of clouds. These amino acids, including serine, glycine, alanine, valine, methionine and phenylalanine, are categorized into hydrophilic and hydrophobic species according to their affinities to water. Different amino acids show distinct effects on the surface tension; even the same amino acid has different influence on the surface tension of planar and spherical interfaces. Finally the curvature dependence of the surface tension is modeled by a quadratic polynomial function of the inverse of droplet radius, and such relationship is used to improve the Köhler equation in predicting the critical supersaturation of droplet activation.

  • 40.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hede, Thomas
    Tu, Yaoquan
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Surface-Active cis-Pinonic Acid in Atmospheric Droplets: A Molecular Dynamics Study2010In: Journal of Physical Chemistry Letters, ISSN 1948-7185, Vol. 1, no 4, p. 769-773Article in journal (Refereed)
    Abstract [en]

    Water vapor in the atmosphere can condensate and form cloud droplets when there is a certain amount of humidity and a presence of cloud condensation nuclei, and organic solutes called surfactants can significantly lower the surface tension of water-one of the parameters determining cloud droplet population. We here present a molecular dynamics study of the behavior of cis-pinonic acid, a commonly found organic compound in cloud condensation nuclei, and its effect on the surface tension of water clusters. Specifically, the decrease in surface tension is found to depend on not only the concentration of the organic compound but also the droplet size due to the spontaneous assembly of the surfactant molecules on the droplet surface. This leads to the conclusion that the partitioning of the surfactant between the bulk and surface plays an important role in the behavior of atmospheric aerosol particles and thus in their availability for cloud formation.

  • 41.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hua, Weijie
    Wang, Bo-Yao
    Pong, Way-Faung
    Glans, Per-Anders
    Guo, Jinghua
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dopant Size Dependent Electronic Structure of Boron Nitride-Doped GrapheneManuscript (preprint) (Other academic)
  • 42.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
    Hua, Weijie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Bo-Yao
    Pong, Way-Faung
    Glans, Per-Anders
    Guo, Jinghua
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
    Effects of domain size on x-ray absorption spectra of boron nitride doped graphenes2016In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 109, no 8, article id 081601Article in journal (Refereed)
    Abstract [en]

    Doping is an efficient way to open the zero band gap of graphene. The control of the dopant domain size allows us to tailor the electronic structure and the properties of the graphene. We have studied the electronic structure of boron nitride doped graphenes with different domain sizes by simulating their near-edge X-ray absorption fine structure (NEXAFS) spectra at the N K-edge. Six different doping configurations (five quantum dot type and one phase-separated zigzag-edged type) were chosen, and N K-edge NEXAFS spectra were calculated with large truncated cluster models by using the density functional theory with hybrid functional and the equivalent core hole approximation. The opening of the band gap as a function of the domain size is revealed. We found that nitrogens in the dopant boundary contribute a weaker, red-shifted pi* peak in the spectra as compared to those in the dopant domain center. The shift is related to the fact that these interfacial nitrogens dominate the lowest conduction band of the system. Upon increasing the domain size, the ratio of interfacial atom decreases, which leads to a blue shift of the pi* peak in the total NEXAFS spectra. The spectral evolution agrees well with experiments measured at different BN-dopant concentrations and approaches to that of a pristine h-BN sheet.

  • 43.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kao, Fu-Jen
    Chuang, Chien-Chin
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering.
    Enhancing fluorescence of quantum dots by silica-coated gold nanorods under one- and two-photon excitation2010In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 18, no 11, p. 11335-11346Article in journal (Refereed)
    Abstract [en]

    Nano-composites of quantum dots (QDs) and gold nanorods (GNRs) or silica-coated GNRs (GNRs_SiO2) were synthesized. The attached GNRs modify the excitation intensity and spontaneous emission of QDs through the surface plasmonic effects. The fluorescence from QDs is enhanced and can be optimized by modifying the thickness of silica coated on GNRs, under both one-and two-photon excitations. The measurements of fluorescence intensity and lifetime demonstrate that the enhancement may be attributed to the matching of the localized surface plasmon resonance of GNR to the excitation wavelength. In addition to enhancing QD-fluorescence in QD-GNR@SiO2, GNRs also present as an effective contrast agent for bio-imaging, through light scattering and or two-photon emission, as well as for photo-thermal therapy. The composite's multifunctional characteristics are highly valuable and to be exploited in bio-applications. (C) 2010 Optical Society of America

  • 44.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Leck, Caroline
    Sun, Lu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hede, Thomas
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cross-Linked Polysaccharide Assemblies in Marine Gels: An Atomistic Simulation2013In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, no 16, p. 2637-2642Article in journal (Refereed)
    Abstract [en]

    Marine polymeric gels or colloidal nano- and microgels have been shown to contribute significantly to the primary marine aerosol and cloud condensation nuclei over remote marine areas. A microscopic understanding of such biologically derived matter at the sea air interface is important for future development of global climate models, but unfortunately cannot be obtained from modern characterization techniques. In this contribution, we employ molecular dynamics simulations to reveal the atomistic details of marine polymeric gels represented by anionic polysaccharide assemblies. The ionic bonds formed between polysaccharides and metal ions in seawater as well as the hydrophobic contribution to surface area are investigated in detail, and destabilization of the assemblies upon removal of Ca2+ or acidification is explained. These results provide insight into physicochemical properties of polysaccharide-Ca2+ structures and enable future studies of their roles of in the wetting process of cloud droplet activation.

  • 45.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Prendergast, David
    Guo, Jinghua
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Electronic Structure of Lithium Intercalated Graphite from First-Principles SimulationsManuscript (preprint) (Other academic)
  • 46.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic Simulations and First-Principles Calculations2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4766-4774Article in journal (Refereed)
    Abstract [en]

    Electron paramagnetic resonance (EPR) imaging techniques provide a promising approach to detect amyloid structures which are of paramount importance in early-stage diagnosis of conformational diseases. Here, we report a combined molecular dynamics and density functional theory/molecular mechanics computational scheme for evaluation of the binding mechanism between a multifunctional spin label and the target amyloid protein. In addition, we consider evaluation of EPR spin Hamiltonian parameters with the aim of providing a better microscopic understanding and interpretation of EPR spectroscopy. The results from molecular dynamics simulations suggest that the oligothiophene conjugate part of the spin label interacts with hydrophobic residues of the amyloid protein through hydrophobic attraction and that both the N-O bond length and the N-O out-of-plane tilt angle in the nitroxide group are slightly diminished after, complexation with the protein. The translational and rotational motions of the protein bound spin label are considerably slowed compared to those of the free spin label in aqueous solution, but interestingly, hydrogen bonds formed between the nitroxide oxygen group and the surrounding water molecules are hardly affected by the presence Of the amyloid protein. First principles calculation's suggest that EPR spin Hamiltonian parameters including the nitroxide nitrogen hyperfine coupling tensor A(N) and electronic g tensor suffer noticeable changes upon complexation with the protein. The magnitude of the A(N) tensor is found,to:be. closely related to the nitroxide N-O out tilt angle, while the g tensor is affected by both the nitroxide N-O bond length as well as the interaction between the spin label and the amyloid protein With this work we show that state-of-the-art simulation techniques represent a promising way of providing a detailed understanding of the microscopic mechanisms responsible for the formation and stability of a spin label complexed with amyloid structures as well as the magnetic properties of the free and protein-bound spin label.

  • 47.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 36, p. 11347-11352Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the Cd-113(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium-water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic Shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in Cd-113 NMR experiments, due to the mutual cancelation between individual relativistic corrections.

  • 48.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 31, p. 10916-10922Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the F-19 NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O-2 partial pressure. Molecular dynamics Simulations are carried out to determine the dominant structures of O-2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of F-19 chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O-2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the F-19 NMR chemical shifts, where the Fermi contact interaction plays the key role. The O-2-induced paramagnetic F-19 chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling F-19 NMR chemical shifts in the presence of paramagnetic agents in ail aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including H-1, C-13, N-15, and F-19 is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.

  • 49.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 11, p. 5833-5840Article in journal (Refereed)
    Abstract [en]

    To promote a more comprehensive understanding of the influence of metal-adsorbate interaction for molecules at metallo surfaces or metallo nanoparticles in solvent environments on their electronic circular dichroism (ECD) spectra, we evaluate the application of a recently derived quantum mechanics capacitance molecular mechanics (QMCMM) model for ECD. Using helicene absorbed on gold surfaces in protic and aprotic solvents as illustration, we elucidate the detailed effects on excitation energies, transition moments, rotatory strengths, orientation dependence of ECD spectra, and the different roles of aprotic and protic solvents and the induced charge distribution patterns on the surface. These changes are decomposed in terms of surface alone, solvent alone, and combined surface solvent influence, and furthermore into the indirect contributions by the surface-induced restructuring of the helicene. Much of the salient changes of the ECD can be rationalized to the substantial redistribution of charge at the gold surface induced by the presence of the helicene. The study indicates that through the QMCMNI model the effects of a metallic surface on the circular dichroism spectra of adsorbed organic molecules can be tackled by extended QM calculations coupled to polarizability-capacitance force fields for large metallic clusters representing surfaces or nanoparticles.

  • 50.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Two-Photon Absorption of Metal-Assisted Chromophores2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, p. 5630-5639Article in journal (Refereed)
    Abstract [en]

    Aiming to understand the effect of a metal surface on nonlinear optical properties and the combined effects of surface and solvent environments on such properties, we present a multiscale response theory study, integrated with dynamics of the two-photon absorption of 4-nitro-4'-amino-trans-stilbene physisorbed on noble metal surfaces, considering two such surfaces, Ag(111) and Au(111), and two solvents, cyclohexane and water, as cases for demonstration. A few conclusions of general character could be drawn: While the geometrical change of the chromophore induced by the environment was found to notably alter (diminish) the two-photon absorption cross section in the polar medium, the effects of the metal surface and solvent on the electronic structure of the chromophore surpasses the geometrical effects and leads to a considerably enhanced two-photon absorption cross section in the polar solvent. This enhancement of two-photon absorption arises essentially from the metal charge image induced enlargement of the difference between the dipole moment of the excited state and the ground state. The orientation-dependence of the two-photon absorption is found to connect with the lateral rotation of the chromophore, where the two-photon absorption reaches its maximum when the polarization of the incident light coincides with the long-axis of the chromophore. Our results demonstrate a distinct enhancement of the two-photon absorption by a metal surface and a polar medium and envisage the employment of metal-chromophore composite materials for future development of nonlinear optical materials with desirable properties.

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