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  • 1
    Language: English
    In: The journal of physical chemistry. A, 01 March 2012, Vol.116(8), pp.1939-49
    Description: Anharmonic vibrational frequency shifts of the phenol(+) O-H stretching mode upon complex formation with the open-shell ligand O(2) were computed at several DFT and MP2 levels of theory, with various basis sets, up to 6-311++G(2df,2pd). It was found that all DFT levels of theory significantly outperform the MP2 method with this respect. The best agreement with the experimental frequency shift for the hydrogen-bonded minimum on the potential energy surfaces was obtained with the HCTH/407 functional (-93.7 cm(-1) theoretical vs -86 cm(-1) experimental), which is a significant improvement over other, more standard DFT functionals (such as, e.g., B3LYP, PBE1PBE), which predict too large downshifts (-139.9 and -147.7 cm(-1), respectively). Good agreement with the experiment was also obtained with the mPW1B95 functional proposed by Truhlar et al. (-109.2 cm(-1)). We have attributed this trend due to the corrected long-range behavior of the HCTH/407 and mPW1B95 functionals, despite the fact that they have been designed primarily for other purposes. MP2 method, even with the largest basis set used, manages to reproduce only less than 50% of the experimentally detected frequency downshift for the hydrogen-bonded dimer. This was attributed to the much more significant spin contamination of the reference HF wave function (compared to DFT Kohn-Sham wave functions), which was found to be strongly dependent on the O-H stretching vibrational coordinate. All DFT levels of theory outperform MP2 in the case of computed anharmonic OH stretching frequency shifts upon ionization of the neutral phenol molecule as well. Besides the hydrogen-bonded minimum, DFT levels of theory also predict existence of two other minima, corresponding to stacked arrangement of the phenol(+) and O(2) subunits. mPW1B95 and PBE1PBE functionals predict a very slight blue shift of the phenol(+) O-H stretching mode in the case of stacked dimer with the nearly perpendicular orientation of oxygen molecule with respect to the phenolic ring, which is entirely of electrostatic origin, in agreement with the experimental observations of an additional band in the IR photodissociation spectra of phenol(+)-O(2) dimer [Patzer, A.; Knorke, H.; Langer, J.; Dopfer, O. Chem. Phys. Lett. 2008, 457, 298]. The structural features of the minima on the studied PESs were discussed in details as well, on the basis of NBO and AIM analyses.
    Keywords: Quantum Theory ; Oxygen -- Chemistry ; Phenol -- Chemistry
    ISSN: 10895639
    E-ISSN: 1520-5215
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  • 2
    Language: English
    In: Journal of Physical Chemistry A, March 1, 2012, Vol.116(8), p.1939-1949
    Keywords: Density Functional Theory -- Usage ; Hydrogen Bonds -- Analysis ; Ionization -- Analysis ; Phenol (Compound) -- Chemical Properties ; Phenol (Compound) -- Electric Properties ; Photolysis -- Analysis ; Potential Energy -- Measurement
    ISSN: 1089-5639
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: The Journal of Chemical Physics, 28 December 2015, Vol.143(24)
    Description: A theoretical proof of the concept that a particularly designed graphene-based moletronics device, constituted by two semi-infinite graphene subunits, acting as source and drain electrodes, and a central benzenoid ring rotator (a “quantum dot”), could act as a field-controllable molecular switch is outlined and analyzed with the density functional theory approach. Besides the ideal (0 K) case, we also consider the operation of such a device under realistic operating (i.e., finite-temperature) conditions. An in-depth insight into the physics behind device controllability by an external field was gained by thorough analyses of the torsional potential of the dot under various conditions (absence or presence of an external gating field with varying strength), computing the torsional correlation time and transition probabilities within the Bloembergen-Purcell-Pound formalism. Both classical and quantum mechanical tunneling contributions to the intramolecular rotation were considered in the model. The main idea that we put forward in the present study is that intramolecular rotors can be controlled by the gating field even in cases when these groups do not possess a permanent dipole moment (as in cases considered previously by us [I. Petreska et al. , J. Chem. Phys. 134 , 014708-1–014708-12 (2011)] and also by other groups [P. E. Kornilovitch et al. , Phys. Rev. B 66 , 245413-1–245413-7 (2002)]). Consequently, one can control the molecular switching properties by an external electrostatic field utilizing even nonpolar intramolecular rotors (i.e., in a more general case than those considered so far). Molecular admittance of the currently considered graphene-based molecular switch under various conditions is analyzed employing non-equilibrium Green’s function formalism, as well as by analysis of frontier molecular orbitals’ behavior.
    Keywords: Articles
    ISSN: 0021-9606
    E-ISSN: 1089-7690
    Source: © 2015 AIP Publishing LLC (AIP)
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  • 4
    Language: English
    In: The Journal of chemical physics, 28 December 2015, Vol.143(24), pp.244704
    Description: A theoretical proof of the concept that a particularly designed graphene-based moletronics device, constituted by two semi-infinite graphene subunits, acting as source and drain electrodes, and a central benzenoid ring rotator (a "quantum dot"), could act as a field-controllable molecular switch is outlined and analyzed with the density functional theory approach. Besides the ideal (0 K) case, we also consider the operation of such a device under realistic operating (i.e., finite-temperature) conditions. An in-depth insight into the physics behind device controllability by an external field was gained by thorough analyses of the torsional potential of the dot under various conditions (absence or presence of an external gating field with varying strength), computing the torsional correlation time and transition probabilities within the Bloembergen-Purcell-Pound formalism. Both classical and quantum mechanical tunneling contributions to the intramolecular rotation were considered in the model. The main idea that we put forward in the present study is that intramolecular rotors can be controlled by the gating field even in cases when these groups do not possess a permanent dipole moment (as in cases considered previously by us [I. Petreska et al., J. Chem. Phys. 134, 014708-1-014708-12 (2011)] and also by other groups [P. E. Kornilovitch et al., Phys. Rev. B 66, 245413-1-245413-7 (2002)]). Consequently, one can control the molecular switching properties by an external electrostatic field utilizing even nonpolar intramolecular rotors (i.e., in a more general case than those considered so far). Molecular admittance of the currently considered graphene-based molecular switch under various conditions is analyzed employing non-equilibrium Green's function formalism, as well as by analysis of frontier molecular orbitals' behavior.
    Keywords: Articles;
    ISSN: 00219606
    E-ISSN: 1089-7690
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  • 5
    Language: English
    In: The Journal of Chemical Physics, 07 January 2011, Vol.134(1)
    Description: A bistable, dipolar stator-rotor molecular system-candidate for molecular electronics is investigated. We demonstrate that it is possible to control the intramolecular torsional states and dynamics in this system by applying an appropriate additional electric field (instead of biasing one), achieving fine tuning and modulation of the relevant properties. The electric field effects on the quantities responsible for torsional dynamics (potential energy surface, potential barrier height, quantum and classical transition probabilities, correlation time, HOMO-LUMO gap) are studied from first principles. Our results indicate that it is possible to artificially stabilize the metastable conformational state of the studied molecule. The importance of this is evident, as the current-voltage characteristics of the metastable state are clearly distinguishable from the current-voltage characteristics of the two stable states. We report for the first time exact calculations related to the possibilities to control the thermally induced stochastic switching, and reduce the noise in a practical application. Thus, we believe that the molecule studied in this paper could operate as a field-switchable molecular device under real conditions.
    Keywords: Articles
    ISSN: 0021-9606
    E-ISSN: 1089-7690
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  • 6
    Language: English
    In: The Journal of Chemical Physics, 07 August 2013, Vol.139(5)
    Description: A hybrid, sequential statistical physics–quantum mechanical electronic–quantum mechanical nuclei approach has been applied to study the C–H stretching frequencies of bare fluoroform dissolved in liquid krypton under cryogenic conditions (at ∼130 K), as well as upon blue shifting hydrogen bonding interactions with dimethylether in the same solvent. The structure of the liquid at 130 K was generated by Monte Carlo simulations of cryogenic Kr solutions containing either fluoroform or fluoroform and dimethylether molecules. Statistically uncorrelated configurations were appropriately chosen from the equilibrated MC runs and supermolecular clusters containing solute and solvent molecules (either standalone or embedded in the “bulk” part of the solvent treated as a polarizable continuum) were subjected to quantum mechanical electronic (QM el ) and subsequent quantum mechanical nuclei (QM nuc ) calculations. QM el calculations were implemented to generate the in-liquid 1D intramolecular C–H stretching vibrational potential of the fluoroform moiety and subsequently in the QM nuc phase the corresponding anharmonic C–H stretching frequency was computed by diagonalization techniques. Finally, the constructed vibrational density of states histograms were compared to the experimental Raman bands. The calculated anharmonic vibrational frequency shifts of the fluoroform C–H stretching mode upon interaction with dimethylether in liquid Kr are in very good agreement with the experimental data (20.3 at MP2 level vs. 16.6 cm −1 experimentally). Most of this relatively large frequency blue shift is governed by configurations characterized by a direct C–H⋯O contact between monomers. The second population detected during MC simulations, characterized by reversed orientation of the monomers, has a minor contribution to the spectral appearance. The experimentally observed trend in the corresponding bandwidths is also correctly reproduced by our theoretical approach. Solvation of the fluoroform monomer, according to experiment, results in small C–H stretching frequency red shift (∼−2 cm −1 ), while our approach predicts a blue shift of about 10 cm −1 . By a detailed analysis of the anharmonic C–H stretching frequency dependence on the position of the nearest solvent krypton atom and also by analyzing the vibrational Stark effect induced by the local fluctuating field component parallel to the C–H axis, we have derived several conclusions related to these observations. The frequency vs. C⋯Kr distance dependence shows appreciable fluctuations and even changes in sign at R values close to the maximum of the C⋯Kr radial distribution function, so that most of the first-shell Kr atoms are located at positions at which the CH frequency shifts acquire either small negative or small positive values. It so happens, therefore, that even the actual sign of the frequency shift is strongly dependent on the correct description of the first solvation shell around CF 3 H by the Monte Carlo method, much more than the other in-liquid properties calculated by similar approaches.
    Keywords: Articles
    ISSN: 0021-9606
    E-ISSN: 1089-7690
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  • 7
    Language: English
    In: Journal of the American Chemical Society, 15 February 2017, Vol.139(6), pp.2318-2328
    Description: The range of unit cell orientations generated at the kink of a bent single crystal poses unsurmountable challenges with diffraction analysis and limits the insight into the molecular-scale mechanism of bending. On a plastically bent crystal of hexachlorobenzene, it is demonstrated here that spatially resolved microfocus infrared spectroscopy using synchrotron radiation can be applied in conjunction with periodic density functional theory calculations to predict spectral changes or to extract information on structural changes that occur as a consequence of bending. The approach reproduces well the observed trends, such as the wall effects, and provides estimations of the vibrational shifts, unit cell deformations, and intramolecular parameters. Generally, expansion of the lattice induces red-shift while compression induces larger blue-shift of the characteristic ν(C-C) and ν(C-Cl) modes. Uniform or non-uniform expansion or contraction of the unit cell of 0.1 Å results in shifts of several cm, whereas deformation of the cell of 0.5° at the unique angle causes shifts of 〈0.5 cm. Since this approach does not include parameters related to the actual stimulus by which the deformation has been induced, it can be generalized and applied to other mechanically, photochemically, or thermally bent crystals.
    Keywords: Diffraction – Usage ; Molecular Dynamics – Research ; Cytology – Research;
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 8
    Language: English
    In: Surface Science, 2011, Vol.605(15), pp.1522-1533
    Description: The influence of fluorination of microcrystalline γ-alumina on the acidity of Lewis sites was studied by quantum chemical cluster model approach. B3LYP and HF/6-31++G( , ) levels of theory were employed, considering the standard and counterpoise-corrected potential energy surfaces (PESs). Explicit inclusion of dynamical electron correlation effects along with the elimination of the basis set superposition effects in geometry optimization and harmonic vibrational analysis were found to be crucial to reproduce the experimental trends in the shifts of the pyridine ν and ν modes upon fluorination. The acidity of surface-exposed Al-sites was found to increase upon fluorination, which is manifested as a ~ 10% increase of the interaction energies, and also in the characteristics of the electronic density and density Laplacian at the intermolecular bond critical point. Bader analysis of the electronic density has shown that pyridine adsorption on pure and fluorinated γ-alumina can be classified as non-covalent interaction. ► We studied the effects of fluorination of γ-alumina on the Lewis sites' acidity. ► Partial fluorination of the surface increases the acidity of the exposed Al-sites. ► This is manifested as a ~ 10% increase of the interaction energies. ► Shifts of adsorbed pyridine ν and ν modes upon fluorination were calculated. ► Counterpoise-corrected PESs have to be explored to reproduce the experimental data.
    Keywords: Pyridine ; Adsorption ; Gamma-Alumina (Γ-Al 2o 3) ; Fluorinated Γ-Al 2o 3 ; Lewis Acid Adsorption Sites ; Heterogeneous Catalysis ; Non-Covalent Interactions ; Vibrational Frequency Shifts ; Chemistry ; Physics
    ISSN: 0039-6028
    E-ISSN: 1879-2758
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  • 9
    Language: English
    In: Journal of the American Chemical Society, 19 February 2014, Vol.136(7), pp.2757-66
    Description: The growing realization that photoinduced bending of slender photoreactive single crystals is surprisingly common has inspired researchers to control crystal motility for actuation. However, new mechanically responsive crystals are reported at a greater rate than their quantitative photophysical characterization; a quantitative identification of measurable parameters and molecular-scale factors that determine the mechanical response has yet to be established. Herein, a simple mathematical description of the quasi-static and time-dependent photoinduced bending of macroscopic single crystals is provided. This kinetic model goes beyond the approximate treatment of a bending crystal as a simple composite bilayer. It includes alternative pathways for excited-state decay and provides a more accurate description of the bending by accounting for the spatial gradient in the product/reactant ratio. A new crystal form (space group P21/n) of the photoresponsive azo-dye Disperse Red 1 (DR1) is analyzed within the constraints of the aforementioned model. The crystal bending kinetics depends on intrinsic factors (crystal size) and external factors (excitation time, direction, and intensity).
    Keywords: Light ; Mechanical Phenomena ; Models, Molecular ; Azo Compounds -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 10
    Language: English
    In: The journal of physical chemistry. A, 01 April 2010, Vol.114(12), pp.4354-63
    Description: The performance of some recently proposed DFT functionals by Truhlar's group (mPW1B95, mPWLYP1W, PBELYP1W, and PBE1W [Dahlke, E. E.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 317. Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 6908.]) was tested primarily with respect to computation of anharmonic vibrational frequency shifts upon hydrogen bond formation in small molecular/ionic dimers. Five hydrogen-bonded systems with varying hydrogen bond strengths were considered: methanol-fluorobenzene, phenol-carbon monoxide in ground neutral (S(0)) and cationic (D(0)) electronic states, phenol-acetylene, and phenol-benzene(+). Anharmonic OH stretching frequency shifts were calculated from the computed vibrational potentials for free and hydrogen-bonded proton-donor molecules. To test the basis set convergence properties, all calculations were performed with 6-31++G(d,p) and 6-311++G(2df,2pd) basis sets. The mPW1B95 functional was found to perform remarkably better in comparison to more standard functionals (such as B3LYP, mPW1PW91, PBE1PBE) in the case of neutral dimers. In the case of cationic dimers, however, this is not always the case. With respect to prediction of anharmonic OH stretching frequency shifts upon ionization of free phenol, all DFT levels of theory outperform MP2. Some other aspects of the functional performances with respect to computation of interaction and dissociation energies were considered as well.
    Keywords: Natural Sciences ; Chemical Sciences ; Theoretical Chemistry ; Naturvetenskap ; Kemi ; Teoretisk Kemi;
    ISSN: 10895639
    E-ISSN: 1520-5215
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