Artem Eduardovich Masunov
Publications
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Alternative Packing Modes Leading to Amyloid Polymorphism in Five Fragments Studied With Molecular Dynamics
Peptide Science. 01/2012;
wileyonlinelibrary.com). DOI 10.1002/bip.21731 This article was originally published online as an accepted preprint. The ''Published Online'' date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@w... [more] wileyonlinelibrary.com). DOI 10.1002/bip.21731 This article was originally published online as an accepted preprint. The ''Published Online'' date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com INTRODUCTION
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2.34Impact points
Unique example of amyloid aggregates stabilized by mainchain H-bond instead of the steric zipper: moleculardynamics study of the amyloidogenic segment of amylinwild-type and mutants
Journal of Molecular Modeling. 01/2012;
Most proteins do not aggregate while in their native functional states. However, they may be disturbed from their native conformation by certain change in the environment, and form unwanted oligomeric or polymeric aggregates. Recent experimental data demonstrate that soluble oligomers of amyloidogen... [more] Most proteins do not aggregate while in their native functional states. However, they may be disturbed from their native conformation by certain change in the environment, and form unwanted oligomeric or polymeric aggregates. Recent experimental data demonstrate that soluble oligomers of amyloidogenic proteins are responsi-ble for amyloidosis and its cytotoxicity. Human islet amyloid polypeptide (IAPP or amylin) is a 37-residue hormone found as fibrillar deposits in pancreatic extracts of nearly all type II diabetics. In this study we performed in silico mutation analysis to examine the stability of the double layer five strand aggregates formed by heptapeptide NNFGAIL segment from amyline peptide. This segment is one of the shortest fragments that can form amyloid fibrils similar to those formed by the full length peptide. The mutants obtained by single glycine replacement were also studied to investigate the specificity of the dry self-complementary interface between the neighboring β-sheet layers. The molecular dynamics simulations of the aggre-gates run for 20 ns at 330 K, the degree of the aggregate disassembly was investigated using several geometry analysis tools: the root mean square deviations of the C α atoms, root mean square fluctuations per residue, twist angles, interstrand distances, fraction of the secondary structure elements, and number of H-bonds. The analysis shows that most mutations make the aggregates unstable, and their stabilities were dependent to a large extent on the position of replaced residues. Our mutational simu-lations are in agreement with the pervious experimental observations. We also used free binding energy calcu-lations to determine the role of different components: nonpolar effects, electrostatics and entropy in binding. Nonpolar effects remained consistently more favorable in wild type and mutants reinforcing the importance of hydrophobic effects in protein-protein binding. While entropy systematically opposed binding in all cases, there was no clear trend in the entropy difference between wildtype and glycine mutants. Free energy decomposi-tion shows residues situated at the interface were found to make favorable contributions to the peptide-peptide association. The study of the wild type and mutants in an explicit solvent could provide valuable insight into the future computer guided design efforts for the amyloid aggregation inhibitor. Keywords Aggregation . Amylin . Amyloid fibril . β sheet . Binding free energy . Cross-β structure . Hydrogen bond . MM-PBSA . Molecular dynamic simulation . NNFGAIL . Oligomer . Secondary structure Introduction
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2.61Impact points
Alternative packing modes leading to amyloid polymorphism in five fragments studied with molecular dynamics.
Biopolymers. 10/2011;
Amyloid aggregates have been implicated in the pathogenesis of diseases such as type 2 diabetes, Alzheimer's, Parkinson's and prion disease. Recently determined microcrystal structures of several short peptide segments derived from fibril-forming proteins revealed co-existence of alternative... [more] Amyloid aggregates have been implicated in the pathogenesis of diseases such as type 2 diabetes, Alzheimer's, Parkinson's and prion disease. Recently determined microcrystal structures of several short peptide segments derived from fibril-forming proteins revealed co-existence of alternative aggregation modes (amyloid polymorphism) formed by the same segment. This polymorphism may help in understanding the influence of the side chain packing on the amyloid stability. Here we use Molecular Dynamics (MD) simulation to analyze the stability of five pairs of polar and nonpolar polymorphic oligomers. MD simulation shows polymorphs with steric zipper interface containing large polar and/or aromatic side chains (GNNQQNY, and NNQNTF) are more stable than steric zipper interfaces made of small or hydrophobic residues (SSTNGVG, VQIVYK, and MVGGVV). Several geometric analyses revealed that larger sheet to sheet interface of the dry steric zipper through polar Q/N rich side chains holds the sheets together. Mutant simulations (Q/N→G) show substitutions with glycine disrupt the steric zipper, leading to unstable oligomers. Stability of Q/N rich oligomers was found to result from the large average number of hydrogen bonds. The molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method reports the nonpolar component of free energy to be favorable, while electrostatic solvation is unfavorable for β-sheet association. Knowledge of structural properties of these fibrils might be useful for developing therapeutic agents against amyloidoses as well as for developing biomaterials. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2011.
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2.61Impact points
Molecular dynamic simulation of wild type and mutants of the polymorphic amyloid NNQNTF segments of elk prion: structural stability and thermodynamic of association.
Biopolymers. 03/2011; 95(9):573-90.
A hexapeptide with amino acid sequence NNQNTF from the elk prion protein forms amyloid fibrils. Here we use molecular dynamic simulations of the oligomers and their single point glycine mutants to study their stability. In an effort to probe the structural stability and association thermodynamic in ... [more] A hexapeptide with amino acid sequence NNQNTF from the elk prion protein forms amyloid fibrils. Here we use molecular dynamic simulations of the oligomers and their single point glycine mutants to study their stability. In an effort to probe the structural stability and association thermodynamic in a realistic environment, all wildtype of NNQNTF polymorphic forms with different size and their corresponding double layer 5 strands single point glycine mutants were subjected to a total of 500 ns of explicit-solvent molecular dynamics (MD) simulation. Our results show that the structural stability of the NNQNTF oligomers increases with increasing the number of β-strands for double layers. Our results also demonstrated that hydrophobic interaction is the principle driving force to stabilize the adjacent β-strands while the steric zipper is responsible for holding the neighboring β-sheet layers together. We used MM-PBSA approach free energy calculations to determine the role of nonpolar effects, electrostatics and entropy in binding. Nonpolar effects remained consistently more favorable in wild type and mutants reinforcing the importance of hydrophobic effects in protein-protein binding. While entropy systematically opposed binding in all cases, there was no observed trend in the entropy difference between wildtype and glycine mutant. Free energy decomposition shows residues situated at the interface were found to make favorable contributions to the peptide-peptide association. The study of the wild type and mutants in an explicit solvent may provide valuable insight for amyloid aggregation inhibitor design efforts.
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2.34Impact points
Near-field enhancement of infrared intensities for f-f transitions in Er3+ ions close to the surface of silicon nanoparticles.
Journal of molecular modeling. 03/2011; 17(3):423-8.
Erbium doped waveguide amplifiers can be used in optical integrated circuits to compensate for signal losses. Such amplifiers use stimulated emission from the first excited state ((4) I (13/2)) to the ground state ((4) I (15/2)) of Er(3+) at 1.53 µm, the standard wavelength for optical communication... [more] Erbium doped waveguide amplifiers can be used in optical integrated circuits to compensate for signal losses. Such amplifiers use stimulated emission from the first excited state ((4) I (13/2)) to the ground state ((4) I (15/2)) of Er(3+) at 1.53 µm, the standard wavelength for optical communication. Since the intra-f transitions are parity forbidden for free Er(3+) ions, the absorption and the emission cross sections are quite small for such doped amplifiers. To enhance the absorption, Si nanoclusters can be embedded in silica matrix. Here we investigate the effect of the Si nanocluster on the Er(3+) emission using ab initio theory for the first time. We combine multi-reference configuration interaction with one-electron spin-orbit Hamiltonian and relativistic effective core potentials. Our calculations show that the presence of a polarizable Be atom at 5Ǻ from the Er(3+) ion in a crystalline environment can lead to an enhancement in the emission by a factor of three. The implications of this effect in designing more efficient optical gain materials are discussed.
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2.34Impact points
Can molecular dynamics simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN Steric zipper
Journal of Molecular Modeling. 01/2011; 17(17:2423–2442):2423--2442.
The aggregation modes of hexapeptide fragments of Tau, Insulin and Aβ peptide (VQIVYK, MVGGVV and LYQLEN) were found from their microcrystalline struc-tures that had been recently resolved by X-ray analysis. The atomic structures reveal a dry self-complementary interface between the neighboring β-sh... [more] The aggregation modes of hexapeptide fragments of Tau, Insulin and Aβ peptide (VQIVYK, MVGGVV and LYQLEN) were found from their microcrystalline struc-tures that had been recently resolved by X-ray analysis. The atomic structures reveal a dry self-complementary interface between the neighboring β-sheet layers, termed "steric zipper". In this study we perform several all-atom molec-ular dynamics simulations with explicit water to analyze stability of the crystalline fragments of 2-10 hexapeptides each and their analogs with single glycine replacement mutations to investigate the structural stability, aggregation behavior and thermodynamic of the amyloid oligomers. Upon comparing single and double layer models, our results reveal that additional strands contribute significantly to the structural stability of the peptide oligomers for double layer model, while in the case of single layer model the stability decreases (or remains the same in the case of LYQLEN). This is in agreement with the previous studies performed on different types of amyloid models. We also replaced the side-chains participating in the steric zipper interfaces with glycine. None of the mutants were structur-ally stable compared to the respective wild type model, except for mutants V2G and V6G in MVGGVV2 case. The exception can be explained by structural features of this particular polymorph. The double layer decamer and dodecamer aggregates of the wild type hexapeptides appear to be stable at 300K, which is confirmed by the conservation of high anti-parallel β-sheet content through-out the whole simulation time. Deletions of the side chains resulted in decline of secondary structure content compared to corresponding wild type indicating that the role of the replaced amino acid in stabilizing the structure. Detailed analysis of the binding energy reveals that stability of these peptide aggregates is determined mainly by the van der Waals and hydrophobic forces that can serve as quantitative measure of shape complementarities between the side chains. This observation implies that interactions among side chains forming the dehydrated steric zipper, rather than among those exposed to water, are the major structural determinant. The electrostatic repulsion destabilizes the studied double layer aggregates in two cases, while stabilizes the other two. Negative total binding free energy indicates that both wild type and mutants complex formation is favorable. However, the mutants complexation is less favorable than the wild type's. The present study provides the atomic level understanding of the aggregation behavior and the driving force for the amyloid aggregates, and could be useful for rational design of amyloid inhibitors and amyloid-specific biomarkers for diagnostic purposes. Keywords Aggregation . Amyloid fibril . β sheet . Binding free energy . Cross-β structure . MM-PBSA . Molecular dynamic simulation . Oligomer . Secondary structure .
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5.44Impact points
Phosphate ester hydrolysis of biologically relevant molecules by cerium oxide nanoparticles.
Nanomedicine : nanotechnology, biology, and medicine. 12/2010; 6(6):738-44.
In an effort to characterize the interaction of cerium oxide nanoparticles (CNPs) in biological systems, we explored the reactivity of CNPs with the phosphate ester bonds of p-nitrophenylphosphate (pNPP), ATP, o-phospho-l-tyrosine, and DNA. The activity of the bond cleavage for pNPP at pH 7 is calcu... [more] In an effort to characterize the interaction of cerium oxide nanoparticles (CNPs) in biological systems, we explored the reactivity of CNPs with the phosphate ester bonds of p-nitrophenylphosphate (pNPP), ATP, o-phospho-l-tyrosine, and DNA. The activity of the bond cleavage for pNPP at pH 7 is calculated to be 0.860 ± 0.010 nmol p-nitrophenol/min/μg CNPs. Interestingly, when CNPs bind to plasmid DNA, no cleavage products are detected. While cerium(IV) complexes generally exhibit the ability to break phosphorus-oxygen bonds, the reactions we report appear to be dependent on the availability of cerium(III) sites, not cerium(IV) sites. We investigated the dephosphorylation mechanism from the first principles and find the reaction proceeds through inversion of the phosphate group similar to an S(N)2 mechanism. The ability of CNPs to interact with phosphate ester bonds of biologically relevant molecules has important implications for their use as potential therapeutics.
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3.09Impact points
Thermally controlled preferential molecular aggregation state in a thiacarbocyanine dye.
The Journal of chemical physics. 10/2010; 133(13):134508.
Herein we report the experimental and theoretical study of the temperature dependence of a thiacarbocyanine dye in its monomer, H- and J-aggregates states. We demonstrate the ability to control the ratio of monomer, H- and/or J-aggregates with heat. We link such a control to the conformation depende... [more] Herein we report the experimental and theoretical study of the temperature dependence of a thiacarbocyanine dye in its monomer, H- and J-aggregates states. We demonstrate the ability to control the ratio of monomer, H- and/or J-aggregates with heat. We link such a control to the conformation dependence of the molecule. An alternative way to gain access to the dominating species without changing the concentration as a complete switching mechanism between all the present species is proposed. The results presented in this work lead to a better understanding of thiacarbocyanine dye's behavior.
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3.47Impact points
Fluorene-based metal-ion sensing probe with high sensitivity to Zn2+ and efficient two-photon absorption.
The journal of physical chemistry. B. 07/2010; 114(28):9313-21.
The photophysical, photochemical, two-photon absorption (2PA) and metal ion sensing properties of a new fluorene derivative (E)-1-(7-(4-(benzo[d]thiazol-2-yl)styryl)-9,9-bis(2-(2-ethoxyethoxy)ethyl)-9H-fluoren-2-yl)-3-(2-(9,10,16,17,18,19,21,22,23,24-decahydro-6H dibenzo[h,s][1,4,7,11,14,17]trioxatr... [more] The photophysical, photochemical, two-photon absorption (2PA) and metal ion sensing properties of a new fluorene derivative (E)-1-(7-(4-(benzo[d]thiazol-2-yl)styryl)-9,9-bis(2-(2-ethoxyethoxy)ethyl)-9H-fluoren-2-yl)-3-(2-(9,10,16,17,18,19,21,22,23,24-decahydro-6H dibenzo[h,s][1,4,7,11,14,17]trioxatriazacycloicosin-20(7H)-yl)ethyl)thiourea (1) were investigated in organic and aqueous media. High sensitivity and selectivity of 1 to Zn(2+) in tetrahydrofuran and a water/acetonitrile mixture were shown by both absorption and fluorescence titration. The observed complexation processes corresponded to 1:1 stoichiometry with the range of binding constants approximately (2-3) x 10(5) M(-1). The degenerate 2PA spectra of 1 and 1/Zn(2+) complex were obtained in the 640-900 nm spectral range with the maximum values of two-photon action cross section for ligand/metal complex approximately (90-130) GM, using a standard two-photon induced fluorescence methodology under femtosecond excitation. The nature of the 2PA bands was analyzed by quantum chemical methods and a specific dependence on metal ion binding processes was shown. Ratiometric fluorescence detection (420/650 nm) provided a good dynamic range (10(-4) to 10(-6) M) for detecting Zn(2+), which along with the good photostability and 2PA properties of probe 1 makes it a good candidate in two-photon fluorescence microscopy imaging and sensing of Zn ions.
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3.09Impact points
Weak antiferromagnetic coupling in molecular ring is predicted correctly by density functional theory plus Hubbard U.
The Journal of chemical physics. 06/2010; 132(24):244104.
We apply density functional theory with empirical Hubbard U parameter (DFT+U) to study Mn-based molecular magnets. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the s... [more] We apply density functional theory with empirical Hubbard U parameter (DFT+U) to study Mn-based molecular magnets. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to pi-back bonding, inverting spin polarization of the acetate oxygen atoms relative to that predicted from superexchange mechanism. This inversion may affect the performance of the models that assume strict localization of the spins on magnetic centers for the complexes with bridging acetate ligands. Next, we apply DFT+U methodology to Mn(12) molecular wheel and find antiparallel spin alignment for the weakly interacting fragments Mn(6), in agreement with experimental observations. Using the optimized geometry of the ground spin state instead of less accurate experimental geometry was found to be crucial for this good agreement. The protocol tested in this study can be applied for the rational design of single molecule magnets for molecular spintronics and quantum computing applications.
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2.28Impact points
Natural polyphenols as inhibitors of amyloid aggregation. Molecular dynamics study of GNNQQNY heptapeptide decamer.
Biophysical chemistry. 06/2010; 149(1-2):12-21.
Amyloid-like fibrils had been associated with many fatal diseases, and the rational design of the fibrillization inhibitors holds the great promise of finding the prevention and treatment options. The understanding of the mechanisms by which the small molecules can inhibit the aggregation plays the ... [more] Amyloid-like fibrils had been associated with many fatal diseases, and the rational design of the fibrillization inhibitors holds the great promise of finding the prevention and treatment options. The understanding of the mechanisms by which the small molecules can inhibit the aggregation plays the key role in such design. Here we present the results of MD simulations that provide the atomistic details of the process, by which the small molecules may destabilize the ordered amyloid oligomers formed by the model hexapeptide. We select a heptapeptide fragment (GNNQQNY) from Sup-35 yeast prion protein, which is capable to form both amyloid fibrils and microcrystals. Atomic-resolution structures of its crystals were reported by Eisenberg et al. (Nature 447:453, 2007). We analyze several MD trajectories describing the evolution of the decamer fragment taken from this crystal structure, both by itself and in the presence of myricetin and kaempferol (two naturally occurring polyphenols, found to be strong and weak aggregation inhibitors). While the decamer of GNNQQNY demonstrates remarkable stability of its structure after 2ns simulation, myricretin disturbs the aggregation. The simulations show myricetin interacts with the beta-sheet due to polar interactions with side chains of the peptide weakening the interstrand hydrogen bonds, wrapping the beta-sheet and disaggregating the outer layer. Both backbone to backbone and side chain to side chain hydrogen bonds are lost, and the beta-sheets are moving away from each other. This leads to the loss of backbone H-bonding and eventual separation of one beta-strands from the outer layer. We also test several AMBER force fields and implicit solvent models for their ability to keep the decamer of GNNQQNY aggregated. The RMSDs of decamer of GNNQQNY with force field 99SB and implicit solvent models of igb2 and igb5, were maintained at less than 4A.
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3.90Impact points
Tuning hydrated nanoceria surfaces: experimental/theoretical investigations of ion exchange and implications in organic and inorganic interactions.
Langmuir : the ACS journal of surfaces and colloids. 05/2010; 26(10):7188-98.
Long-term stability and surface properties of colloidal nanoparticles have significance in many applications. Here, surface charge modified hydrated cerium oxide nanoparticles (CNPs, also known as nanoceria) are synthesized, and their dynamic ion exchange interactions with the surrounding medium are... [more] Long-term stability and surface properties of colloidal nanoparticles have significance in many applications. Here, surface charge modified hydrated cerium oxide nanoparticles (CNPs, also known as nanoceria) are synthesized, and their dynamic ion exchange interactions with the surrounding medium are investigated in detail. Time-dependent zeta (zeta) potential (ZP) variations of CNPs are demonstrated as a useful characteristic for optimizing their surface properties. The surface charge reversal of CNPs observed with respect to time, concentration, temperature, and doping is correlated to the surface modification of CNPs in aqueous solution and the ion exchange reaction between the surface protons (H(+)) and the neighboring hydroxyls ions (OH(-)). Using density functional theory (DFT) calculations, we have demonstrated that the adsorption of H(+) ions on the CNP surface is kinetically more favorable while the adsorption of OH(-) ions on CNPs is thermodynamically more favorable. The importance of selecting CNPs with appropriate surface charges and the implications of dynamic surface charge variations are exemplified with applications in microelectronics and biomedical.
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2.34Impact points
Density functional study of oxygen vacancy formation and spin density distribution in octahedral ceria nanoparticles.
Journal of molecular modeling. 03/2010; 16(10):1617-23.
We report plane wave basis density functional theory (DFT) calculations of the oxygen vacancies formation energy in nanocrystalline CeO2-x in comparison with corresponding results for bulk and (111) CeO2 surface. Effects of strong electronic correlation of Ce4f states are taken into account through ... [more] We report plane wave basis density functional theory (DFT) calculations of the oxygen vacancies formation energy in nanocrystalline CeO2-x in comparison with corresponding results for bulk and (111) CeO2 surface. Effects of strong electronic correlation of Ce4f states are taken into account through the use of an effective on-site Coulomb repulsive interaction within DFT+U approach. Different combinations of exchange-correlation functionals and corresponding U values reported in the literature are tested and the obtained results compared with experimental data. We found that both absolute values and trends in oxygen vacancy formation energy depend on the value of U and associated with degree of localization of Ce4f states. Effect of oxygen vacancy and geometry optimization method on spatial spin distribution in model ceria nanoparticles is also discussed.
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2.34Impact points
Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?
Journal of Molecular Modeling. 01/2010;
We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (α, β and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* a... [more] We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (α, β and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conforma-tional changes for peptides during amyloid formation. Keywords Polyglutamic acid . Assignment of Raman spectra . Density function theory . Conformational transition . Amide vibrational band . Peptide conformational change Introduction
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2.34Impact points
Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?
Journal of molecular modeling. 11/2009;
We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (alpha, beta and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6... [more] We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (alpha, beta and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.
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2.90Impact points
Electronic Hyperpolarizabilities for Donor-Acceptor Molecules with Long Conjugated Bridges: Calculations versus Experiment.
The journal of physical chemistry. A. 09/2009;
We investigate the molecular first hyperpolarizability (beta) for donor/acceptor (D/A) substituted pi-conjugated organic molecules with different D/A groups and pi-systems (including up to eight pi-bonds). The results of the MP2 and density functional theory (PBE0, BMK, M05, M05-2X) calculations are... [more] We investigate the molecular first hyperpolarizability (beta) for donor/acceptor (D/A) substituted pi-conjugated organic molecules with different D/A groups and pi-systems (including up to eight pi-bonds). The results of the MP2 and density functional theory (PBE0, BMK, M05, M05-2X) calculations are compared to those obtained from experimental data. The goal of this study is to select a protocol with optimal quality/cost ratio to be used for systematic prediction of molecular nonlinear optical (NLO) properties. This goal is closely related to the way in which theoretical betas are compared to experimental ones and to the accuracy and consistency of experimental hyperpolarizabilities used to test theoretical predictions. We found that two DFT functionals with the larger fraction of Hartree-Fock exchange (BMK and especially M05-2X) provide the best agreement to the experiment, comparable to that of the MP2 method. Due to high computational cost of MP2 method, we recommend to use the M05-2X functional as a tool for systematic prediction of molecular hyperpolarizabilities.
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2.90Impact points
Theoretical Study of Photochromic Compounds. 1. Bond Length Alternation and Absorption Spectra for the Open and Closed Forms of 29 Diarylethene Derivatives.
The journal of physical chemistry. A. 08/2009;
We apply several exchange-correlation functionals in combination with time-dependent density functional theory to predict the maximum wavelengths in the absorption spectra for 29 diarylethene derivatives in both open and closed isomeric forms. Solvent effects and accurate molecular geometries are fo... [more] We apply several exchange-correlation functionals in combination with time-dependent density functional theory to predict the maximum wavelengths in the absorption spectra for 29 diarylethene derivatives in both open and closed isomeric forms. Solvent effects and accurate molecular geometries are found to be important to obtain good agreement with experimental absorption wavelengths. In order to evaluate the quality of geometry optimization, we compare predicted bond length alternation parameters with experimental ones. We find the TD-M05/6-31G*/PCM//M05-2x/6-31G*/PCM theory level to give the best predictions for the structural and spectral parameters of the diarylethene derivatives. Applications of the photochromic diarylethene compounds as materials for optical switching and data storage based on their photocyclization properties are also discussed.
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3.09Impact points
Quantum chemistry of quantum dots: effects of ligands and oxidation.
The Journal of chemical physics. 08/2009; 131(4):044106.
We report Gaussian basis set density functional theory (DFT) calculations of the structure and spectra of several colloidal quantum dots (QDs) with a (CdSe)(n) core (n=6,15,17), that are either passivated by trimethylphosphine oxide ligands, or unpassivated and oxidized. From the ground state geomet... [more] We report Gaussian basis set density functional theory (DFT) calculations of the structure and spectra of several colloidal quantum dots (QDs) with a (CdSe)(n) core (n=6,15,17), that are either passivated by trimethylphosphine oxide ligands, or unpassivated and oxidized. From the ground state geometry optimization results we conclude that trimethylphosphine oxide ligands preserve the wurtzite structure of the QDs. Evaporation of the ligands may lead to surface reconstruction. We found that the number of two-coordinated atoms on the nanoparticle's surface is the critical parameter defining the optical absorption properties. For (CdSe)(15) wurtzite-derived QD this number is maximal among all considered QDs and the optical absorption spectrum is strongly redshifted compared to QDs with threefold coordinated surface atoms. According to the time-dependent DFT results, surface reconstruction is accompanied by a significant decrease in the linear absorption. Oxidation of QDs destroys the perfection of the QD surface, increases the number of two-coordinated atoms and results in the appearance of an infrared absorption peak close to 700 nm. The vacant orbitals responsible for this near infrared transition have strong Se-O antibonding character. Conclusions of this study may be used in optimization of engineered nanoparticles for photodetectors and photovoltaic devices.
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2.90Impact points
DFT-based methods in the design of two-photon operated molecular switches.
The journal of physical chemistry. A. 07/2009; 113(25):7080-9.
Conjugated organic molecules with photochromic properties are being extensively studied as prospective optical switching and data storage materials. Among different photochromic compounds, diarylethenes demonstrate thermal stability, fatigue resistance, and high quantum yield. The mechanism of photo... [more] Conjugated organic molecules with photochromic properties are being extensively studied as prospective optical switching and data storage materials. Among different photochromic compounds, diarylethenes demonstrate thermal stability, fatigue resistance, and high quantum yield. The mechanism of photoswitching in diarylethenes involves a symmetry-allowed conrotatory electrocyclic reaction, initiated by UV light. Replacement of one UV photon with two near-IR ones would offer a number of practical advantages, including drastic increase in storage capacity via three-dimensional multilayer design. For this purpose we designed a prototype molecule with a two-photon absorbing (2PA) pendant substituent, attached to the photochromic diarylethene moiety. However, this molecule was experimentally shown to have lost the photoswitching properties. We analyze reasons for this loss using quantum chemistry tools. Analysis of the nodal structure of the frontier Kohn-Sham orbitals, allowed us to trace the route of the problem to the lone pair orbital of the 2PA substituent falling within the HOMO-LUMO (highest occupied molecular orbital-lowest unoccupied molecular orbital) gap of the photoreactive diarylethene moiety. We suggest a chemical modification of the 2PA substituent in order to restore the order of the orbitals. Potential energy plots along the reaction coordinate at the M05-2X/6-31G* theory level for the prototype 2PA photochromic molecule before and after the modification confirm the predictive capability of the proposed orbital approach. The Slater transition state method was used to obtain geometries along the reaction pathway by the constrained optimization of excited states, whereas potential energy curves were plotted using the recently proposed (Mikhailov, I. A.; Tafur, S.; Masunov, A. E. Phys. Rev. A 2008, 77 (1), 012510) a posteriori Tamm-Dancoff approximation to the time-dependent density functional theory in second order of the external field. We show that this combination is able to produce accurate potential surfaces for 1B and 2A excited states, as compared to available experimental data and results of high-level multireference wave function theory methods.
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2.90Impact points
Quantum Chemical Study of Trimolecular Reaction Mechanism between Nitric Oxide and Oxygen in the Gas Phase.
The journal of physical chemistry. A. 07/2009;
Singlet and triplet potential energy surfaces of the reaction between molecular oxygen and two nitric oxide(II) molecules were studied by quantum chemical methods (coupled cluster, CASSCF, and density functional theory: B3LYP, TPSS, VSXC, BP86, PBE, B2-PLYP, B2K-PLYP). Elementary steps involving var... [more] Singlet and triplet potential energy surfaces of the reaction between molecular oxygen and two nitric oxide(II) molecules were studied by quantum chemical methods (coupled cluster, CASSCF, and density functional theory: B3LYP, TPSS, VSXC, BP86, PBE, B2-PLYP, B2K-PLYP). Elementary steps involving various N(2)O(4) isomers (cyclic, cis-cis-, cis-trans-, trans-trans-ONOONO, cis- and trans-ONONO(2), O(2)NNO(2)) were considered, as well as weakly bound molecular clusters preceding formation of O(2)NNO(2), and Coupe-type quasi-aromatic hexagonal ring intermediate NO(2).O(2)N. We found that activation energy strongly depends on the conformation of ONOONO peroxide, which is formed barrierlessly. The best agreements with experimental values were achieved by the B3LYP functional with aug-pc3 basis set. The lowest transition state (TS) energies correspond to the following reaction channel: 2NO + O(2) (0 kJ/mol) --> cis-cis-ONOONO (-45 kJ/mol) --> TS1 --> NO(2).O(2)N (-90 kJ/mol) --> TS2 --> cis-ONONO(2) (-133 kJ/mol)--> TS3 --> trans-ONONO(2) (-144 kJ/mol) --> TS4 --> O(2)NNO(2) (-193 kJ/mol). A valley ridge inflection (VRI) point is located on the minimum energy path (MEP) connecting NO(2).O(2)N and cis-ONONO(2). The energy landscape between NO(2).O(2)N and CC-TS2 can be classified as a downhill valley-pitchfork VRI bifurcation according to a recent classification of bifurcation events [Quapp, W. J. Mol. Struct. 2004, 95, 695-696]. The first and second transition states correspond to barrier heights of 10.6 and 37.0 kJ/mol, respectively. These values lead to the negative temperature dependence of the rate constant. The apparent activation enthalpy of the overall reaction was calculated to be Delta(r)H()(0) = -4.5 kJ/mol, in perfect agreement with the experimental value.
Following (17)
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Nora Konopka
CRC Press Online -
Lee Chow
University of Central Florida -
Yoshiyuki Kawazoe
Tohoku University -
Marysue Griffin
Q-Chem, Inc. -
Alexander Bagaturyants
Photochemistry Center, Russian Academy of Science
