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ABSTRACT: The changes in structural ordering, packing entropy, free energy, and film morphologies in the initial nucleation processes of pentacene (Pn), 6, 13-bis(t-butylethynyl) pentacene (t-Bu Pn), and 6, 13-bis(triisopropylsilylethynyl) pentacene (TIPS Pn) on the SiO(2) substrate were investigated, by using the molecular dynamics simulations. During the nucleation, the rod-like Pn molecules tend to diffuse rapidly and have different orientations on the SiO(2) surface. At the low coverage, the t-Bu Pn and TIPS Pn molecules with the branched topological structures almost lie flat on the substrate. On the basis of statistical distribution of various packing configurations of the functionalized Pn pairs, the packing entropy is estimated according to the Boltzmann formula. The packing entropy abruptly decreases in the early stage of deposition. Once the critical nucleus size is reached, the packing entropy converges to a constant value. As the coverage increases, the monolayer films of Pn and its branched derivatives become more ordered. The TIPS Pn with the relatively larger molecular area would occasionally stand on the surface during the nucleation, resulting in the dramatic changes in free energy. In the monolayers, the functionalized Pn molecules are packing more orderly than those in amorphous solids, but less orderly than those in crystals. The degree of order of these monolayers increases as the size of the substituents increases. The understanding of substituent effects on nucleation processes and packing structures is helpful to fabricate organic thin films with well-predefined molecular orientations.
The Journal of chemical physics 08/2012; 137(7):074708. · 3.09 Impact Factor
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ABSTRACT: A multi-layer coarse-graining (CG) model is presented for treating the electrostatic interactions of solvated α-conotoxin peptides. According to the sensitivity to the electrostatic environment, a hybrid set of electrostatic parameters, such as secondary-structure- and residue-based dipoles, and atom-centered partial charges, are adopted. For the polarization "inert" secondary-structures and residues, the fragment dipole moments are distributed within narrow ranges with the magnitude close to zero. The coarse-graining fragment dipoles are parameterized from a large training set (10,000 configurations) to reproduce the electrostatic features of molecular fragments. In contrast, the electrostatically "sensitive" atoms exhibit large fluctuations of charges with the varied environments. The environment-dependent variable charges are updated in each energetic calculation. The electrostatic interaction of the whole chemical system is hence partitioned into several sub-terms coming from the fragment dipole-dipole, (fragment) dipole-(atom) charge, and atom charge-charge interactions. A large number of test calculations on the relative energies of cyclo-peptide conformers have demonstrated that the multi-layer CG electrostatic model presents better performance than the non-polarized force fields, in comparison with the density-functional theory and the fully polarized force field model. The selection of CG fragment centers, mass or geometric center, has little influence on the fragment-based dipole-dipole interactions. The multi-layer partition of electrostatic polarization is expected to be applied to many biologically interesting and complicated phenomena.
The Journal of chemical physics 04/2012; 136(13):134105. · 3.09 Impact Factor
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Journal of Computational Chemistry. 01/2012; 33:34-43.
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ABSTRACT: The double-cage fluorinated fullerene (C 20 F 18 (NH) 2 C 20 F 18) has been suggested to be a new kind of molecular quantum-dot cellular automata (MQCA) candidate. The possibility of noncovalently binding these candidate molecules on silver substrates is explored by molecular dynamics (MD) simulations. It is demonstrated that the candidate molecules can deposit on Ag(100) surface and form ordered MQCA arrays in both head-to-tail and side-by-side styles. The side-by-side array can keep intact even at room temperature, while the head-to-tail array shows larger thermal fluctuations. In comparison with the Ag(100) surface, ordered arrays can only be observed in the side-by-side style at low temperatures on Ag(111) surface. Density functional theory (DFT) calculations of the charge redistribution of the candidate, in response to an electrostatic driver, show that the QCA function of the candidate still maintains with the introduction of the Ag surface. In addition, a simple (Coulomb) electrostatic model is proposed to simulate the dynamical signal transmission in our MQCA wire. The transmission time is affected by the wire length as well as the long-range intercellular electrostatic interactions.
The Journal of Physical Chemistry C 01/2012; · 4.80 Impact Factor
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ABSTRACT: The photocyclization behavior and dynamic conformational transition of photochromic switches of diarythene derivatives in solutions are investigated by using the density functional theory (DFT) and molecular dynamics (MD) simulations. Three possible conformations, antiparallel (anti), parallel (para), and twist, for the open-ring isomers of 1,2-bis(2-methylbenzothiophene-3-yl)maleic anhydride are located. Both PCM-B3LYP/6-31G* calculations and MD simulations demonstrate that anti and twist open-ring isomers can interconvert freely in n-hexane and acetonitrile solutions at room temperature. The statistical ratio of twist to anti isomers from MD simulations is 2.09 in n-hexane and 1.07 in CH(3)CN, in qualitative agreement with those (1.18 in n-hexane and 1.05 in CH(3)CN) estimated from Arrhenius analysis of DFT activation energies. The solvent polarity has little influence on the isomerization of open-ring isomers in the ground state. Due to the evident charge transfer upon excitations, the solvent effects on the electronic structures and absorption spectra of low-lying excited states (S(1) and S(2)) are more significant. For such charge-transfer excited states, the long-range corrected functional CAM-B3LYP gives better agreement with the experimental spectra than B3LYP. The solvent polarity and polarization of the charge-transfer excited states are crucial for fabricating the novel functionalized photochromic molecular switches.
The Journal of Physical Chemistry A 12/2011; 116(3):913-23. · 2.95 Impact Factor
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ABSTRACT: a b s t r a c t The singlet–triplet energy gap of biradicals created in benzene and polyacenes is investigated by density-functional-theory calculations. For the biradicals in benzene, naphthalene, anthracene, tetracene, penta-cene, and hexacene, we find that the singlet state is energetically favored over the triplet state by 189, 191, 184, 199, 218, and 244 meV, respectively. The monotonous increase of the singlet–triplet energy gap from anthracene to hexacene is attributed to the enhanced stability of the singlet state for longer polyacenes. Our analysis shows that the spin density of the singlet state is delocalized over all benzene rings, but such a spin delocalization is not present for the triplet state.
Chemical Physics Letters 11/2011; · 2.34 Impact Factor
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ABSTRACT: The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.
Journal of Computational Chemistry 09/2011; 33(1):34-43. · 4.58 Impact Factor
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ABSTRACT: The influence of environments (THF solvents and electric field) and molecular self-aggregations on the structure and optical properties of 4-(4-hydroxyphenylazo)nitrobenzene has been investigated by molecular dynamics (MD) simulations and quantum chemical calculations. Long-range electrostatic effects and the hydrogen bond interactions between the solute and the THF solvent molecules lead to the augments of nonlinear optical (NLO) response by about two times from the gas phase to THF solution, accompanied by considerable red-shift of more than 40 nm in the maximum absorption wavelengths of the ground (S(0)) and low-lying excited states (S(1), S(2), and S(3)). The solvated chromophore reorients quickly (within 300 ps) under external electric field of 1.0 V/nm, even when the direction of the applied electric field is antiparallel to the dipole moment of the solute. Nonequilibrium MD simulations demonstrate that the light-induced cis-trans isomerization in THF solution and external electric field need longer relaxation time (about 1.0 ps) than that in gas phase (about 500 fs). The dipole-dipole interactions and intermolecular hydrogen bonds facilitate the self-aggregations of solute molecules in solution. The V-shaped dimer exhibits higher hyperpolarizability value by about 1.2 times of the monomer, whereas the antiparallel alignment leads to a cancellation of dipole moment and hence dramatic decrease in hyperpolarizability (one-third of the monomer). However, the Boltzmann-weighted contribution to hyperpolarizability from these two aggregations (with 82% V-shaped and 18% antiparallel) is close to that of the monomer. Orientations of D-π-A dipoles in various environments and molecular aggregations are important to modulate the optical properties of materials.
The Journal of Physical Chemistry A 08/2011; 115(36):10136-45. · 2.95 Impact Factor
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ABSTRACT: The proton-binding behavior of solvated tetraamido/diamino quaternized macrocyclic compounds with rigid phenyl and flexible phenyl bridges in the absence or presence of an external electric field is investigated by molecular dynamics simulation. The proton can be held through H-bonding interactions with the two carbonyl oxygen atoms in macrocycles containing rigid (phenyl) and flexible (propyl) bridges. The solute-solvent H-bonding interactions cause the macrocyclic backbones to twist to different extents, depending on the different bridges. The macrocycle with the rigid phenyl linkages folds into a cuplike shape due to π-π interaction, while the propyl analogue still maintains the ellipsoidal ringlike shape with just a slight distortion. The potential energy required for proton transfer is larger in the phenyl-containing macrocycle than in the compound with propyl units. When an external electric field with a strength of 2.5 V nm(-1) is exerted along the carbonyl oxygen atoms, a difference in proton encircling is exhibited for macrocycles with rigid and flexible bridges. In contrast to encapsulation of a proton in the propyl analogue, the intermolecular solute-solvent H-bonding and intramolecular π-π stacking between the two rigid phenyl spacers leads to loss of the proton from the highly distorted cuplike macrocycle with phenyl bridges. The competition between intra- and intermolecular interactions governs the behavior of proton encircling in macrocycles.
ChemPhysChem 08/2011; 12(13):2453-60. · 3.41 Impact Factor
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ABSTRACT: A new type of molecular quantum-dot cellular automata (MQCA) candidates is suggested using the double-cage fluorinated fullerene molecules, e(-)@C(20)F(18)(XH)(2)C(20)F(18) (X = N, B), which have bistable charge configurations that could be used to encode binary information. The electron switch between the two cages leads to the QCA function.
Physical Chemistry Chemical Physics 08/2011; 13(36):16134-7. · 3.57 Impact Factor
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ABSTRACT: Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.
The Journal of chemical physics 08/2011; 135(5):054504. · 3.09 Impact Factor
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ABSTRACT: Simulations of vibrational circular dichroism (VCD) spectroscopy of optical active aggregates of chiral molecules in the amorphous solid encounter great difficulties in the description of complicated intermolecular interactions by using the conventional quantum mechanical (QM) methods. The fragmentation approach is applied to calculate the VCD spectra of the covalently bonded oligomers and nonbonded molecular aggregates of (S)-alternarlactam, a new fungal cytotoxin with cyclopentenone and isoquinolinone scaffolds. Starting from the statistically averaged configurations that are sampled from the molecular dynamic simulations, the target oligomers or packing systems are divided into several fragments with a proper treatment of boundary effects on the separated segments. Each fragment is embedded in the background point charges centered on the distant atoms to simulate the long-range electrostatic interactions. The total VCD signals are assembled from the rotational strength of all the fragments. Test calculations on the σ-bonded oligomers and molecular aggregates using fragmentation method show good agreement with the conventional QM results. The packing effects on the infrared (IR) absorption and VCD spectroscopies of amorphous (S)-alternarlactam solid are investigated with density of 0.5 and 0.8 g/cm(3), respectively. The fragment-based VCD calculations on (S)-alternarlactam aggregates give a better agreement with experimental spectra than the Boltmann-weighted spectra of various possible monomeric, dimeric, and trimeric configurations. Hydrogen-bonded networks are the dominant packing configurations at the density of 0.5 g/cm(3). The (C═)O···H-N hydrogen-bonding interactions result in the signal splitting of IR and VCD spectra at the C═O stretching vibrational regions. When the density is increased to 0.8 g/cm(3), π-π stacking turns to be the dominating intermolecular interaction pattern. The computational cost of fragmentation calculation scales linearly with the number of the molecular fragments, facilitating the future applications to a wide range of the large-sized chiral systems.
The Journal of Physical Chemistry B 03/2011; 115(12):2801-13. · 3.70 Impact Factor
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Journal of Physical Organic Chemistry 10/2010; 24(7):568 - 577. · 1.96 Impact Factor
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ABSTRACT: The lying-down and standing-up CuPc and F(16)CuPc films on HOPG (highly ordered pyrolytic graphite) and C8-SAM/Au(111) (octane-1-thiol terminated Au(111)) substrates are investigated by using a hybrid strategy combing the molecular dynamic (MD) simulations with density functional theory (DFT) calculations, in order to understand the influence of packing orientation on charge carrier mobilities. On the basis of the periodic slab model and consistent-valence force field, MD simulations show the populations of various packing configurations and radial distribution of intermolecular distance in the films at room temperature. It is also demonstrated that the external electric field (parallel or perpendicular to the substrate) perturbs the intermolecular distances in CuPc and F(16)CuPc films, especially for the slipped edge-to-face stackings. DFT calculations are then used to evaluate two key charge-transfer parameters, reorganization energy and transfer integral. An electrostatics embedding model is employed to approximately consider the external electrostatics contributions to reorganization energy. The thermal-averaged mobility is consequently estimated by taking account of both electronic structures of charge-hopping pairs and dynamic fluctuations in film morphologies under various experimental conditions. It is found that CuPc has smaller reorganization energy and larger hole (electron) mobilities than F(16)CuPc. Under the external electric field of 10(4)-10(7) V cm(-1), both hole and electron mobilities of CuPc and F(16)CuPc films would decrease to 1-3 orders of magnitude. CuPc (F(16)CuPc) films show substantial orientation dependence of mobilities on the ratio of standing-up versus lying-down orientations falling in the range of 10-1000.
Physical Chemistry Chemical Physics 10/2010; 12(38):12177-87. · 3.57 Impact Factor
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ABSTRACT: (-)-Alternarlactam [(-)-1], a new promising cytotoxin against two human cancer cell lines, was isolated from an endophyte culture and synthesized (along with (+)-1) from readily available starting materials. The absolute configuration, chirality-activity relevance and self-aggregation of (-)-1 were assigned by a combination of synthetic, spectroscopic and computational approaches. The full characterization of the new fungal cytotoxin may provide valuable information in the discovery of new antitumor agents.
Chemistry 10/2010; 16(48):14479-85. · 5.93 Impact Factor
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ABSTRACT: The roles of the disulfide bridge, electrostatics, and hydrophobic/hydrophilic effects in the structural stability and conformational changes of six single-disulfide analogues of alpha-conotoxin GI(2-7;3-13) in aqueous solution are investigated by using molecular dynamics simulations with a fragment-based polarization model (J. Phys. Chem. A 2008, 112, 9854.). It is found that the relative stabilities are largely determined by the dipole-dipole interactions between secondary structure-based fragments, revealing the favorable effect of polar residues on conformational stabilities. The loop size closely correlates to not only the thermodynamic stability but also the local geometry of disulfide bridge. The disulfide loops with no more than five residues [GI(2-7), GI(3-7), and GI(7-13)] choose the left-handed disulfide conformation, while the larger loops [with nine and 10 residues in GI(3-13) and GI(2-13)] and a smaller disulfide loop [GI(2-3) without intercysteine residue] prefer the right-handed configuration. In the left-handed analogues, the dihedral angles concerning disulfide bonds decrease subtly along with the enlargement of disulfide loops. A converse dihedral angle and loop size relationship is found in the right-handed isomers. These results are rationalized by the strain energy of the disulfide bond as well as the electrostatic and van der Waals interactions between cysteine pairs. The single-disulfide analogues also exhibit much higher conformational diversity than the native GI. The important role of the size of hydrophobic core in the conformational evolution is also demonstrated in terms of the radius of gyration of the hydrophobic region. The radial distribution functions show the significant solvent-solute hydrogen bonding, implying that the interplay between the intermolecular and the intramolecular interactions control the dynamic process of GI single-disulfide analogues.
The Journal of Physical Chemistry B 09/2010; 114(34):11241-50. · 3.70 Impact Factor
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ABSTRACT: Two novel resveratrol aneuploids, hopeachinols A (1) and B (2), as well as a potent immunosuppressive polyphenol diptoindonesin G (3) were characterized from the ethanol extract of Hopea chinensis stem barks. The structure of the polyphenols was accommodated by comprehensive spectroscopic analysis with the absolute stereochemistry determined by the CD approach coupled with theoretical ECD spectra computer-generated through the Gaussian 03 program. The distinct structure and biological profile of 3 recommended it as a starting molecule for the relevant drug discovery.
Chemistry 06/2010; 16(21):6338-45. · 5.93 Impact Factor
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ABSTRACT: Three new phloroglucinols, named lysidicins F-H (1-3), were isolated from the roots of Lysidice rhodostegia. These compounds have a unprecedented benzyl benzo[b]furo[3,2-d]furan skeleton, and lysidicin F (1) is the first example of natural product with trans-fused furan rings. Their structures were established on the basis of extensive spectroscopic analysis, and the absolute configurations of them were determined by computational methods. A possible biosynthetic pathway for 1-3 was also postulated.
Organic Letters 05/2010; 12(10):2390-3. · 5.86 Impact Factor
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ABSTRACT: A local contracted single and double configuration interaction (LC-CISD) method, which introduces contracted singly and doubly excited vectors within the framework of bond functions, has been recently proposed [P. Reinhardt et al., J. Chem. Phys. 129, 164106 (2008)]. The present work improves this method by introducing a coupled-electron pair approximation (CEPA-3) dressing and by incorporating the leading part of linked effects of triples (T) and quadruples (Q) through a series of local four-electron full CI calculations. Two different ways have been adopted to incorporate this linked TQ effect. One consists of dressing the first column/line of the whole LC-CISD matrix. The other one introduces an additional contracted wave function responsible for the linked effect for each bond pair. The present LC-CEPA-3+TQ treatments have been applied to the evaluation of equilibrium bond lengths and harmonic frequencies of diatomic molecules (HF, BF, CuH, N(2), F(2), and Cl(2)) and single bond breaking in HF, CH(4), ClCH(3), ClSiH(3), n-butane, and F(2) molecules, symmetrical stretching of the two OH bonds in a water molecule, and symmetrical expansion of a triangular Be(3) cluster. The results show that the performance of the LC-CEPA-3+TQs compares favorably with coupled-cluster singles and doubles (CCSD) and CCSD(T) methods, presenting similar behaviors around equilibrium and better ones for stretched geometries. The LC-CEPA-3 method is strictly separable, and the size consistency error of our treatment of triples and quadruples is extremely small. The strict separability can be further achieved by dressing the doubly excited bond functions with the linked TQ effect. The efficiency of truncations on the bielectronic integrals has also been tested.
The Journal of chemical physics 01/2010; 132(3):034108. · 3.09 Impact Factor
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ABSTRACT: Over the last three decades the rational design of diradicals has been a challenging issue because of their special features and activities in organic reactions and biological processes. The orbital phase theory has been developed for understanding the properties of diradicals and designing new candidates for synthesis. The orbital phase is an important factor in promoting the cyclic orbital interaction. When all of the conditions: (1) the electron-donating orbitals are out of phase; (2) the accepting orbitals are in phase; and (3) the donating and accepting orbitals are in phase, are simultaneously satisfied, the system is stabilized by the effective delocalization and polarization. Otherwise, the system is less stable. According to the orbital phase continuity requirement, we can predict the spin preference of π-conjugated diradicals and relative stabilities of constitutional isomers. Effects of the intramolecular interaction of bonds and unpaired electrons on the spin preference, thermodynamic and kinetic stabilities of the singlet and triplet states of localized 1,3-diradicals were also investigated by orbital phase theory. Taking advantage of the ring strains, several monocyclic and bicyclic systems were designed with appreciable singlet preference and kinetic stabilities. Substitution effects on the ground state spin and relative stabilities of diradicals were rationalized by orbital interactions without loss of generality. Orbital phase predictions were supported by available experimental observations and sophisticated calculation results. In comparison with other topological models, the orbital phase theory has some advantages. Orbital phase theory can provide a general model for both π-conjugated and localized diradicals. The relative stabilities and spin preference of all kinds of diradicals can be uniformly rationalized by the orbital phase property. The orbital phase theory is applied to the conformations of diradicals and the geometry-dependent behaviors. The insights gained from the orbital phase theory are useful in a rational design of stable 1,3-diradicals.
Topics in current chemistry 01/2010; 289:219-63. · 4.29 Impact Factor
