"Sis Cat" as Ethnographer: Self-Presentation and Self-Inscription in Zora Neale Hurston's "Mules and Men."

ERIC Educational Resources Information Center

Boxwell, D. A.

1992-01-01

Examines Zora Neale Hurston's work, particularly her collection of folklore and ethnography of the American South, "Mules and Men." Looks at the author's role, the ways the ethnographer inscribes herself into the text, and speculates about Hurston's understanding of the limits of the impersonal researcher. (JB)

"Sisters Under the Skin": Race and Gender in Zora Neale Hurston's "Tell My Horse."

ERIC Educational Resources Information Center

Meisenhelder, Susan

1995-01-01

No work by Zora Neale Hurston has received harsher critical evaluation than her anthropological study of Haiti and Jamaica, "Tell My Horse." Although her aim in part was to write a commercially successful popular book, she also aimed, with some success, to offer significant social commentary. (SLD)

First example of a high-level correlated calculation of the indirect spin-spin coupling constants involving tellurium: tellurophene and divinyl telluride.

PubMed

Rusakov, Yury Yu; Krivdin, Leonid B; Østerstrøm, Freja F; Sauer, Stephan P A; Potapov, Vladimir A; Amosova, Svetlana V

2013-08-21

This paper documents the very first example of a high-level correlated calculation of spin-spin coupling constants involving tellurium taking into account relativistic effects, vibrational corrections and solvent effects for medium sized organotellurium molecules. The (125)Te-(1)H spin-spin coupling constants of tellurophene and divinyl telluride were calculated at the SOPPA and DFT levels, in good agreement with experimental data. A new full-electron basis set, av3z-J, for tellurium derived from the "relativistic" Dyall's basis set, dyall.av3z, and specifically optimized for the correlated calculations of spin-spin coupling constants involving tellurium was developed. The SOPPA method shows a much better performance compared to DFT, if relativistic effects calculated within the ZORA scheme are taken into account. Vibrational and solvent corrections are next to negligible, while conformational averaging is of prime importance in the calculation of (125)Te-(1)H spin-spin couplings. Based on the performed calculations at the SOPPA(CCSD) level, a marked stereospecificity of geminal and vicinal (125)Te-(1)H spin-spin coupling constants originating in the orientational lone pair effect of tellurium has been established, which opens a new guideline in organotellurium stereochemistry.

"Different by Degree": Ella Cara Deloria, Zora Neale Hurston, and Franz Boas Contend with Race and Ethnicity.

ERIC Educational Resources Information Center

Hoefel, Roseanne

2001-01-01

American Indian ethnographer and linguist Ella Cara Deloria and African American folklorist and writer Zora Neale Hurston did fieldwork for Franz Boas, the father of modern anthropology. Both were shocked by how American racism empowered white people's historical actions. By correcting stereotypes through their work, they reasserted the role of…

DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin).

PubMed

Mihaylov, Tzvetan; Trendafilova, Natasha; Georgieva, Ivelina

2008-05-01

Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density distribution and the nucleophilic centers of the deprotonated ligand PhDC(2-) in a solvent environment were estimated on the basis of Hirshfeld atomic charges, electrostatic potential values at the nuclei, and Nalewajski-Mrozek bond orders. In accordance with the empirical formula La(PhDC)(OH)(H(2)O), a chain structure of the complex was simulated by means of two types of molecular fragment: (1) two La(III) cations bound to one PhDC(2-) ligand, and (2) two PhDC(2-) ligands bound to one La(III) cation. Different orientations of PhDC(2-), OH(-) and H(2)O ligands in the La(III) complexes were investigated using 20 possible [La(PhDC(2-))(2)(OH)(H(2)O)](2-) fragments. Energy calculations predicted that the prism-like structure based on "tail-head" cis-LML2 type binding and stabilized via HO...HOH intramolecular hydrogen bonds is the most probable structure for the La(III) complex. The calculated vibrational spectrum of the lowest energy La(III) model fragment is in very good agreement with the experimental IR spectrum of the complex, supporting the suggested ligand binding mode to La(III) in a chain structure, namely, every PhDC(2-) interacts with two La(III) cations through both carbonylic and both hydroxylic oxygens, and every La(III) cation binds four oxygen atoms of two different PhDC(2-).

Nonlinear d10-ML2 Transition-Metal Complexes

PubMed Central

Wolters, Lando P; Bickelhaupt, F Matthias

2013-01-01

We have investigated the molecular geometries of a series of dicoordinated d10-transition-metal complexes ML2 (M=Co−, Rh−, Ir−, Ni, Pd, Pt, Cu+, Ag+, Au+; L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand–metal–ligand (L–M–L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L–M–L angle using quantitative Kohn–Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L–M–L structures is π backdonation. In situations of strong π backdonation, smaller angles increase the overlap of the ligand’s acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor π backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent. PMID:24551547

A Systematic Theoretical Study of UC6: Structure, Bonding Nature, and Spectroscopy.

PubMed

Du, Jiguang; Jiang, Gang

2017-11-20

The study of uranium carbides has received renewed attention in recent years due to the potential use of these compounds as fuels in new generations of nuclear reactors. The isomers of the UC 6 cluster were determined by DFT and ab initio methods. The structures obtained using SC-RECP for U were generally consistent with those obtained using an all-electron basis set (ZORA-SARC). The CCSD(T) calculations indicated that two isomers had similar energies and may coexist in laser evaporation experiments. The nature of the U-C bonds in the different isomers was examined via a topological analysis of the electron density, and the results indicated that the U-C bonds are predominantly closed-shell (ionic) interactions with a certain degree of covalent character in all cases, particularly in the linear species. The IR and UV-vis spectra of the isomers were theoretically simulated to provide information that can be used to identify the isomers of UC 6 in future experiments.

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

PubMed Central

Wolters, Lando P; Bickelhaupt, F Matthias

2012-01-01

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A− and the analogous hydrogen-bonded complexes DH⋅⋅⋅A− (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A− arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A− and the σ* orbital of D–X. PMID:24551497

Connection between the regular approximation and the normalized elimination of the small component in relativistic quantum theory

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2005-02-01

The regular approximation to the normalized elimination of the small component (NESC) in the modified Dirac equation has been developed and presented in matrix form. The matrix form of the infinite-order regular approximation (IORA) expressions, obtained in [Filatov and Cremer, J. Chem. Phys. 118, 6741 (2003)] using the resolution of the identity, is the exact matrix representation and corresponds to the zeroth-order regular approximation to NESC (NESC-ZORA). Because IORA (=NESC-ZORA) is a variationally stable method, it was used as a suitable starting point for the development of the second-order regular approximation to NESC (NESC-SORA). As shown for hydrogenlike ions, NESC-SORA energies are closer to the exact Dirac energies than the energies from the fifth-order Douglas-Kroll approximation, which is much more computationally demanding than NESC-SORA. For the application of IORA (=NESC-ZORA) and NESC-SORA to many-electron systems, the number of the two-electron integrals that need to be evaluated (identical to the number of the two-electron integrals of a full Dirac-Hartree-Fock calculation) was drastically reduced by using the resolution of the identity technique. An approximation was derived, which requires only the two-electron integrals of a nonrelativistic calculation. The accuracy of this approach was demonstrated for heliumlike ions. The total energy based on the approximate integrals deviates from the energy calculated with the exact integrals by less than 5×10-9hartree units. NESC-ZORA and NESC-SORA can easily be implemented in any nonrelativistic quantum chemical program. Their application is comparable in cost with that of nonrelativistic methods. The methods can be run with density functional theory and any wave function method. NESC-SORA has the advantage that it does not imply a picture change.

Relativistic Zeroth-Order Regular Approximation Combined with Nonhybrid and Hybrid Density Functional Theory: Performance for NMR Indirect Nuclear Spin-Spin Coupling in Heavy Metal Compounds.

PubMed

Moncho, Salvador; Autschbach, Jochen

2010-01-12

A benchmark study for relativistic density functional calculations of NMR spin-spin coupling constants has been performed. The test set contained 47 complexes with heavy metal atoms (W, Pt, Hg, Tl, Pb) with a total of 88 coupling constants involving one or two heavy metal atoms. One-, two-, three-, and four-bond spin-spin couplings have been computed at different levels of theory (nonhybrid vs hybrid DFT, scalar vs two-component relativistic). The computational model was based on geometries fully optimized at the BP/TZP scalar relativistic zeroth-order regular approximation (ZORA) and the conductor-like screening model (COSMO) to include solvent effects. The NMR computations also employed the continuum solvent model. Computations in the gas phase were performed in order to assess the importance of the solvation model. The relative median deviations between various computational models and experiment were found to range between 13% and 21%, with the highest-level computational model (hybrid density functional computations including scalar plus spin-orbit relativistic effects, the COSMO solvent model, and a Gaussian finite-nucleus model) performing best.

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

PubMed Central

Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

2018-01-01

Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

Spin-Forbidden Reactions: Adiabatic Transition States Using Spin-Orbit Coupled Density Functional Theory.

PubMed

Gaggioli, Carlo Alberto; Belpassi, Leonardo; Tarantelli, Francesco; Harvey, Jeremy N; Belanzoni, Paola

2018-04-06

A spin-forbidden chemical reaction involves a change in the total electronic spin state from reactants to products. The mechanistic study is challenging because such a reaction does not occur on a single diabatic potential energy surface (PES), but rather on two (or multiple) spin diabatic PESs. One possible approach is to calculate the so-called "minimum energy crossing point" (MECP) between the diabatic PESs, which however is not a stationary point. Inclusion of spin-orbit coupling between spin states (SOC approach) allows the reaction to occur on a single adiabatic PES, in which a transition state (TS SOC) as well as activation free energy can be calculated. This Concept article summarizes a previously published application in which, for the first time, the SOC effects, using spin-orbit ZORA Hamiltonian within density functional theory (DFT) framework, are included and account for the mechanism of a spin-forbidden reaction in gold chemistry. The merits of the MECP and TS SOC approaches and the accuracy of the results are compared, considering both our recent calculations on molecular oxygen addition to gold(I)-hydride complexes and new calculations for the prototype spin-forbidden N 2 O and N 2 Se dissociation reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Spin Multiplicity in O2 Adsorption and Dissociation on Small Bimetallic AuAg Clusters.

PubMed

García-Cruz, Raúl; Poulain, Enrique; Hernández-Pérez, Isaías; Reyes-Nava, Juan A; González-Torres, Julio C; Rubio-Ponce, A; Olvera-Neria, Oscar

2017-08-17

To dispose of atomic oxygen, it is necessary the O 2 activation; however, an energy barrier must be overcome to break the O-O bond. This work presents theoretical calculations of the O 2 adsorption and dissociation on small pure Au n and Ag m and bimetallic Au n Ag m (n + m ≤ 6) clusters using the density functional theory (DFT) and the zeroth-order regular approximation (ZORA) to explicitly include scalar relativistic effects. The most stable Au n Ag m clusters contain a higher concentration of Au with Ag atoms located in the center of the cluster. The O 2 adsorption energy on pure and bimetallic clusters and the ensuing geometries depend on the spin multiplicity of the system. For a doublet multiplicity, O 2 is adsorbed in a bridge configuration, whereas for a triplet only one O-metal bond is formed. The charge transfer from metal toward O 2 occupies the σ* O-O antibonding natural bond orbital, which weakens the oxygen bond. The Au 3 ( 2 A) cluster presents the lowest activation energy to dissociate O 2 , whereas the opposite applies to the AuAg ( 3 A) system. In the O 2 activation, bimetallic clusters are not as active as pure Au n clusters due to the charge donated by Ag atoms being shared between O 2 and Au atoms.

77 FR 66463 - Change in Bank Control Notices; Acquisitions of Shares of a Bank or Bank Holding Company

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-05

... 63166-2034: 1. R. Forest Taylor and Zora Taylor, both of Morgantown, Kentucky, as the largest individual..., Tennessee; Emily Ann Romans, Russellville, Kentucky; Robert Daniel Taylor, and Sharon Kay Taylor, both of...

Serbo-Croatian Workbook. Phase 1. Part 1A,

DTIC Science & Technology

1983-10-25

1 PRACTICE OF NOUN GENDERS * Determine the gender of the following nouns: kiupa zadruga junak me so zora novac stolica voce jastuk Pismo izvinjenje...tamo? (povrce i voce ) 7. Da li ste napisali ?___________________________ (pismo, zadatak, knjiga) 71 8. Koga niste videli? (majka, otac, sin, moji

Modifications of spontaneous oculomotor activity in microgravitational conditions

NASA Astrophysics Data System (ADS)

Kornilova, L. N.; Goncharenko, A. M.; Polyakov, V. V.; Grigorova, V.; Manev, A.

Investigations on spontaneous oculomotor activity were carried out prior to and after (five cosmonauts) and during space flight (two cosmonauts) on the 3rd, 5th and 164th days of the space flight. Recording of oculomotor activity was carried out by electrooculography on automated data acquisition and processing system "Zora" based on personal computers. During the space flight and after it all the cosmonauts with the eyes closed or open and dark-goggled showed an essential increase of the movements' amplitude when removing the eyes into the extreme positions especially in a vertical direction, occurrence of correcting saccadic movements (or nystagmus), an increase in time of fixing reactions.

Books for Summer Reading.

ERIC Educational Resources Information Center

Phi Delta Kappan, 1991

1991-01-01

To help replenish educators' supply of ideas, "Kappan" editors suggest several books for summer reading, including many noncurrent titles not specifically on education such as Peter Novick's "That Noble Dream," Joy Kogawa's "Obasan," Zora Neale Hurston's "Their Eyes Were Watching God," Kate Chopin's "The Awakening," Willa Cather's "My Antonia,"…

An Argument for an Integrated Approach to Teaching Southern Literature

ERIC Educational Resources Information Center

Ellis, Grace

1978-01-01

In addition to such writers as William Faulkner, Flannery O'Connor, Carson McCullers, and Eudora Welty, a good course in modern Southern fiction should include black writers such as Zora Hurston, Nella Larsen, Jean Toomer, Richard Wright, Maya Angelou, and Alice Walker. (MKM)

Anthropology with an Agenda: Four Forgotten Dance Anthropologists

ERIC Educational Resources Information Center

Richter, Katrina

2010-01-01

In response to postcolonial, feminist and subaltern critiques of anthropology, this article seeks to answer the question, "For whom should research be conducted, and by whom should it be used?" by examining the lives and works of four female dance anthropologists. Franziska Boas, Zora Neale Hurston, Katherine Dunham and Pearl Primus used…

Reevaluation of Vegetational Characteristics at the CERC (Coastal Engineering Research Center) Field Research Facility, Duck, North Carolina.

DTIC Science & Technology

1983-03-01

var. cerifera L. Wax myrtle Onagraceae *Ludiigia aZata Ell. W. - r-priurose Oenothera frticoea L. drops 0. hisniflsa Nuttall Evening primrose... Orchidaceae Spiranthee cernua ver. odorata Nodding ladies’ (Nuttall) Correll. tresses Passiflorarese *PassifZora lutea L. Passion-flower Phytolacaceat POytoZaca

Alkali Metal Cation Affinities of Anionic Main Group-Element Hydrides Across the Periodic Table.

PubMed

Boughlala, Zakaria; Fonseca Guerra, Célia; Bickelhaupt, F Matthias

2017-10-05

We have carried out an extensive exploration of gas-phase alkali metal cation affinities (AMCA) of archetypal anionic bases across the periodic system using relativistic density functional theory at ZORA-BP86/QZ4P//ZORA-BP86/TZ2P. AMCA values of all bases were computed for the lithium, sodium, potassium, rubidium and cesium cations and compared with the corresponding proton affinities (PA). One purpose of this work is to provide an intrinsically consistent set of values of the 298 K AMCAs of all anionic (XH n-1 - ) constituted by main group-element hydrides of groups 14-17 along the periods 2-6. In particular, we wish to establish the trend in affinity for a cation as the latter varies from proton to, and along, the alkali cations. Our main purpose is to understand these trends in terms of the underlying bonding mechanism using Kohn-Sham molecular orbital theory together with a quantitative bond energy decomposition analyses (EDA). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The role of E-mentorship in a virtual world for youth transplant recipients.

PubMed

Cantrell, Kathryn; Fischer, Amy; Bouzaher, Alisha; Bers, Marina

2010-01-01

Because of geographic distances, many youth transplant recipients do not have the opportunity to meet and form relationships with peers who have undergone similar experiences. This article explores the role of E-mentorship in virtual environments. Most specifically, by analyzing data from a study conducted with the Zora virtual world with pediatric transplant recipients, suggestions and recommendations are given for conceiving the role of virtual mentors and allocating the needed resources. Zora is a graphical virtual world designed to create a community that offers psychoeducational support and the possibility of participating in virtual activities following a curriculum explicitly designed to address issues of school transition and medical adherence. Activities are designed to foster relationships, teach technological skills, and facilitate the formation of a support network of peers and mentors.This article addresses the research question, "What makes a successful E-mentorship model in virtual worlds for children with serious illnesses?" by looking at E-mentoring patterns such as time spent online, chat analysis, initiation of conversation, initiation of activities, and out-of-world contact.

Theoretical investigation of M@Pb122- and M@Sn122- Zintl clusters (M = Lrn+, Lun+, La3+, Ac3+ and n = 0, 1, 2, 3).

PubMed

Joshi, Meenakshi; Chandrasekar, Aditi; Ghanty, Tapan K

2018-06-06

The positions of lawrencium (Lr), lutetium (Lu), actinium (Ac) and lanthanum (La) in the periodic table have been a controversial topic for quite some time. According to studies carried out by different groups with their justifications, these elements may potentially be placed in the d-block, p-block or all four in a 15 element f-block. The present work looks into this issue from a new perspective, which involves encapsulation of these four elements into Zintl ion clusters, Pb122- and Sn122-, followed by the determination of the structural, thermodynamic and electronic properties of these endohedral M@Pb122- and M@Sn122- clusters (M = Lrn+, Lun+ with n = 0, 1, 2, 3) using first principles based density functional theory (DFT). These parameters are compared with similar clusters encapsulated La3+ and Ac3+ ions in order to seek out similarities and differences to draw conclusions about their placement in the periodic table. For the first time the structural, energetic, and electronic properties of these metal atom/ion encapsulated Pb122- and Sn122- clusters have been investigated thoroughly. Structural parameters such as bond distances, geometry and symmetry, electronic properties viz. the density of states, the molecular orbital ordering, the electron localization function, bond critical point properties and charge distributions have been analyzed. Additionally, the thermodynamic property of the binding energy during the encapsulation process has also been calculated. All M@Pb12+ and M@Sn12+ (M = Lr and Lu) clusters form stable 18 bonding electron magic number systems with shell closing. They show negative values of binding energy and relatively large HOMO-LUMO energy gaps indicating the stability of such clusters. All the calculated parameters for Lr encapsulated clusters closely match with the corresponding calculated parameters of Lu encapsulated clusters, confirming the similarity between Lr and Lu metal atoms in various oxidation states, though their atomic ground state valence electronic configurations are different. The effect of spin orbit coupling has also been investigated using the ZORA approach. It is interesting to discover that La and Ac showed striking similarities to Lr and Lu with respect to all the properties investigated and have formed a stable 18-electron system.

We Need More Drama: A Comparison of Ford, Hurston, and Boykin's African American Characteristics and Instructional Strategies for the Culturally Different Classroom

ERIC Educational Resources Information Center

Trotman Scott, Michelle; Moss-Bouldin, Shondrika

2014-01-01

Teachers who are not considered to be culturally competent may misinterpret many characteristics exhibited by African American students. They may be unaware of the African American linguistic practices and characteristics and they may also be unfamiliar with research conducted by scholars such as Zora Neale Hurston and A. Wade Boykin. This lack of…

DefEX: Hands-On Cyber Defense Exercise for Undergraduate Students

DTIC Science & Technology

2011-07-01

Injection, and 4) File Upload. Next, the students patched the associated flawed Perl and PHP Hypertext Preprocessor ( PHP ) code. Finally, students...underlying script. The Zora XSS vulnerability existed in a PHP file that echoed unfiltered user input back to the screen. To eliminate the...vulnerability, students filtered the input using the PHP htmlentities function and retested the code. The htmlentities function translates certain ambiguous

Activation Strain Analysis of SN2 Reactions at C, N, O, and F Centers

PubMed Central

2017-01-01

Fundamental principles that determine chemical reactivity and reaction mechanisms are the very foundation of chemistry and many related fields of science. Bimolecular nucleophilic substitutions (SN2) are among the most common and therefore most important reaction types. In this report, we examine the trends in the SN2 reactions with respect to increasing electronegativity of the reaction center by comparing the well-studied backside SN2 Cl– + CH3Cl with similar Cl– substitutions on the isoelectronic series with the second period elements N, O, and F in place of C. Relativistic (ZORA) DFT calculations are used to construct the gas phase reaction potential energy surfaces (PES), and activation strain analysis, which allows decomposition of the PES into the geometrical strain and interaction energy, is employed to analyze the observed trends. We find that SN2@N and SN2@O have similar PES to the prototypical SN2@C, with the well-defined reaction complex (RC) local minima and a central barrier, but all stationary points are, respectively, increasingly stable in energy. The SN2@F, by contrast, exhibits only a single-well PES with no barrier. Using the activation strain model, we show that the trends are due to the interaction energy and originate mainly from the decreasing energy of the empty acceptor orbital (σ*A–Cl) on the reaction center A in the order of C, N, O, and F. The decreasing steric congestion around the central atom is also a likely contributor to this trend. Additional decomposition of the interaction energy using Kohn–Sham molecular orbital (KS-MO) theory provides further support for this explanation, as well as suggesting electrostatic energy as the primary reason for the distinct single-well PES profile for the FCl reaction. PMID:28045531

Activation Strain Analysis of SN2 Reactions at C, N, O, and F Centers.

PubMed

Kubelka, Jan; Bickelhaupt, F Matthias

2017-02-02

Fundamental principles that determine chemical reactivity and reaction mechanisms are the very foundation of chemistry and many related fields of science. Bimolecular nucleophilic substitutions (S N 2) are among the most common and therefore most important reaction types. In this report, we examine the trends in the S N 2 reactions with respect to increasing electronegativity of the reaction center by comparing the well-studied backside S N 2 Cl - + CH 3 Cl with similar Cl - substitutions on the isoelectronic series with the second period elements N, O, and F in place of C. Relativistic (ZORA) DFT calculations are used to construct the gas phase reaction potential energy surfaces (PES), and activation strain analysis, which allows decomposition of the PES into the geometrical strain and interaction energy, is employed to analyze the observed trends. We find that S N 2@N and S N 2@O have similar PES to the prototypical S N 2@C, with the well-defined reaction complex (RC) local minima and a central barrier, but all stationary points are, respectively, increasingly stable in energy. The S N 2@F, by contrast, exhibits only a single-well PES with no barrier. Using the activation strain model, we show that the trends are due to the interaction energy and originate mainly from the decreasing energy of the empty acceptor orbital (σ* A-Cl ) on the reaction center A in the order of C, N, O, and F. The decreasing steric congestion around the central atom is also a likely contributor to this trend. Additional decomposition of the interaction energy using Kohn-Sham molecular orbital (KS-MO) theory provides further support for this explanation, as well as suggesting electrostatic energy as the primary reason for the distinct single-well PES profile for the FCl reaction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sim, Eunji; Kim, Min-Cheol; Burke, Kieron

We investigate dissociation of diatomic molecules using standard density functional theory (DFT) and density-corrected density functional theory (DC-DFT) compared with CCSD(T) results as reference. The results show the difference between the HOMO values of dissociated atomic species often can be used as an indicator whether DFT would predict the correct dissociation limit. DFT predicts incorrect dissociation limits and charge distribution in molecules or molecular ions when the fragments have large HOMO differences, while DC-DFT and CCSD(T) do not. The criteria for large HOMO difference is about 2 ∼ 4 eV.

Solid-state (185/187)Re NMR and GIPAW DFT study of perrhenates and Re2(CO)10: chemical shift anisotropy, NMR crystallography, and a metal-metal bond.

PubMed

Widdifield, Cory M; Perras, Frédéric A; Bryce, David L

2015-04-21

Advances in solid-state nuclear magnetic resonance (SSNMR) methods, such as dynamic nuclear polarization (DNP), intricate pulse sequences, and increased applied magnetic fields, allow for the study of systems which even very recently would be impractical. However, SSNMR methods using certain quadrupolar probe nuclei (i.e., I > 1/2), such as (185/187)Re remain far from fully developed due to the exceedingly strong interaction between the quadrupole moment of these nuclei and local electric field gradients (EFGs). We present a detailed high-field (B0 = 21.1 T) experimental SSNMR study on several perrhenates (KReO4, AgReO4, Ca(ReO4)2·2H2O), as well as ReO3 and Re2(CO)10. We propose solid ReO3 as a new rhenium SSNMR chemical shift standard due to its reproducible and sharp (185/187)Re NMR resonances. We show that for KReO4, previously poorly understood high-order quadrupole-induced effects (HOQIE) on the satellite transitions can be used to measure the EFG tensor asymmetry (i.e., ηQ) to nearly an order-of-magnitude greater precision than competing SSNMR and nuclear quadrupole resonance (NQR) approaches. Samples of AgReO4 and Ca(ReO4)2·2H2O enable us to comment on the effects of counter-ions and hydration upon Re(vii) chemical shifts. Calcium-43 and (185/187)Re NMR tensor parameters allow us to conclude that two proposed crystal structures for Ca(ReO4)2·2H2O, which would be considered as distinct, are in fact the same structure. Study of Re2(CO)10 provides insights into the effects of Re-Re bonding on the rhenium NMR tensor parameters and rhenium oxidation state on the Re chemical shift value. As overtone NQR experiments allowed us to precisely measure the (185/187)Re EFG tensor of Re2(CO)10, we were able to measure rhenium chemical shift anisotropy (CSA) for the first time in a powdered sample. Experimental observations are supported by gauge-including projector augmented-wave (GIPAW) density functional theory (DFT) calculations, with NMR tensor calculations also provided for NH4ReO4, NaReO4 and RbReO4. These calculations are able to reproduce many of the experimental trends in rhenium δiso values and EFG tensor magnitudes. Using KReO4 as a prototypical perrhenate-containing system, we establish a correlation between the tetrahedral shear strain parameter (|ψ|) and the nuclear electric quadrupolar coupling constant (CQ), which enables the refinement of the structure of ND4ReO4. Shortcomings in traditional DFT approaches, even when including relativistic effects via the zeroth-order regular approximation (ZORA), for calculating rhenium NMR tensor parameters are identified for Re2(CO)10.

Electron correlation and the self-interaction error of density functional theory

NASA Astrophysics Data System (ADS)

Polo, Victor; Kraka, Elfi; Cremer, Dieter

The self-interaction error (SIE) of commonly used DFT functionals has been systematically investigated by comparing the electron density distribution ρ( r ) generated by self-interaction corrected DFT (SIC-DFT) with a series of reference densities obtained by DFT or wavefunction theory (WFT) methods that cover typical electron correlation effects. Although the SIE of GGA functionals is considerably smaller than that of LDA functionals, it has significant consequences for the coverage of electron correlation effects at the DFT level of theory. The exchange SIE mimics long range (non-dynamic) pair correlation effects, and is responsible for the fact that the electron density of DFT exchange-only calculations resembles often that of MP4, MP2 or even CCSD(T) calculations. Changes in the electron density caused by SICDFT exchange are comparable with those that are associated with HF exchange. Correlation functionals contract the density towards the bond and the valence region, thus taking negative charge out of the van der Waals region where these effects are exaggerated by the influence of the SIE of the correlation functional. Hence, SIC-DFT leads in total to a relatively strong redistribution of negative charge from van der Waals, non-bonding, and valence regions of heavy atoms to the bond regions. These changes, although much stronger, resemble those obtained when comparing the densities of hybrid functionals such as B3LYP with the corresponding GGA functional BLYP. Hence, the balanced mixing of local and non-local exchange and correlation effects as it is achieved by hybrid functionals mimics SIC-DFT and can be considered as an economic way to include some SIC into standard DFT. However, the investigation shows also that the SIC-DFT description of molecules is unreliable because the standard functionals used were optimized for DFT including the SIE.

Investigation of ground state charge transfer complex between paracetamol and p-chloranil through DFT and UV-visible studies

NASA Astrophysics Data System (ADS)

Shukla, Madhulata; Srivastava, Nitin; Saha, Satyen

2012-08-01

The present report deals with the theoretical investigation on ground state structure and charge transfer (CT) transitions in paracetamol (PA)/p-chloranil (CA) complex using Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) method. It is found that Cdbnd O bond length of p-chloranil increases on complexation with paracetamol along with considerable amount of charge transfer from PA to CA. TD-DFT calculations have been performed to analyse the observed UV-visible spectrum of PA-CA charge transferred complex. Interestingly, in addition to expected CT transition, a weak symmetry relieved π-π* transition in the chloranil is also observed.

Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solovyeva, Alisa; Technical University Braunschweig, Institute for Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig; Pavanello, Michele

2012-05-21

Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a {pi}-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations.more » In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.« less

First-principles study of paraelectric and ferroelectric CsH2PO4 including dispersion forces: Stability and related vibrational, dielectric, and elastic properties

NASA Astrophysics Data System (ADS)

Van Troeye, Benoit; van Setten, Michiel Jan; Giantomassi, Matteo; Torrent, Marc; Rignanese, Gian-Marco; Gonze, Xavier

2017-01-01

Using density functional theory (DFT) and density functional perturbation theory (DFPT), we investigate the stability and response functions of CsH2PO4 , a ferroelectric material at low temperature. This material cannot be described properly by the usual (semi)local approximations within DFT. The long-range e--e- correlation needs to be properly taken into account, using, for instance, Grimme's DFT-D methods, as investigated in this work. We find that DFT-D3(BJ) performs the best for the members of the dihydrogenated alkali phosphate family (KH2PO4 , RbH2PO4 , CsH2PO4 ), leading to experimental lattice parameters reproduced with an average deviation of 0.5%. With these DFT-D methods, the structural, dielectric, vibrational, and mechanical properties of CsH2PO4 are globally in excellent agreement with the available experiments (<2 % MAPE for Raman-active phonons). Our study suggests the possible existence of a new low-temperature phase of CsH2PO4 , not yet reported experimentally. Finally, we report the implementation of DFT-D contributions to elastic constants within DFPT.

Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table.

PubMed

Mulder, Joshua R; Guerra, Célia Fonseca; Slootweg, J Chris; Lammertsma, Koop; Bickelhaupt, F Matthias

2016-01-15

A comprehensive theoretical treatment is presented for the electronic excitation spectra of ca. 50 different mono-, di-, and tetrasubstituted naphthalenediimides (NDI) using time-dependent density functional theory (TDDFT) at ZORA-CAM-B3LYP/TZ2P//ZORA-BP86/TZ2P with COSMO for simulating the effect of dichloromethane (DCM) solution. The substituents -XHn are from groups 14-17 and rows 2-5 of the periodic table. The lowest dipole-allowed singlet excitation (S0 -S1 ) of the monosubstituted NDIs can be tuned from 3.39 eV for -F to 2.42 eV for -TeH, while the S0 -S2 transition is less sensitive to substitution with energies ranging between 3.67 eV for -CH3 and 3.44 eV for -SbH2 . In the case of NDIs with group-15 and -16 substituents, the optical transitions strongly depend on the extent to which -XHn is planar or pyramidal as well as on the possible formation of intramolecular hydrogen bonds. The accumulative effect of double and quadruple substitution leads in general to increasing bathochromic shifts, but the increased steric hindrance in tetrasubstituted NDIs can lead to deformations that diminish the effectiveness of the substituents. Detailed analyses of the Kohn-Sham orbital electronic structure in monosubstituted NDIs reveal the mesomeric destabilization of the HOMO as the primary cause of the bathochromic shift of the S0-S1 transition. © 2015 Wiley Periodicals, Inc.

Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

NASA Astrophysics Data System (ADS)

Srivastava, Santosh K.; Singh, Vipin B.

2013-11-01

Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

Density-functional theory applied to d- and f-electron systems

NASA Astrophysics Data System (ADS)

Wu, Xueyuan

Density functional theory (DFT) has been applied to study the electronic and geometric structures of prototype d- and f-electron systems. For the d-electron system, all electron DFT with gradient corrections to the exchange and correlation functionals has been used to investigate the properties of small neutral and cationic vanadium clusters. Results are in good agreement with available experimental and other theoretical data. For the f-electron system, a hybrid DFT, namely, B3LYP (Becke's 3-parameter hybrid functional using the correlation functional of Lee, Yang and Parr) with relativistic effective core potentials and cluster models has been applied to investigate the nature of chemical bonding of both the bulk and the surfaces of plutonium monoxide and dioxide. Using periodic models, the electronic and geometric structures of PuO2 and its (110) surface, as well as water adsorption on this surface have also been investigated using DFT in both local density approximation (LDA) and generalized gradient approximation (GGA) formalisms.

Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

PubMed

Guidez, Emilie B; Gordon, Mark S

2015-03-12

The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hedegård, Erik Donovan, E-mail: erik.hedegard@phys.chem.ethz.ch; Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense; Olsen, Jógvan Magnus Haugaard

2015-03-21

We present here the coupling of a polarizable embedding (PE) model to the recently developed multiconfiguration short-range density functional theory method (MC-srDFT), which can treat multiconfigurational systems with a simultaneous account for dynamical and static correlation effects. PE-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linearmore » response have been implemented in a development version of DALTON. To benchmark the PE-MC-srDFT approach against the literature data, we have investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies. To demonstrate the capabilities of PE-MC-srDFT, we also investigated the retinylidene Schiff base chromophore embedded in the channelrhodopsin protein. While using a much more compact reference wave function in terms of active space, our PE-MC-srDFT approach yields excitation energies comparable in quality to CASSCF/CASPT2 benchmarks.« less

Investigations of Topological Surface States in Sb (111) Ultrathin Films by STM/STS Experiments and DFT Calculations

NASA Astrophysics Data System (ADS)

Luo, Ziyu; Yao, Guanggeng; Xu, Wentao; Feng, Yuanping; Wang, Xue-Sen

2014-03-01

Bulk Sb was regarded as a semimetal with a nontrivial topological order. It is worth exploring whether the Sb ultrathin film has the potential to be an elementary topological insulator. In the presence of quantum confinement effect, we investigated the evolution of topological surface states in Sb (111) ultrathin films with different thickness by the scanning tunneling microscopy/ spectroscopy (STM/STS) experiments and density functional theory (DFT) calculations. By comparing the quasiparticle interference (QPI) patterns obtained from Fourier-transform scanning tunneling spectroscopy (FT-STS) and from DFT calculations, we successfully derive the spin properties of topological surface states on Sb (111) ultrathin films. In addition, based on the DFT calculations, the 8BL Sb (111) ultrathin film was proved to possess up to 30% spinseparated topological surface states within the bandgap. Therefore, the highquality 8BL Sb (111) ultrathin film could be regarded as an elementary topological insulator.

Does defibrotide induce a delay to polymorphonuclear neutrophil engraftment after hematopoietic stem cell transplantation? Observation in a pediatric population.

PubMed

Maximova, Natalia; Pizzol, Antonio; Giurici, Nagua; Granzotto, Marilena

2015-04-01

In recent years, defibrotide (DFT) has emerged as a promising therapy for veno-occlusive disease (VOD). The aim of this study was to investigate whether DFT prophylaxis affects neutrophil engraftment in patients undergoing hematopoietic stem cell transplantation (HSCT). A cohort of 44 consecutive pediatric patients who underwent HSCT was retrospectively analyzed to see the role of DFT on engraftment. Patients were assigned into two groups based on the use or non-use of prophylaxis with DFT. The mean time to engraftment was statistically different between the two groups for both polymorphonuclear neutrophils (PMN) and white blood cells. Our study supports the hypothesis that prophylaxis with DFT for VOD leads to a delay to the engraftment of PMN in pediatric patients that underwent HSCT.

Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

PubMed

Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

2017-12-06

Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 < MoF 3 < MoF 6 before sharply decreasing for MoF 9 , with a similar effect for the supported systems (MoF 0 ≈ MoF 9 < MoF 6 < MoF 3 ). This is consistent with the different kinetic behavior (zeroth order in alkyne for MoF 9 derivatives instead of first order for the others) and the isolation of stable metallacyclobutadiene intermediates of MoF 9 for both molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

Time-dependent i-DFT exchange-correlation potentials with memory: applications to the out-of-equilibrium Anderson model

NASA Astrophysics Data System (ADS)

Kurth, Stefan; Stefanucci, Gianluca

2018-06-01

We have recently put forward a steady-state density functional theory (i-DFT) to calculate the transport coefficients of quantum junctions. Within i-DFT it is possible to obtain the steady density on and the steady current through an interacting junction using a fictitious noninteracting junction subject to an effective gate and bias potential. In this work we extend i-DFT to the time domain for the single-impurity Anderson model. By a reverse engineering procedure we extract the exchange-correlation (xc) potential and xc bias at temperatures above the Kondo temperature T K. The derivation is based on a generalization of a recent paper by Dittmann et al. [N. Dittmann et al., Phys. Rev. Lett. 120, 157701 (2018)]. Interestingly the time-dependent (TD) i-DFT potentials depend on the system's history only through the first time-derivative of the density. We perform numerical simulations of the early transient current and investigate the role of the history dependence. We also empirically extend the history-dependent TD i-DFT potentials to temperatures below T K. For this purpose we use a recently proposed parametrization of the i-DFT potentials which yields highly accurate results in the steady state.

Spectroscopic investigation, HOMO-LUMO and NLO studies on L-histidinium maleate based on DFT approach

NASA Astrophysics Data System (ADS)

Dhanavel, S.; Stephen, A.; Asirvatham, P. Samuel

2017-05-01

The molecular structure of the title compound L-Histidinium Maleate (LHM) was constructed and optimized based on Density Functional Theory method (DFT-B3LYP) with the 6-31G (d,p) basis set. The fundamental vibrational spectral assignment was analyzed with the aid of optimized structure of LHM. The study on electronic properties such as, HOMO-LUMO energies and absorption wavelength were performed using Time dependent DFT (TD-DFT) approach which reveals that energy transfer occur within the molecule. 13C NMR chemical shift values were measured using Gauge independent atomic orbital method (GIAO) and the obtained values are in good agreement with the reported experimental values. Hardness, ionization potential and electrophilicity index also calculated. The electric dipole moment (μtot) and hyperpolarizability (βtot) values of the investigated molecules were computed. The calculated value (β) was 3.7 times higher than that of urea, which confirms the LHM molecule is a potential candidate for NLO applications.

Relativistic (SR-ZORA) quantum theory of atoms in molecules properties.

PubMed

Anderson, James S M; Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W

2017-01-15

The Quantum Theory of Atoms in Molecules (QTAIM) is used to elucidate the effects of relativity on chemical systems. To do this, molecules are studied using density-functional theory at both the nonrelativistic level and using the scalar relativistic zeroth-order regular approximation. Relativistic effects on the QTAIM properties and topology of the electron density can be significant for chemical systems with heavy atoms. It is important, therefore, to use the appropriate relativistic treatment of QTAIM (Anderson and Ayers, J. Phys. Chem. 2009, 115, 13001) when treating systems with heavy atoms. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

No need for external orthogonality in subsystem density-functional theory.

PubMed

Unsleber, Jan P; Neugebauer, Johannes; Jacob, Christoph R

2016-08-03

Recent reports on the necessity of using externally orthogonal orbitals in subsystem density-functional theory (SDFT) [Annu. Rep. Comput. Chem., 8, 2012, 53; J. Phys. Chem. A, 118, 2014, 9182] are re-investigated. We show that in the basis-set limit, supermolecular Kohn-Sham-DFT (KS-DFT) densities can exactly be represented as a sum of subsystem densities, even if the subsystem orbitals are not externally orthogonal. This is illustrated using both an analytical example and in basis-set free numerical calculations for an atomic test case. We further show that even with finite basis sets, SDFT calculations using accurate reconstructed potentials can closely approach the supermolecular KS-DFT density, and that the deviations between SDFT and KS-DFT decrease as the basis-set limit is approached. Our results demonstrate that formally, there is no need to enforce external orthogonality in SDFT, even though this might be a useful strategy when developing projection-based DFT embedding schemes.

Stereochemical and conformational study on fenoterol by ECD spectroscopy and TD-DFT calculations.

PubMed

Tedesco, Daniele; Zanasi, Riccardo; Wainer, Irving W; Bertucci, Carlo

2014-03-01

Fenoterol and its derivatives are selective β2-adrenergic receptor (β2-AR) agonists whose stereoselective biological activities have been extensively investigated in the past decade; a complete stereochemical characterization of fenoterol derivatives is therefore crucial for a better understanding of the effects of stereochemistry on β2-AR binding. In the present project, the relationship between chiroptical properties and absolute stereochemistry of the stereoisomers of fenoterol (1) was investigated by experimental ECD spectroscopy and time-dependent density functional theory (TD-DFT). DFT geometry optimizations were carried out at the RI-B97D/TZVP/IEFPCM(MeOH) level and subsequent TD-DFT calculations were performed using the PBE0 hybrid functional. Despite the large pool of equilibrium conformers found for the investigated compounds and the known limitations of the level of theory employed, the computational protocol was able to reproduce the experimental ECD spectra of the stereoisomers of 1. The main contribution to the overall chiroptical properties was found to arise from the absolute configuration of the chiral center in α-position to the resorcinol moiety. Based on this evidence, a thorough conformational analysis was performed on the optimized DFT conformers, which revealed the occurrence of a different equilibrium between conformational patterns for the diastereomers of fenoterol: the (R,R')/(S,S') enantiomeric pair showed a higher population of folded conformations than the (R,S')/(S,R') pair. Copyright © 2013 Elsevier B.V. All rights reserved.

Nonlinear modeling of crystal system transition of black phosphorus using continuum-DFT model.

PubMed

Setoodeh, A R; Farahmand, H

2018-01-24

In this paper, the nonlinear behavior of black phosphorus crystals is investigated in tandem with dispersion-corrected density functional theory (DFT-D) analysis under uniaxial loadings. From the identified anisotropic behavior of black phosphorus due to its morphological anisotropy, a hyperelastic anisotropic (HA) model named continuum-DFT is established to predict the nonlinear behavior of the material. In this respect, uniaxial Cauchy stresses are employed on both the DFT-D and HA models along the zig-zag and armchair directions. Simultaneously, the transition of the crystal system is recognized at about 4.5 GPa of the applied uniaxial tensile stress along the zig-zag direction on the DFT-D simulation in the nonlinear region. In order to develop the nonlinear continuum model, unknown constants are surveyed with the optimized least square technique. In this regard, the continuum model is obtained to reproduce the Cauchy stress-stretch and density of strain-stretch results of the DFT-D simulation. Consequently, the modified HA model is introduced to characterize the nonlinear behavior of black phosphorus along the zig-zag direction. More importantly, the specific transition of the crystal system is successfully predicted in the new modified continuum-DFT model. The results reveal that the multiscale continuum-DFT model is well defined to replicate the nonlinear behavior of black phosphorus along the zig-zag and armchair directions.

Excited state characterization of carbonyl containing carotenoids: a comparison between single and multireference descriptions

NASA Astrophysics Data System (ADS)

Spezia, Riccardo; Knecht, Stefan; Mennucci, Benedetta

Carotenoids can play multiple roles in biological photoreceptors thanks to their rich photophysics. In the present work, we have investigated six of the most common carbonyl containing carotenoids: Echinenone, Canthaxanthin, Astaxanthin, Fucoxanthin, Capsanthin and Capsorubin. Their excitation properties are investigated by means of a hybrid density functional theory (DFT) and multireference configuration interaction (MRCI) approach to elucidate the role of the carbonyl group: the bright transition is of {\\pi}{\\pi}* character, as expected, but the presence of a C=O moiety reduces the energy of n{\\pi}* transitions which may become closer to the {\\pi}{\\pi}* transition, in particular as the conjugation chain decreases. This can be related to the presence of a low-lying charge transfer state typical of short carbonyl- containing carotenoids. The DFT/MRCI results are finally used to benchmark single- reference time-dependent DFT-based methods: among the investigated functionals, the meta- GGA (and in particular M11L and MN12L) functionals show to perform the best for all six investigated systems.

Ensemble density variational methods with self- and ghost-interaction-corrected functionals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pastorczak, Ewa; Pernal, Katarzyna, E-mail: pernalk@gmail.com

2014-05-14

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introducedmore » by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.« less

Semiempirical and DFT Investigations of the Dissociation of Alkyl Halides

ERIC Educational Resources Information Center

Waas, Jack R.

2006-01-01

Enthalpy changes corresponding to the gas phase heats of dissociation of 12 organic halides were calculated using two semiempirical methods, the Hartree-Fock method, and two DFT methods. These calculated values were compared to experimental values where possible. All five methods agreed generally with the expected empirically known trends in the…

OH-initiated transformation and hydrolysis of aspirin in AOPs system: DFT and experimental studies.

PubMed

He, Lin; Sun, Xiaomin; Zhu, Fanping; Ren, Shaojie; Wang, Shuguang

2017-08-15

Advanced oxidation processes (AOPs) are widely used in wastewater treatment of pharmaceutical and personal care products (PPCPs). In this work, the OH-initiated transformation as well as the hydrolysis of a typical PPCPs, aspirin, was investigated using density functional theory (DFT) calculations and laboratory experiments. For DFT calculations, the frontier electron densities and bond dissociation energies were analyzed. Profiles of the potential energy surface were constructed, and all the possible pathways were discussed. Additionally, rate constants for each pathway were calculated with transition state theory (TST) method. UV/H 2 O 2 experiments of aspirin were performed and degradation intermediates were identified by UPLC-MS-MS analysis. Different findings from previous experimental works were reported that the H-abstraction pathways at methyl position were dominated and OH-addition pathways on benzene ring were also favored. Meantime, hydroxyl ASA was confirmed as the main stable intermediate. Moreover, it was the first time to use DFT method to investigate the hydrolysis mechanisms of organic ester compound. Copyright © 2017 Elsevier B.V. All rights reserved.

Anisotropy induced Kondo splitting in a mechanically stretched molecular junction: A first-principles based study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiaoli; Hou, Dong, E-mail: houdong@ustc.edu.cn; Zheng, Xiao, E-mail: xz58@ustc.edu.cn

2016-01-21

The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy–SH){sub 2} sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It ismore » confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.« less

Spectroscopic (FT-IR/FT-Raman) and computational (HF/DFT) investigation and HOMO/LUMO/MEP analysis on 1,1-difluoro-2-vinyl-cyclopropane

NASA Astrophysics Data System (ADS)

Senthil Raj, P.; Shoba, D.; Ramalingam, S.; Periandy, S.

2015-08-01

All the computational calculations were made in the ground state using the HF and DFT (B3LYP) methods with 6-31++G (d,p) and 6-311++G (d,p) basis sets. Making use of the recorded data, the complete vibrational assignments were made and analysis of the observed fundamental bands of molecule was carried out. The shifting of the frequencies in the vibrational pattern of the title molecule due to the substitutions; sbnd CHdbnd CH2 and F were deeply investigated by the vibrational analysis. Moreover, 13C NMR and 1H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF/B3LYP methods with 6-311++G (d,p). A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Mulliken charges of the 1DF2VCP were also calculated and interpreted. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valsson, Omar; Filippi, Claudia, E-mail: c.filippi@utwente.nl; Casida, Mark E., E-mail: mark.casida@ujf-grenoble.fr

2015-04-14

The excited-state relaxation of retinal protonated Schiff bases (PSBs) is an important test case for biological applications of time-dependent (TD) density-functional theory (DFT). While well-known shortcomings of approximate TD-DFT might seem discouraging for application to PSB relaxation, progress continues to be made in the development of new functionals and of criteria allowing problematic excitations to be identified within the framework of TD-DFT itself. Furthermore, experimental and theoretical ab initio advances have recently lead to a revised understanding of retinal PSB photochemistry, calling for a reappraisal of the performance of TD-DFT in describing this prototypical photoactive system. Here, we re-investigate themore » performance of functionals in (TD-)DFT calculations in light of these new benchmark results, which we extend to larger PSB models. We focus on the ability of the functionals to describe primarily the early skeletal relaxation of the chromophore and investigate how far along the out-of-plane pathways these functionals are able to describe the subsequent rotation around formal single and double bonds. Conventional global hybrid and range-separated hybrid functionals are investigated as the presence of Hartree-Fock exchange reduces problems with charge-transfer excitations as determined by the Peach-Benfield-Helgaker-Tozer Λ criterion and by comparison with multi-reference perturbation theory results. While we confirm that most functionals cannot render the complex photobehavior of the retinal PSB, do we also observe that LC-BLYP gives the best description of the initial part of the photoreaction.« less

Hybrid density functional theory band structure engineering in hematite

NASA Astrophysics Data System (ADS)

Pozun, Zachary D.; Henkelman, Graeme

2011-06-01

We present a hybrid density functional theory (DFT) study of doping effects in α-Fe2O3, hematite. Standard DFT underestimates the band gap by roughly 75% and incorrectly identifies hematite as a Mott-Hubbard insulator. Hybrid DFT accurately predicts the proper structural, magnetic, and electronic properties of hematite and, unlike the DFT+U method, does not contain d-electron specific empirical parameters. We find that using a screened functional that smoothly transitions from 12% exact exchange at short ranges to standard DFT at long range accurately reproduces the experimental band gap and other material properties. We then show that the antiferromagnetic symmetry in the pure α-Fe2O3 crystal is broken by all dopants and that the ligand field theory correctly predicts local magnetic moments on the dopants. We characterize the resulting band gaps for hematite doped by transition metals and the p-block post-transition metals. The specific case of Pd doping is investigated in order to correlate calculated doping energies and optical properties with experimentally observed photocatalytic behavior.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

Torras, Juan; Zanuy, David; Aradilla, David; Alemán, Carlos

2016-09-21

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

Accuracy and Transferability of Ab Initio Electronic Band Structure Calculations for Doped BiFeO3

NASA Astrophysics Data System (ADS)

Gebhardt, Julian; Rappe, Andrew M.

2017-11-01

BiFeO3 is a multiferroic material and, therefore, highly interesting with respect to future oxide electronics. In order to realize such devices, pn junctions need to be fabricated, which are currently impeded by the lack of successful p-type doping in this material. In order to guide the numerous research efforts in this field, we recently finished a comprehensive computational study, investigating the influence of many dopants onto the electronic structure of BiFeO3. In order to allow for this large scale ab initio study, the computational setup had to be accurate and efficient. Here we discuss the details of this assessment, showing that standard density-functional theory (DFT) yields good structural properties. The obtained electronic structure, however, suffers from well-known shortcomings. By comparing the conventional DFT results for alkali and alkaline-earth metal doping with more accurate hybrid-DFT calculations, we show that, in this case, the problems of standard DFT go beyond a simple systematic error. Conventional DFT shows bad transferability and the more reliable hybrid-DFT has to be chosen for a qualitatively correct prediction of doping induced changes in the electronic structure of BiFeO3.

Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

NASA Astrophysics Data System (ADS)

Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

2018-03-01

A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.

KSC kicks off African-American History Month

NASA Technical Reports Server (NTRS)

2000-01-01

Mack McKinney, chief, program resources management at NASA and chairperson for African-American History Month, presents a plaque to Bhetty Waldron at the kick-off ceremony of African-American History Month on Feb. 3 at the NASA Training Auditorium. The award was given in thanks for Waldron's portrayal of Dr. Mary McLeod Bethune and Zora Neal Hurston during the ceremony. The theme for this year's observation is 'Heritage and Horizons: The African-American Legacy and the Challenges of the 21st Century.' February is designated each year as a time to celebrate the achievements and contributions of African Americans to Kennedy Space Center, NASA and the nation.

Additive effect of mesenchymal stem cells and defibrotide in an arterial rat thrombosis model.

PubMed

Dilli, Dilek; Kılıç, Emine; Yumuşak, Nihat; Beken, Serdar; Uçkan Çetinkaya, Duygu; Karabulut, Ramazan; Zenciroğlu, Ayşegu L

2017-06-01

In this study, we aimed to investigate the additive effect of mesenchymal stem cells (MSC) and defibrotide (DFT) in a rat model of femoral arterial thrombosis. Thirty Sprague Dawley rats were included. An arterial thrombosis model by ferric chloride (FeCl3) was developed in the left femoral artery. The rats were equally assigned to 5 groups: Group 1-Sham-operated (without arterial injury); Group 2-Phosphate buffered saline (PBS) injected; Group 3-MSC; Group 4-DFT; Group 5-MSC + DFT. All had two intraperitoneal injections of 0.5 ml: the 1st injection was 4 h after the procedure and the 2nd one 48 h after the 1st injection. The rats were sacrificed 7 days after the 2nd injection. Although the use of human bone marrow-derived (hBM) hBM-MSC or DFT alone enabled partial resolution of the thrombus, combining them resulted in near-complete resolution. Neovascularization was two-fold better in hBM-MSC + DFT treated rats (11.6 ± 2.4 channels) compared with the hBM-MSC (3.8 ± 2.7 channels) and DFT groups (5.5 ± 1.8 channels) (P < 0.0001 and P= 0.002, respectively). The combined use of hBM-MSC and DFT in a rat model of arterial thrombosis showed additive effect resulting in near-complete resolution of the thrombus.

FT IR spectral investigations of toxic material dibrom using DFT

NASA Astrophysics Data System (ADS)

Parvathy, M.; Gopika, M. S.; Mary, B. L. Bincy; Nimmi, D. E.; Praveen, S. G.; Binoy, J.

2018-05-01

Since, dibrom is widely used organophosphate pesticide, the exploration of its structural features is of immense research interest, and can be effectively carried out using infrared spectroscopy aided by DFT simulation. The present work aims to investigate the interrelation between carbon-halogen bond strength and electronegativity halogen. The resonance of phosphate in dibrom and the deviation from resonant structure due to bridging of oxygen by electron donating methyl group has been investigated in detail. The molecular docking study has been performed to explore the bioactivity of dibrom and to assess the strength of interaction of dibrom towards DNA and BSA.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 4-acetylpyridine

NASA Astrophysics Data System (ADS)

Atilgan, A.; Yurdakul, Ş.; Erdogdu, Y.; Güllüoğlu, M. T.

2018-06-01

The spectroscopic (UV-Vis and infrared), structural and some electronic property observations of the 4-acetylpyridine (4-AP) were reported, which are investigated by using some spectral methods and DFT calculations. FT-IR spectra were obtained for 4-AP at room temperature in the region 4000 cm-1- 400 cm-1. In the DFT calculations, the B3LYP functional with 6-311G++G(d,p) basis set was applied to carry out the quantum mechanical calculations. The Fourier Transform Infrared (FT-IR) and FT-Raman spectra were interpreted by using of normal coordinate analysis based on scaled quantum mechanical force field. The present work expands our understanding of the both the vibrational and structural properties as well as some electronic properties of the 4-AP by means of the theoretical and experimental methods.

SeO2 adsorption on CaO surface: DFT and experimental study on the adsorption of multiple SeO2 molecules

NASA Astrophysics Data System (ADS)

Fan, Yaming; Zhuo, Yuqun; Li, Liangliang

2017-10-01

SeO2 adsorption mechanisms on CaO surface were firstly investigated by both density functional theory (DFT) calculations and adsorption experiments. Adsorption of multiple SeO2 on the CaO (001) surface was investigated using slab model. Based on the results of adsorption energy and surface property, a double-layer adsorption mechanisms were proposed. In experiments, the SeO2 adsorption products were prepared in a U-shaped quartz reactor at 200 °C. The surface morphology was investigated by field emission scanning electron microscopy (FE-SEM). The superficial and total SeO2 mass fractions were measured by X-ray photoelectron spectroscopy (XPS) and inductively coupled plasma atomic emission spectroscopy (ICP-AES), respectively. The surface valence state and bulk structure are determined by XPS and X-Ray Diffraction (XRD). The experimental results are in good agreement with the DFT results. In conclusion, the fundamental SeO2 chemisorption mechanisms on CaO surface were suggested.

Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

2018-03-01

Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.

Spectroscopic (FT-IR, FT-Raman and UV-Visible) investigations, NMR chemical shielding anisotropy (CSA) parameters of 2,6-Diamino-4-chloropyrimidine for dye sensitized solar cells using density functional theory.

PubMed

Gladis Anitha, E; Joseph Vedhagiri, S; Parimala, K

2015-02-05

The molecular structure, geometry optimization, vibrational frequencies of organic dye sensitizer 2,6-Diamino-4-chloropyrimidine (DACP) were studied based on Hartree-Fock (HF) and density functional theory (DFT) using B3LYP methods with 6-311++G(d,p) basis set. Ultraviolet-Visible (UV-Vis) spectrum was investigated by time dependent DFT (TD-DFT). Features of the electronic absorption spectrum in the UV-Visible regions were assigned based on TD-DFT calculation. The absorption bands are assigned to transitions. The interfacial electron transfer between semiconductor TiO2 electrode and dye sensitizer DACP is due to an electron injection process from excited dye to the semiconductor's conduction band. The observed and the calculated frequencies are found to be in good agreement. The energies of the frontier molecular orbitals (FMOS) have also been determined. The chemical shielding anisotropic (CSA) parameters are calculated from the NMR analysis, Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-01

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

Ferrocenyl-substituted dinuclear Cu(II) complex: Synthesis, spectroscopy, electrochemistry, DFT calculations and catecholase activity

NASA Astrophysics Data System (ADS)

Emirik, Mustafa; Karaoğlu, Kaan; Serbest, Kerim; Menteşe, Emre; Yilmaz, Ismail

2016-02-01

A new ferrocenyl-substituted heterocyclic hydrazide ligand and its Cu(II) complex were prepared. The DFT calculations were performed to determine the electronic and molecular structures of the title compounds. The electronic spectra were calculated by using time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the compounds. The bands assignments of IR spectra were achieved in the light of the theoretical vibrational spectral data and total energy distribution values calculated at DFT/B3LYP/6-311++G(d,p) level. The redox behaviors of the ferrocene derivatives were investigated by cyclic voltammetry. The compounds show reversible redox couple assignable to Fc+/Fc couple. The copper(II) complex behaves as an effective catalyst towards oxidation of 3,5-di-tert-butylcatechol to its corresponding quinone derivative in DMF saturated with O2. The reaction follows Michaelis-Menten enzymatic reaction kinetics with turnover numbers 2.32 × 103.

Molecular structure, vibrational spectra and DFT molecular orbital calculations (TD-DFT and NMR) of the antiproliferative drug Methotrexate

NASA Astrophysics Data System (ADS)

Ayyappan, S.; Sundaraganesan, N.; Aroulmoji, V.; Murano, E.; Sebastian, S.

2010-09-01

The FT-IR and FT-Raman spectral studies of the Methotrexate (MTX) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of MTX have been investigated with the help of B3LYP density functional theory (DFT) using 6-31G(d) as basis set. Detailed analysis of the vibrational spectra has been made with the aid of theoretically predicted vibrational frequencies. The vibrational analysis confirms the differently acting ring modes, steric repulsion, conjugation and back-donation. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complement with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Good correlations between the experimental 1H and 13C NMR chemical shifts in DMSO solution and calculated GIAO shielding tensors were found.

First principles investigation of structural, vibrational and thermal properties of black and blue phosphorene

NASA Astrophysics Data System (ADS)

Arif Khalil, R. M.; Ahmad, Javed; Rana, Anwar Manzoor; Bukhari, Syed Hamad; Tufiq Jamil, M.; Tehreem, Tuba; Nissar, Umair

2018-05-01

In this investigation, structural, dynamical and thermal properties of black and blue phosphorene (P) are presented through the first principles calculations based on the density functional theory (DFT). These DFT calculations depict that due to the approximately same values of ground state energy at zero Kelvin and Helmholtz free energy at room-temperature, it is expected that both structures can coexist at transition temperature. Lattice dynamics of both phases were investigated by using the finite displacement supercell approach. It is noticed on the basis of harmonic approximation thermodynamic calculations that the blue phase is thermodynamically more stable than the black phase above 155 K.

Telomere dynamics and homeostasis in a transmissible cancer.

PubMed

Ujvari, Beata; Pearse, Anne-Maree; Taylor, Robyn; Pyecroft, Stephen; Flanagan, Cassandra; Gombert, Sara; Papenfuss, Anthony T; Madsen, Thomas; Belov, Katherine

2012-01-01

Devil Facial Tumour Disease (DFTD) is a unique clonal cancer that threatens the world's largest carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii) with extinction. This transmissible cancer is passed between individual devils by cell implantation during social interactions. The tumour arose in a Schwann cell of a single devil over 15 years ago and since then has expanded clonally, without showing signs of replicative senescence; in stark contrast to a somatic cell that displays a finite capacity for replication, known as the "Hayflick limit". In the present study we investigate the role of telomere length, measured as Telomere Copy Number (TCN), and telomerase and shelterin gene expression, as well as telomerase activity in maintaining hyperproliferation of Devil Facial Tumour (DFT) cells. Our results show that DFT cells have short telomeres. DFTD TCN does not differ between geographic regions or between strains. However, TCN has increased over time. Unlimited cell proliferation is likely to have been achieved through the observed up-regulation of the catalytic subunit of telomerase (TERT) and concomitant activation of telomerase. Up-regulation of the central component of shelterin, the TRF1-intercating nuclear factor 2 (TINF2) provides DFT a mechanism for telomere length homeostasis. The higher expression of both TERT and TINF2 may also protect DFT cells from genomic instability and enhance tumour proliferation. DFT cells appear to monitor and regulate the length of individual telomeres: i.e. shorter telomeres are elongated by up-regulation of telomerase-related genes; longer telomeres are protected from further elongation by members of the shelterin complex, which may explain the lack of spatial and strain variation in DFT telomere copy number. The observed longitudinal increase in gene expression in DFT tissue samples and telomerase activity in DFT cell lines might indicate a selection for more stable tumours with higher proliferative potential.

Structure and Bonding analysis of the cationic electrophilic phosphinidene complexes of iron, ruthenium, and osmium [(η(5)-C5Me5)(CO)2M{PN(i)Pr2}]+, [(η(5)-C5H5)(CO)2M{PNR2}]+ (R = Me, (i)Pr), and [(η(5)-C5H5)(PMe3)2M{PNMe2}]+ (M = Fe, Ru, Os).

PubMed

Pandey, Krishna K; Tiwari, Pradeep; Patidar, Pankaj

2012-11-29

Quantum-chemical DFT calculations for the electronic, molecular structure and M-PNR(2) bonding analyses of the experimentally known cationic electrophilic phosphinidene complexes [(η(5)-C(5)Me(5))(CO)(2)M{PN(i)Pr(2)}](+) and of the model complexes [(η(5)-C(5)H(5))(CO)(2)M{PNR(2)}](+) (R = (i)Pr, Me) and [(η(5)-C(5)H(5))(PMe(3))(2)M{PNMe(2)}](+) were carried out using BP86/TZ2P/ZORA level of theory. The calculated geometrical parameters of the studied complexes are in good agreement with the reported experimental values. The short M-P bond distances and calculated Pauling bond orders (range of 1.23-1.68), suggest the presence of M-P multiple bond characters. The Hirshfeld charge analysis shows that the overall charge flows from phosphinidene ligand to metal fragment. The M-P σ-bonding orbitals are well-occupied (>1.80e). The energy decomposition analysis revealed that the contribution of the electrostatic interaction ΔE(elstat) is, in all studied complexes, significantly larger (55.2-62.6%) than the orbital interactions ΔE(orb). The orbital interactions between metal and PNR(2) in [(η(5)-C(5)H(5))(L)(2)M{PNR(2)}](+) arise mainly from M ← PNR(2) σ-donation. The π-bonding contribution (19-36%) is much smaller than the σ-bonding. The interaction energies, as well as bond dissociation energies, depend on the auxiliary ligand framework around the metal and decrease in the order (η(5)-C(5)H(5)) > (η(5)-C(5)Me(5)) and CO > PMe(3). Upon substitution of R = (i)Pr with smaller group R = Me, the M-PNR(2) bond strength slightly decreases.

Density functional studies on the exchange interaction of a dinuclear Gd(iii)-Cu(ii) complex: method assessment, magnetic coupling mechanism and magneto-structural correlations.

PubMed

Rajaraman, Gopalan; Totti, Federico; Bencini, Alessandro; Caneschi, Andrea; Sessoli, Roberta; Gatteschi, Dante

2009-05-07

Density functional calculations have been performed on a [Gd(iii)Cu(ii)] complex [L(1)CuGd(O(2)CCF(3))(3)(C(2)H(5)OH)(2)] () (where L(1) is N,N'-bis(3-ethoxy-salicylidene)-1,2-diamino-2-methylpropanato) with an aim of assessing a suitable functional within the DFT formalism to understand the mechanism of magnetic coupling and also to develop magneto-structural correlations. Encouraging results have been obtained in our studies where the application of B3LYP on the crystal structure of yields a ferromagnetic J value of -5.8 cm(-1) which is in excellent agreement with the experimental value of -4.42 cm(-1) (H = JS(Gd).S(Cu)). After testing varieties of functional for the method assessment we recommend the use of B3LYP with a combination of an effective core potential basis set. For all electron basis sets the relativistic effects should be incorporated either via the Douglas-Kroll-Hess (DKH) or zeroth-order regular approximation (ZORA) methods. A breakdown approach has been adopted where the calculations on several model complexes of have been performed. Their wave functions have been analysed thereafter (MO and NBO analysis) in order to gain some insight into the coupling mechanism. The results suggest, unambiguously, that the empty Gd(iii) 5d orbitals have a prominent role on the magnetic coupling. These 5d orbitals gain partial occupancy via Cu(ii) charge transfer as well as from the Gd(iii) 4f orbitals. A competing 4f-3d interaction associated with the symmetry of the complex has also been observed. The general mechanism hence incorporates both contributions and sets forth rather a prevailing mechanism for the 3d-4f coupling. The magneto-structural correlations reveal that there is no unique parameter which the J values are strongly correlated with, but an exponential relation to the J value found for the O-Cu-O-Gd dihedral angle parameter is the most credible correlation.

Multinuclear Solid-State Magnetic Resonance as a Sensitive Probe of Structural Changes upon the Occurrence of Halogen Bonding in Co-crystals.

PubMed

Widdifield, Cory M; Cavallo, Gabriella; Facey, Glenn A; Pilati, Tullio; Lin, Jingxiang; Metrangolo, Pierangelo; Resnati, Giuseppe; Bryce, David L

2013-09-02

Although the understanding of intermolecular interactions, such as hydrogen bonding, is relatively well-developed, many additional weak interactions work both in tandem and competitively to stabilize a given crystal structure. Due to a wide array of potential applications, a substantial effort has been invested in understanding the halogen bond. Here, we explore the utility of multinuclear ((13)C, (14/15)N, (19)F, and (127)I) solid-state magnetic resonance experiments in characterizing the electronic and structural changes which take place upon the formation of five halogen-bonded co-crystalline product materials. Single-crystal X-ray diffraction (XRD) structures of three novel co-crystals which exhibit a 1:1 stoichiometry between decamethonium diiodide (i.e., [(CH3)3N(+)(CH2)10N(+)(CH3)3][2 I(-)]) and different para-dihalogen-substituted benzene moieties (i.e., p-C6X2Y4, X=Br, I; Y=H, F) are presented. (13)C and (15)N NMR experiments carried out on these and related systems validate sample purity, but also serve as indirect probes of the formation of a halogen bond in the co-crystal complexes in the solid state. Long-range changes in the electronic environment, which manifest through changes in the electric field gradient (EFG) tensor, are quantitatively measured using (14)N NMR spectroscopy, with a systematic decrease in the (14)N quadrupolar coupling constant (CQ) observed upon halogen bond formation. Attempts at (127)I solid-state NMR spectroscopy experiments are presented and variable-temperature (19)F NMR experiments are used to distinguish between dynamic and static disorder in selected product materials, which could not be conclusively established using solely XRD. Quantum chemical calculations using the gauge-including projector augmented-wave (GIPAW) or relativistic zeroth-order regular approximation (ZORA) density functional theory (DFT) approaches complement the experimental NMR measurements and provide theoretical corroboration for the changes in NMR parameters observed upon the formation of a halogen bond. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Au11Re: A hollow or endohedral binary cluster?

NASA Astrophysics Data System (ADS)

MacLeod Carey, Desmond; Muñoz-Castro, Alvaro

2018-06-01

In this letter, we discussed the plausible formation of [Au11Re] as a superatom with an electronic structure accounted by the 1S21P61D10 shell order, denoting similar stability to [W@Au12]. The possible hollow or endohedral structures show a variable HOMO-LUMO gap according to the given structure (from 0.33 to 1.30 eV, at the PBE/ZORA level). Our results show that the energy minimum is an endohedral arrangement, where Re is encapsulated in a D3h-Au11 cage, retaining a higher gold-dopant stoichiometric ratio. This approach is useful for further rationalization and design of novel superatoms expanding the libraries of endohedral clusters.

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile

NASA Astrophysics Data System (ADS)

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K.; Kant, Rajni; Khajuria, Yugal

2015-04-01

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800 nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity.

Cd hyperfine interactions in DNA bases and DNA of mouse strains infected with Trypanosoma cruzi investigated by perturbed angular correlation spectroscopy and ab initio calculations.

PubMed

Petersen, Philippe A D; Silva, Andreia S; Gonçalves, Marcos B; Lapolli, André L; Ferreira, Ana Maria C; Carbonari, Artur W; Petrilli, Helena M

2014-06-03

In this work, perturbed angular correlation (PAC) spectroscopy is used to study differences in the nuclear quadrupole interactions of Cd probes in DNA molecules of mice infected with the Y-strain of Trypanosoma cruzi. The possibility of investigating the local genetic alterations in DNA, which occur along generations of mice infected with T. cruzi, using hyperfine interactions obtained from PAC measurements and density functional theory (DFT) calculations in DNA bases is discussed. A comparison of DFT calculations with PAC measurements could determine the type of Cd coordination in the studied molecules. To the best of our knowledge, this is the first attempt to use DFT calculations and PAC measurements to investigate the local environment of Cd ions bound to DNA bases in mice infected with Chagas disease. The obtained results also allowed the detection of local changes occurring in the DNA molecules of different generations of mice infected with T. cruzi, opening the possibility of using this technique as a complementary tool in the characterization of complicated biological systems.

Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone

NASA Astrophysics Data System (ADS)

Murugavel, S.; Stephen, C. S. Jacob Prasanna; Subashini, R.; Reddy, H. Raveendranatha; AnanthaKrishnan, Dhanabalan

2016-10-01

The title compound 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE) was synthesised effectively by chlorination of 3-acetyl-4-phenylquinolin-2(1H)-one (APQ) using POCl3 reagent. Structural and vibrational spectroscopic studies were performed by utilizing single crystal X-ray diffraction, FTIR and NMR spectral analysis along with DFT method utilizing GAUSSIAN‧ 03 software. Veda program has been employed to perform a detailed interpretation of vibrational spectra. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NBO, Global chemical reactivity descriptors and thermodynamic properties have been examined by (DFT/B3LYP) method with the 6-311G(d,p) basis set level.

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Water at silica/liquid water interfaces investigated by DFT-MD simulations

NASA Astrophysics Data System (ADS)

Gaigeot, Marie-Pierre

This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.

Double counting in the density functional plus dynamical mean-field theory of transition metal oxides

NASA Astrophysics Data System (ADS)

Dang, Hung

2015-03-01

Recently, the combination of density functional theory (DFT) and dynamical mean-field theory (DMFT) has become a widely-used beyond-mean-field approach for strongly correlated materials. However, not only is the correlation treated in DMFT but also in DFT to some extent, a problem arises as the correlation is counted twice in the DFT+DMFT framework. The correction for this problem is still not well-understood. To gain more understanding of this ``double counting'' problem, I provide a detailed study of the metal-insulator transition in transition metal oxides in the subspace of oxygen p and transition metal correlated d orbitals using DFT+DMFT. I will show that the fully charge self-consistent DFT+DMFT calculations with the standard ``fully-localized limit'' (FLL) double counting correction fail to predict correctly materials such as LaTiO3, LaVO3, YTiO3 and SrMnO3 as insulators. Investigations in a wide range of the p- d splitting, the d occupancy, the lattice structure and the double counting correction itself will be presented to understand the reason behind this failure. I will also show that if the double counting correction is chosen to reproduce the p- d splitting consistent with experimental data, the DFT+DMFT approach can still give reasonable results in comparison with experiments.

First principle investigation of structural and optical properties of cubic titanium dioxide

NASA Astrophysics Data System (ADS)

Dash, Debashish; Chaudhury, Saurabh; Tripathy, Susanta K.

2018-05-01

This paper presents an analysis of structural and optical properties of cubic titanium dioxide (TiO2) using Orthogonalzed Linear Combinations of Atomic Orbitals (OLCAO) basis set under the framework of Density Functional Theory (DFT). The structural property, specially the lattice constant `a' and the optical properties such as refractive index, extinction coefficient, and reflectivity are investigated and discussed in the energy range of 0-16 eV. Further, the results have compared with previous theoretical as well as with experimental results. It was found that DFT based simulation results are approximation to experimental results.

Experimental and theoretical investigation on the molecular structure, spectroscopic and electric properties of 2,4-dinitrodiphenylamine, 2-nitro-4-(trifluoromethyl)aniline and 4-bromo-2-nitroaniline

NASA Astrophysics Data System (ADS)

Hernández-Paredes, Javier; Hernández-Negrete, Ofelia; Carrillo-Torres, Roberto C.; Sánchez-Zeferino, Raúl; Duarte-Moller, Alberto; Alvarez-Ramos, Mario E.

2015-10-01

2,4-Dinitrodiphenylamine (I), 2-nitro-4-(trifluoromethyl)aniline (II) and 4-bromo-2-nitroaniline (III) have been investigated by DFT and experimental FTIR, Raman and UV-Vis spectroscopies. The gas-phase molecular geometries were consistent with similar compounds already reported in the literature. From the vibrational analysis, the main functional groups were identified and their absorption bands were assigned. Some differences were found between the calculated and the experimental UV-Vis spectra. These differences were analyzed and explained in terms of the TD-DFT/B3LYP limitations, which were mainly attributed to charge-transfer (CT) effects. These findings were in agreement with previous works, which reported that TD-DFT/B3LYP calculations diverge from experimental results when the electronic transitions involve CT. Despite this, TD-DFT/B3LYP calculations provided satisfactory results and a detailed description of the electronic transitions involved in the absorption bands of the UV-Vis spectra. In terms of the NLO properties, it was found that compound (I) is a good candidate for NLO applications and deserves further study due to its good β values. However, the β values for compounds (II) and (III) were negatively affected compared to those found on o-nitroaniline.

Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of manganese (II) complex of picolinate: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Tamer, Ömer; Avcı, Davut; Atalay, Yusuf; Çoşut, Bünyemin; Zorlu, Yunus; Erkovan, Mustafa; Yerli, Yusuf

2016-02-01

A novel manganese (II) complex with picolinic acid (pyridine 2-carboxylic acid, Hpic), namely, [Mn(pic)2(H2O)2] was prepared and its crystal structure was fully characterized by using single crystal X-ray diffraction. Picolinate (pic) ligands were coordinated to the central manganese(II) ion as bidentate N,O-donors through the nitrogen atoms of pyridine rings and the oxygen atoms of carboxylate groups forming five-membered chelate rings. The spectroscopic characterization of Mn(II) complex was performed by the applications of FT-IR, Raman, UV-vis and EPR techniques. In order to support these studies, density functional theory (DFT) calculations were carried out by using B3LYP level. IR and Raman spectra were simulated at B3LYP level, and obtained results indicated that DFT calculations generally give compatible results to the experimental ones. The electronic structure of the Mn(II) complex was predicted using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength were investigated by applying natural bond orbital (NBO) analysis. Nonlinear optical properties of Mn(II) complex were investigated by the determining of molecular polarizability (α) and hyperpolarizability (β) parameters.

Tetramer model of leukoemeraldine-emeraldine electrochemistry in the presence of trihalogenoacetic acids. DFT approach.

PubMed

Barbosa, Nuno Almeida; Grzeszczuk, Maria; Wieczorek, Robert

2015-01-15

First results of the application of the DFT computational approach to the reversible electrochemistry of polyaniline are presented. A tetrameric chain was used as the simplest model of the polyaniline polymer species. The system under theoretical investigation involved six tetramer species, two electrons, and two protons, taking part in 14 elementary reactions. Moreover, the tetramer species were interacting with two trihalogenoacetic acid molecules. Trifluoroacetic, trichloroacetic, and tribromoacetic acids were found to impact the redox transformation of polyaniline as shown by cyclic voltammetry. The theoretical approach was considered as a powerful tool for investigating the main factors of importance for the experimental behavior. The DFT method provided molecular structures, interaction energies, and equilibrium energies of all of the tetramer-acid complexes. Differences between the energies of the isolated tetramer species and their complexes with acids are discussed in terms of the elementary reactions, that is, ionization potentials and electron affinities, equilibrium constants, electrode potentials, and reorganization energies. The DFT results indicate a high impact of the acid on the reorganization energy of a particular elementary electron-transfer reaction. The ECEC oxidation path was predicted by the calculations. The model of the reacting system must be extended to octamer species and/or dimeric oligomer species to better approximate the real polymer situation.

Probing the electronic structure of β,β‧-fused quinoxalino porphyrins and tetraazaanthracene-bridged bis-porphyrins with resonance Raman spectroscopy and density functional theory

NASA Astrophysics Data System (ADS)

Elliott, Anastasia B. S.; Gordon, Keith C.; Khoury, Tony; Crossley, Maxwell J.

2012-12-01

A number of π-extended porphyrins and bis-porphyrins were characterised by resonance Raman spectroscopy and density functional theory (DFT) calculations, using both B3LYP and CAM-B3LYP functionals. Single porphyrin species, incorporating a β,β'-fused quinoxalino unit, and tetraazaanthracene-bridged bis-porphyrins were investigated. Geometry optimisation predicted all species were planar with respect to the porphyrin core(s). Comparison of experimental with simulated vibrational spectra, obtained via DFT calculations [B3LYP/6-31G(d)], verified the modelling; demonstrated by a mean absolute deviation (MAD) between experimental and calculated band positions of less than 10 cm-1. Simulated electronic transitions obtained via time-dependent DFT [TD-DFT, B3LYP and CAM-B3LYP/6-31G(d)] lay within 0.4 eV of experimental bands and calculations showed perturbation of the frontier molecular orbitals (FMOs) following substitution of the porphyrin core. The nature of transitions that were investigated experimentally via resonance Raman enhancement showed consistency with the character of calculated transitions. A wavepacket analysis of the resonance Raman intensities provided electronic parameters, such as reorganisation energy, as well as normal mode displacements (Δi) that were also consistent with the nature of the specific vibrational modes and probed optical transitions. The largest vibrational reorganisation value obtained was for the Bsh band of compound (1). This result is consistent with the greater electron density shift of the transition found from DFT and resonance Raman and also the less symmetrical nature of (1).

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

DFT-Assisted Polymorph Identification from Lattice Raman Fingerprinting

PubMed Central

2017-01-01

A combined experimental and theoretical approach, consisting of lattice phonon Raman spectroscopy and density functional theory (DFT) calculations, is proposed as a tool for lattice dynamics characterization and polymorph phase identification. To illustrate the reliability of the method, the lattice phonon Raman spectra of two polymorphs of the molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]benzothiophene are investigated. We show that DFT calculations of the lattice vibrations based on the known crystal structures, including many-body dispersion van der Waals (MBD-vdW) corrections, predict experimental data within an accuracy of ≪5 cm–1 (≪0.6 meV). Due to the high accuracy of the simulations, they can be used to unambiguously identify different polymorphs and to characterize the nature of the lattice vibrations and their relationship to the structural properties. More generally, this work implies that DFT-MBD-vdW is a promising method to describe also other physical properties that depend on lattice dynamics like charge transport. PMID:28731723

Equation of state of mixtures: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, R. J.; Root, S.; Haill, T. A.; Schroen, D. G.; Mattsson, T. R.; Flicker, D. G.; Sandia National Laboratories Collaboration

2011-06-01

Mixtures of materials are expected to behave quite differently from their isolated constituents, particularly when the constituents atomic numbers differ significantly. To investigate the mixture behavior, we performed density functional theory (DFT) calculations on xenon/hydrogen, xenon/ethane, and platinum/hydrocarbon mixtures. In addition, we performed shock compression experiments on platinum-doped hydrocarbon foams up to 480 GPa using the Sandia Z-accelerator. Since the DFT simulations treat electrons and nuclei generically, simulations of pure and mix systems are expected to be of comparable accuracy. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. The role of de-mixing and the relative contributions of the enthalpy of mixing are explored. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Constrained subsystem density functional theory.

PubMed

Ramos, Pablo; Pavanello, Michele

2016-08-03

Constrained Subsystem Density Functional Theory (CSDFT) allows to compute diabatic states for charge transfer reactions using the machinery of the constrained DFT method, and at the same time is able to embed such diabatic states in a molecular environment via a subsystem DFT scheme. The CSDFT acronym is chosen to reflect the fact that on top of the subsystem DFT approach, a constraining potential is applied to each subsystem. We show that CSDFT can successfully tackle systems as complex as single stranded DNA complete of its backbone, and generate diabatic states as exotic as a hole localized on a phosphate group as well as on the nucleobases. CSDFT will be useful to investigators needing to evaluate the environmental effect on charge transfer couplings for systems in condensed phase environments.

A theoretical insight for solvent effect on myoglobin assay of W(CO)4L2 type novel complexes with DFT/TDDFT

NASA Astrophysics Data System (ADS)

Üstün, Elvan; Demi˙r, Serpil; Coşkun, Feyzullah; Kaloğlu, Murat; Şahi˙n, Onur; Büyükgüngör, Orhan; Özdemi˙r, İsmail

2016-11-01

Novel tetracarbonyl complexes of type W(CO)4L2 (L: 4-chlorobenzylimidazoline; 4-methylbenzylimidazoline; 3,5-dimethylbenzylimidazoline; 2,4,6-trimethylbenzylimidazoline; 2,3,5,6- tetramethylbenzylimidazoline) were synthesized. Then newly synthesized novel compounds were characterized by IR, 1H NMR, 13C NMR and LC-MS. The characterizations of two of the complexes have also been confirmed with single crystal X-Ray diffraction and DFT optimization results of these complexes have been compared with single crystal results. We have investigated the solvent effect on the structure and metal-to-ligand charge transfer (MLCT) transitions with DFT/TDDFT calculations with ORCA package program with BP86 functional.

Electronic structure, transport, and collective effects in molecular layered systems.

PubMed

Hahn, Torsten; Ludwig, Tim; Timm, Carsten; Kortus, Jens

2017-01-01

The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc) and a flourinated copper phthalocyanine-manganese phthalocyanine (F 16 CoPc/MnPc) heterostructure, are investigated by means of density functional theory (DFT) and the non-equilibrium Green's function (NEGF) approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

Telomere Dynamics and Homeostasis in a Transmissible Cancer

PubMed Central

Ujvari, Beata; Pearse, Anne-Maree; Taylor, Robyn; Pyecroft, Stephen; Flanagan, Cassandra; Gombert, Sara; Papenfuss, Anthony T.; Madsen, Thomas; Belov, Katherine

2012-01-01

Background Devil Facial Tumour Disease (DFTD) is a unique clonal cancer that threatens the world's largest carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii) with extinction. This transmissible cancer is passed between individual devils by cell implantation during social interactions. The tumour arose in a Schwann cell of a single devil over 15 years ago and since then has expanded clonally, without showing signs of replicative senescence; in stark contrast to a somatic cell that displays a finite capacity for replication, known as the “Hayflick limit”. Methodology/Principal Findings In the present study we investigate the role of telomere length, measured as Telomere Copy Number (TCN), and telomerase and shelterin gene expression, as well as telomerase activity in maintaining hyperproliferation of Devil Facial Tumour (DFT) cells. Our results show that DFT cells have short telomeres. DFTD TCN does not differ between geographic regions or between strains. However, TCN has increased over time. Unlimited cell proliferation is likely to have been achieved through the observed up-regulation of the catalytic subunit of telomerase (TERT) and concomitant activation of telomerase. Up-regulation of the central component of shelterin, the TRF1-intercating nuclear factor 2 (TINF2) provides DFT a mechanism for telomere length homeostasis. The higher expression of both TERT and TINF2 may also protect DFT cells from genomic instability and enhance tumour proliferation. Conclusions/Significance DFT cells appear to monitor and regulate the length of individual telomeres: i.e. shorter telomeres are elongated by up-regulation of telomerase-related genes; longer telomeres are protected from further elongation by members of the shelterin complex, which may explain the lack of spatial and strain variation in DFT telomere copy number. The observed longitudinal increase in gene expression in DFT tissue samples and telomerase activity in DFT cell lines might indicate a selection for more stable tumours with higher proliferative potential. PMID:22952882

Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes.

PubMed

Holland, Jason P; Green, Jennifer C

2010-04-15

The electronic absorption spectra of a range of copper and zinc complexes have been simulated by using time-dependent density functional theory (TD-DFT) calculations implemented in Gaussian03. In total, 41 exchange-correlation (XC) functionals including first-, second-, and third-generation (meta-generalized gradient approximation) DFT methods were compared in their ability to predict the experimental electronic absorption spectra. Both pure and hybrid DFT methods were tested and differences between restricted and unrestricted calculations were also investigated by comparison of analogous neutral zinc(II) and copper(II) complexes. TD-DFT calculated spectra were optimized with respect to the experimental electronic absorption spectra by use of a Matlab script. Direct comparison of the performance of each XC functional was achieved both qualitatively and quantitatively by comparison of optimized half-band widths, root-mean-squared errors (RMSE), energy scaling factors (epsilon(SF)), and overall quality-of-fit (Q(F)) parameters. Hybrid DFT methods were found to outperform all pure DFT functionals with B1LYP, B97-2, B97-1, X3LYP, and B98 functionals providing the highest quantitative and qualitative accuracy in both restricted and unrestricted systems. Of the functionals tested, B1LYP gave the most accurate results with both average RMSE and overall Q(F) < 3.5% and epsilon(SF) values close to unity (>0.990) for the copper complexes. The XC functional performance in spin-restricted TD-DFT calculations on the zinc complexes was found to be slightly worse. PBE1PBE, mPW1PW91 and B1LYP gave the most accurate results with typical RMSE and Q(F) values between 5.3 and 7.3%, and epsilon(SF) around 0.930. These studies illustrate the power of modern TD-DFT calculations for exploring excited state transitions of metal complexes. 2009 Wiley Periodicals, Inc.

An Electronic Structure Approach to Charge Transfer and Transport in Molecular Building Blocks for Organic Optoelectronics

NASA Astrophysics Data System (ADS)

Hendrickson, Heidi Phillips

A fundamental understanding of charge separation in organic materials is necessary for the rational design of optoelectronic devices suited for renewable energy applications and requires a combination of theoretical, computational, and experimental methods. Density functional theory (DFT) and time-dependent (TD)DFT are cost effective ab-initio approaches for calculating fundamental properties of large molecular systems, however conventional DFT methods have been known to fail in accurately characterizing frontier orbital gaps and charge transfer states in molecular systems. In this dissertation, these shortcomings are addressed by implementing an optimally-tuned range-separated hybrid (OT-RSH) functional approach within DFT and TDDFT. The first part of this thesis presents the way in which RSH-DFT addresses the shortcomings in conventional DFT. Environmentally-corrected RSH-DFT frontier orbital energies are shown to correspond to thin film measurements for a set of organic semiconducting molecules. Likewise, the improved RSH-TDDFT description of charge transfer excitations is benchmarked using a model ethene dimer and silsesquioxane molecules. In the second part of this thesis, RSH-DFT is applied to chromophore-functionalized silsesquioxanes, which are currently investigated as candidates for building blocks in optoelectronic applications. RSH-DFT provides insight into the nature of absorptive and emissive states in silsesquioxanes. While absorption primarily involves transitions localized on one chromophore, charge transfer between chromophores and between chromophore and silsesquioxane cage have been identified. The RSH-DFT approach, including a protocol accounting for complex environmental effects on charge transfer energies, was tested and validated against experimental measurements. The third part of this thesis addresses quantum transport through nano-scale junctions. The ability to quantify a molecular junction via spectroscopic methods is crucial to their technological design and development. Time dependent perturbation theory, employed by non-equilibrium Green's function formalism, is utilized to study the effect of quantum coherences on electron transport and the effect of symmetry breaking on the electronic spectra of model molecular junctions. The fourth part of this thesis presents the design of a physical chemistry course based on a pedagogical approach called Writing-to-Teach. The nature of inaccuracies expressed in student-generated explanations of quantum chemistry topics, and the ability of a peer review process to engage these inaccuracies, is explored within this context.

First principle study of a potential bioactive molecule with tetrahydroisoquinoline, carbothiomide and adamantane scaffolds

NASA Astrophysics Data System (ADS)

Al-Shehri, Mona M.; Al-Majed, Abdul-Rahman A.; Aljohar, Haya I.; El-Emam, Ali A.; Pathak, Shilendra K.; Sachan, Alok K.; Prasad, Onkar; Sinha, Leena

2017-09-01

The FT-Raman and FT-IR spectra of N-(adamantan-1-yl)-1,2,3,4-tetrahydroisoquinoline-2-carbothioamide were recorded and investigated. The DFT/M06-2X/6-311++G(d,p) method was used to compute the vibrational wavenumbers. The effect of solvents (water, carbon tetrachloride and chloroform) on the dipole moment and polarizability has been evaluated. UV-Vis spectrum of the title compound was recorded and compared with the theoretical spectrum calculated by TD-DFT approach. To investigate the movement of electrons within the system when excited, the difference of the excited and ground state densities has also been plotted. The molecular docking studies reveals that the investigated compound may exhibit HIV-1 Protease inhibitory activity.

Acid base chemistry of luteolin and its methyl-ether derivatives: A DFT and ab initio investigation

NASA Astrophysics Data System (ADS)

Amat, Anna; De Angelis, Filippo; Sgamellotti, Antonio; Fantacci, Simona

2008-09-01

The acid-base chemistry of luteolin, a flavonoid with important pharmacological and dyeing properties, and of the related methyl ether derivatives have been investigated by DFT and MP2 methods, testing different computational setups. We calculate the pK's of all the possible deprotonation sites, for which no experimental assignment could be achieved. The calculated pK's deliver a different acidity order for the two most acidic deprotonation sites between luteolin and its methyl ether derivatives, due to intramolecular hydrogen bonding in luteolin. A lowest p Ka of 6.19 is computed for luteolin, in good agreement with available experimental data.

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile.

PubMed

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K; Kant, Rajni; Khajuria, Yugal

2015-04-05

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity. Copyright © 2014 Elsevier B.V. All rights reserved.

Polymorphism and thermodynamic ground state of silver fulminate studied from van der Waals density functional calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yedukondalu, N.; Vaitheeswaran, G., E-mail: gvsp@uohyd.ernet.in

2014-06-14

Silver fulminate (AgCNO) is a primary explosive, which exists in two polymorphic phases, namely, orthorhombic (Cmcm) and trigonal (R3{sup ¯}) forms at ambient conditions. In the present study, we have investigated the effect of pressure and temperature on relative phase stability of the polymorphs using planewave pseudopotential approaches based on Density Functional Theory (DFT). van der Waals interactions play a significant role in predicting the phase stability and they can be effectively captured by semi-empirical dispersion correction methods in contrast to standard DFT functionals. Based on our total energy calculations using DFT-D2 method, the Cmcm structure is found to bemore » the preferred thermodynamic equilibrium phase under studied pressure and temperature range. Hitherto Cmcm and R3{sup ¯} phases denoted as α- and β-forms of AgCNO, respectively. Also a pressure induced polymorphic phase transition is seen using DFT functionals and the same was not observed with DFT-D2 method. The equation of state and compressibility of both polymorphic phases were investigated. Electronic structure and optical properties were calculated using full potential linearized augmented plane wave method within the Tran-Blaha modified Becke-Johnson potential. The calculated electronic structure shows that α, β phases are indirect bandgap insulators with a bandgap values of 3.51 and 4.43 eV, respectively. The nature of chemical bonding is analyzed through the charge density plots and partial density of states. Optical anisotropy, electric-dipole transitions, and photo sensitivity to light of the polymorphs are analyzed from the calculated optical spectra. Overall, the present study provides an early indication to experimentalists to avoid the formation of unstable β-form of AgCNO.« less

Local and average structure of Mn- and La-substituted BiFeO3

NASA Astrophysics Data System (ADS)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.

The role of the van der Waals interactions in the adsorption of anthracene and pentacene on the Ag(111) surface

NASA Astrophysics Data System (ADS)

Morbec, Juliana M.; Kratzer, Peter

2017-01-01

Using first-principles calculations based on density-functional theory (DFT), we investigated the effects of the van der Waals (vdW) interactions on the structural and electronic properties of anthracene and pentacene adsorbed on the Ag(111) surface. We found that the inclusion of vdW corrections strongly affects the binding of both anthracene/Ag(111) and pentacene/Ag(111), yielding adsorption heights and energies more consistent with the experimental results than standard DFT calculations with generalized gradient approximation (GGA). For anthracene/Ag(111) the effect of the vdW interactions is even more dramatic: we found that "pure" DFT-GGA calculations (without including vdW corrections) result in preference for a tilted configuration, in contrast to the experimental observations of flat-lying adsorption; including vdW corrections, on the other hand, alters the binding geometry of anthracene/Ag(111), favoring the flat configuration. The electronic structure obtained using a self-consistent vdW scheme was found to be nearly indistinguishable from the conventional DFT electronic structure once the correct vdW geometry is employed for these physisorbed systems. Moreover, we show that a vdW correction scheme based on a hybrid functional DFT calculation (HSE) results in an improved description of the highest occupied molecular level of the adsorbed molecules.

Local and average structure of Mn- and La-substituted BiFeO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO 3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO 3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.« less

Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices

DTIC Science & Technology

2012-06-14

implemented a prototype DFT simulation software using two different open source Finite Element (FE) libraries: DEALII and FENICS . These two libraries have been...ATK. In the first part of this Phase I project we investigated two different candidate finite element libraries, DEAL II and FENICS . Although both...element libraries, Deal.II and FEniCS /dolfin, for use as back-ends to a finite element DFT in ATK, Quantum Insight and QuantumWise A/S, October 2011.

Experimental and theoretical investigation on the molecular structure, spectroscopic and electric properties of 2,4-dinitrodiphenylamine, 2-nitro-4-(trifluoromethyl)aniline and 4-bromo-2-nitroaniline.

PubMed

Hernández-Paredes, Javier; Hernández-Negrete, Ofelia; Carrillo-Torres, Roberto C; Sánchez-Zeferino, Raúl; Duarte-Moller, Alberto; Alvarez-Ramos, Mario E

2015-10-05

2,4-Dinitrodiphenylamine (I), 2-nitro-4-(trifluoromethyl)aniline (II) and 4-bromo-2-nitroaniline (III) have been investigated by DFT and experimental FTIR, Raman and UV-Vis spectroscopies. The gas-phase molecular geometries were consistent with similar compounds already reported in the literature. From the vibrational analysis, the main functional groups were identified and their absorption bands were assigned. Some differences were found between the calculated and the experimental UV-Vis spectra. These differences were analyzed and explained in terms of the TD-DFT/B3LYP limitations, which were mainly attributed to charge-transfer (CT) effects. These findings were in agreement with previous works, which reported that TD-DFT/B3LYP calculations diverge from experimental results when the electronic transitions involve CT. Despite this, TD-DFT/B3LYP calculations provided satisfactory results and a detailed description of the electronic transitions involved in the absorption bands of the UV-Vis spectra. In terms of the NLO properties, it was found that compound (I) is a good candidate for NLO applications and deserves further study due to its good β values. However, the β values for compounds (II) and (III) were negatively affected compared to those found on o-nitroaniline. Copyright © 2015 Elsevier B.V. All rights reserved.

DFT and PCM-TD-DFT investigation of the electronic structures and spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinone derivatives

NASA Astrophysics Data System (ADS)

El-Taher, Sabry; Metwaly, Mohamed

2017-04-01

UV-Visible absorption spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinones (5pR-PPTT, R = H, CH3, CH3O, and N(CH3)2) were measured in different solvents and investigated using the theoretical PCM-TD-DFT scheme. A benchmark evaluation against experimental results on the accuracy of different DFT functionals has been performed. The best agreement with X-ray data is achieved by using the long-range corrected LC-wPBE functional, while the PBE0 functional provided the most accurate λmax for the studied compounds. The thionic forms of the ZE isomers of the studied compounds are found to be the most stable tautomers. The assignation debate of the second absorption band of rhodanine [2-thioxo-4-thiazolidinone (Rd)] has been solved by confirming on its π-π∗ nature. It was found that the expansion of the π-conjugation system at position 5 of Rd ring leads to significant bathochromic shift. The CT lengths (Δr) and dipole moment change (ΔμCT) indices showed that the charge transfer character of the electronic transitions is directly proportional to the electron-releasing strength of substituted phenyl ring. It was concluded that the red shifting of the maximum absorption is mainly regulated by the solvent polarizability and much less by solvent polarity.

Molecular structure, vibrational spectra, AIM, HOMO-LUMO, NBO, UV, first order hyperpolarizability, analysis of 3-thiophenecarboxylic acid monomer and dimer by Hartree-Fock and density functional theory

NASA Astrophysics Data System (ADS)

Issaoui, Noureddine; Ghalla, Houcine; Muthu, S.; Flakus, H. T.; Oujia, Brahim

2015-02-01

In this work, the molecular structure, harmonic vibrational frequencies, UV, NBO and AIM of 3-thiophenecarboxilic acid (abbreviated as 3-TCA) monomer and dimer has been investigated. The FT-IR and FT-Raman spectra were recorded. The ground-state molecular geometry and vibrational frequencies have been calculated by using the Hartree-Fock (HF) and density functional theory (DFT)/B3LYP methods and 6-311++G(d,p) as a basis set. The fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with VEDA program. Comparison of the observed fundamental vibrational frequencies of 3-TCA with calculated results by HF and DFT methods indicates that B3LYP is better to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title compound have been constructed. A study on the Mulliken atomic charges, the electronic properties were performed by time-dependent DFT (TD-DFT) approach, frontier molecular orbitals (HOMO-LUMO), molecular electrostatic potential (MEP) and thermodynamic properties have been performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been also computed.

Molecular structure, vibrational spectra, AIM, HOMO-LUMO, NBO, UV, first order hyperpolarizability, analysis of 3-thiophenecarboxylic acid monomer and dimer by Hartree-Fock and density functional theory.

PubMed

Issaoui, Noureddine; Ghalla, Houcine; Muthu, S; Flakus, H T; Oujia, Brahim

2015-02-05

In this work, the molecular structure, harmonic vibrational frequencies, UV, NBO and AIM of 3-thiophenecarboxilic acid (abbreviated as 3-TCA) monomer and dimer has been investigated. The FT-IR and FT-Raman spectra were recorded. The ground-state molecular geometry and vibrational frequencies have been calculated by using the Hartree-Fock (HF) and density functional theory (DFT)/B3LYP methods and 6-311++G(d,p) as a basis set. The fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with VEDA program. Comparison of the observed fundamental vibrational frequencies of 3-TCA with calculated results by HF and DFT methods indicates that B3LYP is better to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title compound have been constructed. A study on the Mulliken atomic charges, the electronic properties were performed by time-dependent DFT (TD-DFT) approach, frontier molecular orbitals (HOMO-LUMO), molecular electrostatic potential (MEP) and thermodynamic properties have been performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, molecular structure, vibrational spectroscopy, optical investigation and DFT study of a novel hybrid material: 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate

NASA Astrophysics Data System (ADS)

Kessentini, A.; Dammak, T.; Belhouchet, M.

2017-12-01

In his work we investigate a new halogenotin (IV) organic inorganic material. The structure, determined by single-crystal X-ray diffraction at 293 K of 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate abbreviated 3,3‧(DDS)SnCl6, can be viewed as inorganic layers built from (SnCl6)2- octahedra and H2O molecules, between which, the organic entities [C12H14N2O2S]2+ are inserted. Experimental room-temperature X-ray studies were supported by theoretical methods using density functional theory (DFT). The detailed examination of the vibrational spectra of our material was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. The optical properties in the UV-visible region have been explored by the UV-visible absorption. This material shows a single absorption band centred at 325 nm (318 eV). The energy difference between Occupied, HOMO and Lowest Unoccupied, LUMO orbital which is called energy gap can be used to predict the strength and stability of metal complexes, as well as in determining molecular electrical transport properties. For the calculation of excitation energies in the optical studies we used Time-Dependent Density Functional Theory (TD-DFT). In addition, Mulliken population method and molecular electrostatic potential (MEP) of the title material have been theoretically studied by GAUSSIAN 03 package.

Charge Transfer Enhancement in the D-π-A Type Porphyrin Dyes: A Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) Study.

PubMed

Kang, Guo-Jun; Song, Chao; Ren, Xue-Feng

2016-11-25

The electronic geometries and optical properties of two D-π-A type zinc porphyrin dyes (NCH₃-YD2 and TPhe-YD) were systematically investigated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) to reveal the origin of significantly altered charge transfer enhancement by changing the electron donor of the famous porphyrin-based sensitizer YD2-o-C8. The molecular geometries and photophysical properties of dyes before and after binding to the TiO₂ cluster were fully investigated. From the analyses of natural bond orbital (NBO), extended charge decomposition analysis (ECDA), and electron density variations (Δρ) between the excited state and ground state, it was found that the introduction of N(CH₃)₂ and 1,1,2-triphenylethene groups enhanced the intramolecular charge-transfer (ICT) character compared to YD2-o-C8. The absorption wavelength and transition possess character were significantly influenced by N(CH₃)₂ and 1,1,2-triphenylethene groups. NCH₃-YD2 with N(CH₃)₂ groups in the donor part is an effective way to improve the interactions between the dyes and TiO₂ surface, light having efficiency (LHE), and free energy change (ΔG inject ), which is expected to be an efficient dye for use in dye-sensitized solar cells (DSSCs).

DFT-GGA errors in NO chemisorption energies on (111) transition metal surfaces

NASA Astrophysics Data System (ADS)

Huang, Xu; Mason, Sara E.

2014-03-01

We investigate whether well-known DFT-GGA errors in predicting the chemisorption energy (Echem) of CO on transition metal surfaces manifest in analogous NO chemisorption systems. While widely investigated in the case of CO/metal, analogous DFT-GGA errors have long been claimed to be absent in NO/metal chemisorption. Here, we provide theoretical evidence of systematic enhanced back-donation in NO/metal chemisorption at the DFT-GGA level. We use electronic structure analysis to show that the partially filled molecular NO 2π* orbital rehybridizes with the transition metal d-band to form new bonding and anti-bonding states. We relate the back-donation charge transfer associated with chemisorption to the promotion of an electron from the 5σ orbital to the 2π* orbital in the gas-phase NO G2Σ- ← X2Π excitation. We establish linear relationships between Echem and ΔEG ← X and formulate an Echem correction scheme in the style of Mason et al. [Physical Review B 69, 161401(R)]. We apply the NO Echem correction method to the (111) surfaces of Pt, Pd, Rh, and Ir, with NO chemisorption modeled at a coverage of 0.25 ML. We note that the slope of Echemvs. ΔEG ← X and the dipole moment depend strongly on adsorption site for each metal, and we construct an approximate correction scheme which we test using NO/Pt(100) chemisorption.

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

PubMed

Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

2014-11-18

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Sweetman, A. M.; Lekkas, I.; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2015-02-01

The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images.

Superoxide dismutase activity of Cu-bound prion protein

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry

2009-03-01

Misfolding of the prion protein, PrP, has been linked to a group of neurodegenerative diseases, including the mad cow disease in cattle and the Creutzfeldt-Jakob disease in humans. The normal function of PrP is still unknown, but it was found that the PrP can efficiently bind Cu(II) ions. Early experiments suggested that Cu-PrP complex possesses significant superoxide dismutase (SOD) activity, but later experiments failed to confirm it and at present this issue remains unresolved. Using a recently developed hybrid DFT/DFT method, which combines Kohn-Sham DFT for the solute and its first solvation shells with orbital-free DFT for the remainder of the solvent, we have investigated SOD activity of PrP. The PrP is capable of incorporating Cu(II) ions in several binding modes and our calculations find that each mode has a different SOD activity. The highest activity found is comparable to those of well-known SOD proteins, suggesting that the conflicting experimental results may be due to different bindings of Cu(II) in those experiments.

Copper attachment to a non-octarepeat site in prion protein

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Bernholc, Jerry

2010-03-01

Prion protein, PrP, plays a causative role in several neurodegenerative diseases, including mad cow disease in cattle and Creutzfeldt-Jakob disease in humans. The PrP is known to efficiently bind copper ions and this ability has been linked to its function. PrP contains up to six binding sites, four of which are located in the so-called octarepeat region and are now well known. The binding sites outside this region are still largely undetermined, despite evidence of their relevance to prion diseases. Using a hybrid DFT/DFT, which combines Kohn-Sham DFT with orbital-free DFT to achieve accurate and efficient description of solvent effects in ab initio calculations, we have investigated copper attachment to the sequence GGGTH, which represents the copper binding site located at His96. We have considered both NNNN and NNNO types of copper coordination, as suggested by experiments. Our calculations have determined the geometry of copper attachment site and its energetics. Comparison to the already known binding sites provides insight into the process of copper uptake in PrP.

Water dissociation and CO oxidation over Au/anatase catalyst. A DFT-D2 study

NASA Astrophysics Data System (ADS)

Saqlain, Muhammad Adnan; Hussain, Akhtar; Siddiq, Muhammad; Leitão, Alexandre A.

2018-03-01

With the help of DFT-D2 methodology, we have investigated the adsorption of water on clean anatase(001) and Au/anatase(001). In the former case, adsorption energies of H2O differ to small extent computed employing GGA = PW91 and DFT-D2 methods. While the GGA = PW91 predicts that water would desorb close to 650 K on the TiO2 surface, the DFT-D2 predicts that desorption is most likely to occur above 700 K. A comparison of water adsorption on TiO2 and Au/TiO2 surfaces shows that the TiO2 prefers dimer adsorption whereas the Au/TiO2 prefers monomer adsorption. We found that the diffusion of surface hydroxyls on to the Au cluster from the Au/TiO2 periphery is unlikely and it seems that the CO oxidation would occur at the Au/TiO2 boundary. The results show that water dissociation and CO oxidation steps occur easily on Au/TiO2 indicating that this could be good alternative catalyst for water gas shift reaction industry.

Multiscale Investigations of the Early Stage Oxidation on Cu Surfaces

NASA Astrophysics Data System (ADS)

Zhu, Qing; Xiao, Penghao; Lian, Xin; Yang, Shen-Che; Henkelman, Grame; Saidi, Wissam; Yang, Judith; University of Pittsburgh Team; University of Texas at Austin Team

Previous in situ TEM experiments have shown that the oxidation of the three low index Cu surfaces (100), (110) and (111) exhibit different oxide nucleation rates, and the resulting oxides have 3-dimensional (3D) island shapes or 2D rafts under different conditions. In order to better understand these results, we have investigated the early stages of Cu oxidation using a multiscale computational approach that employs density functional theory (DFT), reactive force field (ReaxFF), and kinetic Mote Carlo (KMC). With DFT calculation, we have compared O2 dissociation barriers on Cu (100), (110) and (111) surfaces at high oxygen coverage to evaluate the kinetic barrier of sublayer oxidization. We found that O2 dissociation barriers on Cu(111) surface are all lower than those on (110) and (100) surfaces. This trend agrees with experimental observations that (111) surface is easier to oxidize. These DFT calculated energy barriers are then incorporated into KMC simulations. The large scale ReaxFF molecular dynamics and KMC simulations detail the oxidation dynamics of the different Cu surfaces, and show the formation of various oxide morphologies that are consistent with experimental observations.

Lattice and Valence Electronic Structures of Crystalline Octahedral Molybdenum Halide Clusters-Based Compounds, Cs2[Mo6X14] (X = Cl, Br, I), Studied by Density Functional Theory Calculations.

PubMed

Saito, Norio; Cordier, Stéphane; Lemoine, Pierric; Ohsawa, Takeo; Wada, Yoshiki; Grasset, Fabien; Cross, Jeffrey S; Ohashi, Naoki

2017-06-05

The electronic and crystal structures of Cs 2 [Mo 6 X 14 ] (X = Cl, Br, I) cluster-based compounds were investigated by density functional theory (DFT) simulations and experimental methods such as powder X-ray diffraction, ultraviolet-visible spectroscopy, and X-ray photoemission spectroscopy (XPS). The experimentally determined lattice parameters were in good agreement with theoretically optimized ones, indicating the usefulness of DFT calculations for the structural investigation of these clusters. The calculated band gaps of these compounds reproduced those experimentally determined by UV-vis reflectance within an error of a few tenths of an eV. Core-level XPS and effective charge analyses indicated bonding states of the halogens changed according to their sites. The XPS valence spectra were fairly well reproduced by simulations based on the projected electron density of states weighted with cross sections of Al K α , suggesting that DFT calculations can predict the electronic properties of metal-cluster-based crystals with good accuracy.

DFT investigation on the electronic structure of Faujasite

NASA Astrophysics Data System (ADS)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

2013-11-01

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

Adsorption of beryllium atoms and clusters both on graphene and in a bilayer of graphite investigated by DFT.

PubMed

Ferro, Yves; Fernandez, Nicolas; Allouche, Alain; Linsmeier, Christian

2013-01-09

We herein investigate the interaction of beryllium with a graphene sheet and in a bilayer of graphite by means of periodic DFT calculations. In all cases, we find the beryllium atoms to be more weakly bonded on graphene than in the bilayer. Be(2) forms both magnetic and non-magnetic structures on graphene depending on the geometrical configuration of adsorption. We find that the stability of the Be/bilayer system increases with the size of the beryllium clusters inserted into the bilayer of graphite. We also find a charge transfer from beryllium to the graphite layers. All these results are analysed in terms of electronic structure.

Molecular modeling the microstructure and phase behavior of bulk and inhomogeneous complex fluids

NASA Astrophysics Data System (ADS)

Bymaster, Adam

Accurate prediction of the thermodynamics and microstructure of complex fluids is contingent upon a model's ability to capture the molecular architecture and the specific intermolecular and intramolecular interactions that govern fluid behavior. This dissertation makes key contributions to improving the understanding and molecular modeling of complex bulk and inhomogeneous fluids, with an emphasis on associating and macromolecular molecules (water, hydrocarbons, polymers, surfactants, and colloids). Such developments apply broadly to fields ranging from biology and medicine, to high performance soft materials and energy. In the bulk, the perturbed-chain statistical associating fluid theory (PC-SAFT), an equation of state based on Wertheim's thermodynamic perturbation theory (TPT1), is extended to include a crossover correction that significantly improves the predicted phase behavior in the critical region. In addition, PC-SAFT is used to investigate the vapor-liquid equilibrium of sour gas mixtures, to improve the understanding of mercaptan/sulfide removal via gas treating. For inhomogeneous fluids, a density functional theory (DFT) based on TPT1 is extended to problems that exhibit radially symmetric inhomogeneities. First, the influence of model solutes on the structure and interfacial properties of water are investigated. The DFT successfully describes the hydrophobic phenomena on microscopic and macroscopic length scales, capturing structural changes as a function of solute size and temperature. The DFT is used to investigate the structure and effective forces in nonadsorbing polymer-colloid mixtures. A comprehensive study is conducted characterizing the role of polymer concentration and particle/polymer size ratio on the structure, polymer induced depletion forces, and tendency towards colloidal aggregation. The inhomogeneous form of the association functional is used, for the first time, to extend the DFT to associating polymer systems, applicable to any association scheme. Theoretical results elucidate how reversible bonding governs the structure of a fluid near a surface and in confined environments, the molecular connectivity (formation of supramolecules, star polymers, etc.) and the phase behavior of the system. Finally, the DFT is extended to predict the inter- and intramolecular correlation functions of polymeric fluids. A theory capable of providing such local structure is important to understanding how local chemistry, branching, and bond flexibility affect the thermodynamic properties of polymers.

DFT/TD-DFT study of solvent effect as well the substituents influence on the different features of TPP derivatives for PDT application

NASA Astrophysics Data System (ADS)

Dulski, Mateusz; Kempa, Marta; Kozub, Patrycja; Wójcik, Justyna; Rojkiewicz, Marcin; Kuś, Piotr; Szurko, Agnieszka; Ratuszna, Alicja; Wrzalik, Roman

2013-03-01

Spectral characteristics study of meso-tetraphenylporphyrin derivatives (TPP1 and TPP2) used as photosensitizers for utilization in photodynamic therapy (PDT) has been performed by density functional theory (DFT) and time dependent DFT (TD-DFT) calculations at B3LYP/6-31G(d) level of theory using PCM solvation model. The geometrical parameters of porphyrins have been studied for ground and excited-state geometry to deduce the influence of various substituents as well as solvent effect on the deformation of porphyrin ring. Two theoretical approaches - linear response (LR) and external iteration (EI) - have been performed to replicate absorption and fluorescence emission spectra. Experimental and theoretical investigations have shown that EI method reproduces the absorption energies very well for both singlet-singlet and triplet-triplet transitions, whereas the LR approach is more coherent with experimental fluorescence emission spectra. Spectral features and HOMO-LUMO band gap analysis have shown that TPP1 can be more useful in PDT. Calculations have revealed that two the highest occupied and two the lowest unoccupied molecular orbitals are responsible for the Q-band absorption and are located mainly on the porphyrin ring. In order to verify the substituent effect on the activity of tested compounds in their ground and excited states, the molecular electrostatic potential surfaces have been analyzed.

Properties of a planar electric double layer under extreme conditions investigated by classical density functional theory and Monte Carlo simulations.

PubMed

Zhou, Shiqi; Lamperski, Stanisław; Zydorczak, Maria

2014-08-14

Monte Carlo (MC) simulation and classical density functional theory (DFT) results are reported for the structural and electrostatic properties of a planar electric double layer containing ions having highly asymmetric diameters or valencies under extreme concentration condition. In the applied DFT, for the excess free energy contribution due to the hard sphere repulsion, a recently elaborated extended form of the fundamental measure functional is used, and coupling of Coulombic and short range hard-sphere repulsion is described by a traditional second-order functional perturbation expansion approximation. Comparison between the MC and DFT results indicates that validity interval of the traditional DFT approximation expands to high ion valences running up to 3 and size asymmetry high up to diameter ratio of 4 whether the high valence ions or the large size ion are co- or counter-ions; and to a high bulk electrolyte concentration being close to the upper limit of the electrolyte mole concentration the MC simulation can deal with well. The DFT accuracy dependence on the ion parameters can be self-consistently explained using arguments of liquid state theory, and new EDL phenomena such as overscreening effect due to monovalent counter-ions, extreme layering effect of counter-ions, and appearance of a depletion layer with almost no counter- and co-ions are observed.

Spectroscopic and molecular structure investigation of 2-furanacrylic acid monomer and dimer using HF and DFT methods

NASA Astrophysics Data System (ADS)

Ghalla, H.; Issaoui, N.; Govindarajan, M.; Flakus, H. T.; Jamroz, M. H.; Oujia, B.

2014-02-01

In the present work, we reported a combined experimental and theoretical study on molecular structure and vibrational spectra of 2-furanacrylic acid (abbreviated as 2FAA). The FT-IR and FT-Raman spectra of 2FAA have been recorded in the regions 4000-400 and 4000-100 cm-1. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The monomer and dimer structures of the title molecule have been obtained from Hartree-Fock (HF) and density functional theory (DFT) B3LYP methods with 6-311++G(d,p) as basis set calculations. The vibrational frequencies were calculated by DFT method and compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. Intermolecular OH⋯O hydrogen bonds are discussed in dimer structure of the molecule. The infrared and Raman spectra were also predicted from the calculated intensities. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. A study on the electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. In addition, Milliken atomic charges, possible charge transfer, natural bond orbital (NBO) and AIM topological analysis were performed. Moreover, molecular electrostatic potential (MEP) and the thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

Spectroscopic and DFT-based computational studies on the molecular electronic structural characteristics and the third-order nonlinear property of an organic NLO crystal: (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide

NASA Astrophysics Data System (ADS)

Sasikala, V.; Sajan, D.; Joseph, Lynnette; Balaji, J.; Prabu, S.; Srinivasan, P.

2017-04-01

Single crystals of (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide (CBMBSH) have been grown by slow evaporation crystal growth method. The structure stabilizing intramolecular donor-acceptor interactions and the presence of the Nsbnd H⋯O, Csbnd H⋯O and Csbnd H⋯C(π) hydrogen bonds in the crystal were confirmed by vibrational spectroscopic and DFT methods. The linear optical absorption characteristics of the solvent phase of CBMBSH were investigated using UV-Vis-NIR spectroscopic and TD-DFT approaches. The 2PA assisted RSA nonlinear absorption and the optical limiting properties of CBMBSH were studied using the open-aperture Z-scan method. The topological characteristics of the electron density have been determined using the quantum theory of atoms in molecules method.

A Parallel Framework with Block Matrices of a Discrete Fourier Transform for Vector-Valued Discrete-Time Signals.

PubMed

Soto-Quiros, Pablo

2015-01-01

This paper presents a parallel implementation of a kind of discrete Fourier transform (DFT): the vector-valued DFT. The vector-valued DFT is a novel tool to analyze the spectra of vector-valued discrete-time signals. This parallel implementation is developed in terms of a mathematical framework with a set of block matrix operations. These block matrix operations contribute to analysis, design, and implementation of parallel algorithms in multicore processors. In this work, an implementation and experimental investigation of the mathematical framework are performed using MATLAB with the Parallel Computing Toolbox. We found that there is advantage to use multicore processors and a parallel computing environment to minimize the high execution time. Additionally, speedup increases when the number of logical processors and length of the signal increase.

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Chemical degradation mechanisms of membranes for alkaline membrane fuel cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choe, Yoong-Kee; Henson, Neil J.; Kim, Yu Seung

2015-12-31

Chemical degradation mechanisms of membranes for alkaline membrane fuel cells have been investigated using density functional theory (DFT). We have elucidated that the aryl-ether moiety of membranes is one of the weakest site against attack of hydroxide ions. The results of DFT calculations for hydroxide initiated aryl-ether cleavage indicated that the aryl-ether cleavage occurred prior to degradation of cationic functional group. Such a weak nature of the aryl-ether group arises from the electron deficiency of the aryl group as well as the low bond dissociation energy. The DFT results suggests that removal of the aryl-ether group in the membrane shouldmore » enhance the stability of membranes under alkaline conditions. In fact, an ether fee poly(phenylene) membrane exhibits excellent stability against the attack from hydroxide ions.« less

Calorimetric, FTIR and 1H NMR measurements in combination with DFT calculations for monitoring solid-state changes of dynamics of sibutramine hydrochloride.

PubMed

Pajzderska, Aleksandra; Chudoba, Dorota M; Mielcarek, Jadwiga; Wąsicki, Jan

2012-10-01

Two forms of sibutramine hydrochloride, monohydrate and anhydrous, have been investigated by calorimetric methods, Fourier transform infrared (FTIR) absorption and (1) H nuclear magnetic resonance (NMR) measurements as well as by density functional theory (DFT) of vibrational frequencies and infrared intensities, calculations of steric hindrances and Monte Carlo simulations. The results of FTIR spectra combined with DFT calculations permitted identification of the bands corresponding to the dynamics and vibrations of water molecules. NMR study and Monte Carlo simulations revealed the occurrence of reorientation jumps of the methyl groups in sibutramine cation and also revealed that the reorientation of isopropyl group is possible only in sibutramine monohydrate hydrochloride. The hydration of sibutramine hydrochloride causes a change in the conformation of sibutramine cation. Copyright © 2012 Wiley-Liss, Inc.

Anatase-rutile phase transformation of titanium dioxide bulk material: a DFT + U approach

NASA Astrophysics Data System (ADS)

Vu, Nam H.; Le, Hieu V.; Cao, Thi M.; Pham, Viet V.; Le, Hung M.; Nguyen-Manh, Duc

2012-10-01

The anatase-rutile phase transformation of TiO2 bulk material is investigated using a density functional theory (DFT) approach in this study. According to the calculations employing the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Vanderbilt ultrasoft pseudopotential, it is suggested that the anatase phase is more energetically stable than rutile, which is in variance with the experimental observations. Consequently, the DFT + U method is employed in order to predict the correct structural stability in titania from electronic-structure-based total energy calculations. The Hubbard U term is determined by examining the band structure of rutile with various values of U from 3 to 10 eV. At U = 5 eV, a theoretical bandgap for rutile is obtained as 3.12 eV, which is in very good agreement with the reported experimental bandgap. Hence, we choose the DFT + U method (with U = 5 eV) to investigate the transformation pathway using the newly-developed solid-state nudged elastic band (ss-NEB) method, and consequently obtain an intermediate transition structure that is 9.794 eV per four-TiO2 above the anatase phase. When the Ti-O bonds in the transition state are examined using charge density analysis, seven Ti-O bonds (out of 24 bonds in the anatase unit cell) are broken, and this result is in excellent agreement with a previous experimental study (Penn and Banfield 1999 Am. Miner. 84 871-6).

Global and local curvature in density functional theory.

PubMed

Zhao, Qing; Ioannidis, Efthymios I; Kulik, Heather J

2016-08-07

Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a "+U" correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc-Cu) and ligand strength (CO, NH3, and H2O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide.

Quantum mechanics study of repulsive π-π interaction and flexibility of phenyl moiety in the iron azodioxide complex

NASA Astrophysics Data System (ADS)

Liu, Yuemin; Liu, Yucheng; Murru, Siva; Tzeng, Nianfeng; Srivastava, Radhey S.

2015-10-01

In this study, repulsive π-π interactions within iron azodioxide complex Fe[Ph(O)NN(O)Ph]3 were quantum mechanically characterized using DFT, MP2 and CCSD(T) methods. Flexibility of six phenyl moieties in this complex structure was also investigated by structural optimization approach using the DFT methods. Our MP2 and CCSD(T) calculations of the closest pair provided interaction energy of 6.62 and 8.29 kcal/mol respectively, which indicate a strongest repulsion among these intra-molecular π-π interactions. Interaction energy of the particular π-π pair calculated from 24 hybrid DFT methods ranges from 4.56 kcal/mol from BHandH method to 15.15 kcal/mol from O3LYP method. Cares should be exercised when interpreting interaction energy and geometry optimization from DFT simulation of systems containing π-π interaction. Comparison between the DFT results and the benchmark CCSD(T) results shows that the DFT calculations of π-π interaction are reasonable but still need to be interpreted with caution. Furthermore, MP2 interaction energy of -44.69 kcal/mol between two substituted π systems/phenyl rings Ph(O)N-moieties suggested that above energetically unfavorable π-π interaction can be compensated by the covalent bond N-N in a single ligand Ph(O)NN(O)Ph, which allows for a reasonable stability across the complex molecules. Optimizations of the entire complex molecule using B3LYP and M06HF methods produced a large variation of π-π distances and orientations, which implied that the complex molecule may perform catalysis at room temperature.

A simplified Tamm-Dancoff density functional approach for the electronic excitation spectra of very large molecules

NASA Astrophysics Data System (ADS)

Grimme, Stefan

2013-06-01

Two approximations in the Tamm-Dancoff density functional theory approach (TDA-DFT) to electronically excited states are proposed which allow routine computations for electronic ultraviolet (UV)- or circular dichroism (CD) spectra of molecules with 500-1000 atoms. Speed-ups compared to conventional time-dependent DFT (TD-DFT) treatments of about two to three orders of magnitude in the excited state part at only minor loss of accuracy are obtained. The method termed sTDA ("s" for simplified) employs atom-centered Löwdin-monopole based two-electron repulsion integrals with the asymptotically correct 1/R behavior and perturbative single excitation configuration selection. It is formulated generally for any standard global hybrid density functional with given Fock-exchange mixing parameter ax. The method performs well for two standard benchmark sets of vertical singlet-singlet excitations for values of ax in the range 0.2-0.6. The mean absolute deviations from reference data are only 0.2-0.3 eV and similar to those from standard TD-DFT. In three cases (two dyes and one polypeptide), good mutual agreement between the electronic spectra (up to 10-11 eV excitation energy) from the sTDA method and those from TD(A)-DFT is obtained. The computed UV- and CD-spectra of a few typical systems (e.g., C60, two transition metal complexes, [7]helicene, polyalanine, a supramolecular aggregate with 483 atoms and about 7000 basis functions) compare well with corresponding experimental data. The method is proposed together with medium-sized double- or triple-zeta type atomic-orbital basis sets as a quantum chemical tool to investigate the spectra of huge molecular systems at a reliable DFT level.

Experimental demonstration of OFDM/OQAM transmission with DFT-based channel estimation for visible laser light communications

NASA Astrophysics Data System (ADS)

He, Jing; Shi, Jin; Deng, Rui; Chen, Lin

2017-08-01

Recently, visible light communication (VLC) based on light-emitting diodes (LEDs) is considered as a candidate technology for fifth-generation (5G) communications, VLC is free of electromagnetic interference and it can simplify the integration of VLC into heterogeneous wireless networks. Due to the data rates of VLC system limited by the low pumping efficiency, small output power and narrow modulation bandwidth, visible laser light communication (VLLC) system with laser diode (LD) has paid more attention. In addition, orthogonal frequency division multiplexing/offset quadrature amplitude modulation (OFDM/OQAM) is currently attracting attention in optical communications. Due to the non-requirement of cyclic prefix (CP) and time-frequency domain well-localized pulse shapes, it can achieve high spectral efficiency. Moreover, OFDM/OQAM has lower out-of-band power leakage so that it increases the system robustness against inter-carrier interference (ICI) and frequency offset. In this paper, a Discrete Fourier Transform (DFT)-based channel estimation scheme combined with the interference approximation method (IAM) is proposed and experimentally demonstrated for VLLC OFDM/OQAM system. The performance of VLLC OFDM/OQAM system with and without DFT-based channel estimation is investigated. Moreover, the proposed DFT-based channel estimation scheme and the intra-symbol frequency-domain averaging (ISFA)-based method are also compared for the VLLC OFDM/OQAM system. The experimental results show that, the performance of EVM using the DFT-based channel estimation scheme is improved about 3dB compared with the conventional IAM method. In addition, the DFT-based channel estimation scheme can resist the channel noise effectively than that of the ISFA-based method.

Elastically frustrated rehybridization: Origin of chemical order and compositional limits in InGaN quantum wells

NASA Astrophysics Data System (ADS)

Lymperakis, L.; Schulz, T.; Freysoldt, C.; Anikeeva, M.; Chen, Z.; Zheng, X.; Shen, B.; Chèze, C.; Siekacz, M.; Wang, X. Q.; Albrecht, M.; Neugebauer, J.

2018-01-01

Nominal InN monolayers grown by molecular beam epitaxy on GaN(0001) are investigated combining in situ reflection high-energy electron diffraction (RHEED), transmission electron microscopy (TEM), and density functional theory (DFT). TEM reveals a chemical intraplane ordering never observed before. Employing DFT, we identify a novel surface stabilization mechanism elastically frustrated rehybridization, which is responsible for the observed chemical ordering. The mechanism also sets an incorporation barrier for indium concentrations above 25% and thus fundamentally limits the indium content in coherently strained layers.

Discrete Fourier Transform Analysis in a Complex Vector Space

NASA Technical Reports Server (NTRS)

Dean, Bruce H.

2009-01-01

Alternative computational strategies for the Discrete Fourier Transform (DFT) have been developed using analysis of geometric manifolds. This approach provides a general framework for performing DFT calculations, and suggests a more efficient implementation of the DFT for applications using iterative transform methods, particularly phase retrieval. The DFT can thus be implemented using fewer operations when compared to the usual DFT counterpart. The software decreases the run time of the DFT in certain applications such as phase retrieval that iteratively call the DFT function. The algorithm exploits a special computational approach based on analysis of the DFT as a transformation in a complex vector space. As such, this approach has the potential to realize a DFT computation that approaches N operations versus Nlog(N) operations for the equivalent Fast Fourier Transform (FFT) calculation.

DFT investigation on the electronic structure of Faujasite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian

2013-11-13

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed formore » describing atomic charge distribution in the chosen systems.« less

Investigation of copper(II) binding to the protein precursor of Non-Amyloid-Beta Component of Alzheimer Disease Amyloid Plaque

NASA Astrophysics Data System (ADS)

Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

2007-03-01

The Non-Amyloid-Beta Component Precursor (NACP) is a natively unfolded synaptic protein that is implicated in Alzheimers and Parkinsons diseases. Its aggregation into fibrillar structures is accelerated by the binding of copper(II). Experimental studies suggest that the dominant copper binding site is located at the histidine residue in NACP. Based on this evidence we assembled a model fragment of the binding site and used DFT to analyze the conformational details of the most probable binding motifs. We investigated the overall conformational effects with classical MD by constraining the copper binding site to the most energetically favorable geometry obtained from the DFT calculations. These results are compared and contrasted with those of the unbound NACP.

The study of intermolecular interactions in NLO crystal melaminium chloride hemihydrate using DFT simulation and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Sangeetha, K.; Kumar, V. R. Suresh; Marchewka, M. K.; Binoy, J.

2018-05-01

Since, the intermolecular interactions play a crucial role in the formation of crystalline network, its analysis throws light on structure dependent crystalline properties. In the present study, DFT based vibrational spectral investigation has been performed in the stretching region (3500 cm-1 - 2800 cm-1) of IR and Raman spectra of melaminium chloride hemihydrates. The intermolecular interaction has been investigated by analyzing the half width of the OH and NH stretching profile of the deconvoluted spectra. Correlation of vibrational spectra with Hirshfeld surface analysis and finger print plot has been contemplated and molecular docking studies has been performed on melaminium chloride hemihydrate to assess its role in the drug transport mechanism and toxicity to human body.

An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(iii)(HPDO3A)(H2O)

NASA Astrophysics Data System (ADS)

Khan, Shehryar; Pollet, Rodolphe; Vuilleumier, Rodolphe; Kowalewski, Jozef; Odelius, Michael

2017-12-01

In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field—CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates.

Self-consistent DFT +U method for real-space time-dependent density functional theory calculations

NASA Astrophysics Data System (ADS)

Tancogne-Dejean, Nicolas; Oliveira, Micael J. T.; Rubio, Angel

2017-12-01

We implemented various DFT+U schemes, including the Agapito, Curtarolo, and Buongiorno Nardelli functional (ACBN0) self-consistent density-functional version of the DFT +U method [Phys. Rev. X 5, 011006 (2015), 10.1103/PhysRevX.5.011006] within the massively parallel real-space time-dependent density functional theory (TDDFT) code octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of noncollinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition-metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self-consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the nonequilibrium properties of correlated systems.

Quantitative structure-activity relationships of the antimalarial agent artemisinin and some of its derivatives - a DFT approach.

PubMed

Rajkhowa, Sanchaita; Hussain, Iftikar; Hazarika, Kalyan K; Sarmah, Pubalee; Deka, Ramesh Chandra

2013-09-01

Artemisinin form the most important class of antimalarial agents currently available, and is a unique sesquiterpene peroxide occurring as a constituent of Artemisia annua. Artemisinin is effectively used in the treatment of drug-resistant Plasmodium falciparum and because of its rapid clearance of cerebral malaria, many clinically useful semisynthetic drugs for severe and complicated malaria have been developed. However, one of the major disadvantages of using artemisinins is their poor solubility either in oil or water and therefore, in order to overcome this difficulty many derivatives of artemisinin were prepared. A comparative study on the chemical reactivity of artemisinin and some of its derivatives is performed using density functional theory (DFT) calculations. DFT based global and local reactivity descriptors, such as hardness, chemical potential, electrophilicity index, Fukui function, and local philicity calculated at the optimized geometries are used to investigate the usefulness of these descriptors for understanding the reactive nature and reactive sites of the molecules. Multiple regression analysis is applied to build up a quantitative structure-activity relationship (QSAR) model based on the DFT based descriptors against the chloroquine-resistant, mefloquine-sensitive Plasmodium falciparum W-2 clone.

Computational study of AuSi{sub n} (n=1-9) nanoalloy clusters invoking DFT based descriptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ranjan, Prabhat; Kumar, Ajay; Chakraborty, Tanmoy, E-mail: tanmoy.chakraborty@jaipur.manipal.edu, E-mail: tanmoychem@gmail.com

2016-04-13

Nanoalloy clusters formed between Au and Si are topics of great interest today from both scientific and technological point of view. Due to its remarkable catalytic, electronic, mechanical and magnetic properties Au-Si nanoalloy clusters have extensive applications in the field of microelectronics, catalysis, biomedicine, and jewelry industry. Density Functional Theory (DFT) is a new paradigm of quantum mechanics, which is very much popular to study the electronic properties of materials. Conceptual DFT based descriptors have been invoked to correlate the experimental properties of nanoalloy clusters. In this venture, we have systematically investigated AuSi{sub n} (n=1-9) nanoalloy clusters in the theoreticalmore » frame of the B3LYP exchange correlation. The experimental properties of AuSi{sub n} (n=1-9) nanoalloy clusters are correlated in terms of DFT based descriptors viz. HOMO-LUMO gap, Electronegativity (χ), Global Hardness (η), Global Softness (S) and Electrophilicity Index (ω). The calculated HOMO-LUMO gap exhibits interesting odd-even alteration behaviour, indicating that even numbered clusters possess higher stability as compare to their neighbour odd numbered clusters. This study also reflects a very well agreement between experimental bond length and computed data.« less

A computational DFT study of structural transitions in textured solid-fluid interfaces

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Parry, Andrew O.; Kalliadasis, Serafim

2015-11-01

Fluids adsorbed at walls, in capillary pores and slits, and in more exotic, sculpted geometries such as grooves and wedges can exhibit many new phase transitions, including wetting, pre-wetting, capillary-condensation and filling, compared to their bulk counterparts. As well as being of fundamental interest to the modern statistical mechanical theory of inhomogeneous fluids, these are also relevant to nanofluidics, chemical- and bioengineering. In this talk we will show using a microscopic Density Functional Theory (DFT) for fluids how novel, continuous, interfacial transitions associated with the first-order prewetting line, can occur on steps, in grooves and in wedges, that are sensitive to both the range of the intermolecular forces and interfacial fluctuation effects. These transitions compete with wetting, filling and condensation producing very rich phase diagrams even for relatively simple geometries. We will also discuss practical aspects of DFT calculations, and demonstrate how this statistical-mechanical framework is capable of yielding complex fluid structure, interfacial tensions, and regions of thermodynamic stability of various fluid configurations. As a side note, this demonstrates that DFT is an excellent tool for the investigations of complex multiphase systems. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031.

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

PubMed

Cerný, Jirí; Hobza, Pavel

2005-04-21

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

Structural, thermodynamic, and electronic properties of Laves-phase NbMn2 from first principles, x-ray diffraction, and calorimetric experiments

NASA Astrophysics Data System (ADS)

Yan, X.; Chen, Xing-Qiu; Michor, H.; Wolf, W.; Witusiewicz, V. T.; Bauer, E.; Podloucky, R.; Rogl, P.

2018-03-01

By combining theoretical density functional theory (DFT) and experimental studies, structural and magnetic phase stabilities and electronic structural, elastic, and vibrational properties of the Laves-phase compound NbMn2 have been investigated for the C14, C15, and C36 crystal structures. At low temperatures C14 is the ground-state structure, with ferromagnetic and antiferromagnetic orderings being degenerate in energy. The degenerate spin configurations result in a rather large electronic density of states at Fermi energy for all magnetic cases, even for the spin-polarized DFT calculations. Based on the DFT-derived phonon dispersions and densities of states, temperature-dependent free energies were derived for the ferromagnetic and antiferromagnetic C14 phase, demonstrating that the spin-configuration degeneracy possibly exists up to finite temperatures. The heat of formation Δ298H0=-45.05 ±3.64 kJ (molf .u .NbMn2) -1 was extracted from drop isoperibolic calorimetry in a Ni bath. The DFT-derived enthalpy of formation of NbMn2 is in good agreement with the calorimetric measurements. Second-order elastic constants for NbMn2 as well as for related compounds were calculated.

Electromechanical and Chemical Sensing at the Nanoscale: DFT and Transport Modeling

NASA Astrophysics Data System (ADS)

Maiti, Amitesh

Of the many nanoelectronic applications proposed for near to medium-term commercial deployment, sensors based on carbon nanotubes (CNT) and metal-oxide nanowires are receiving significant attention from researchers. Such devices typically operate on the basis of the changes of electrical response characteristics of the active component (CNT or nanowire) when subjected to an externally applied mechanical stress or the adsorption of a chemical or bio-molecule. Practical development of such technologies can greatly benefit from quantum chemical modeling based on density functional theory (DFT), and from electronic transport modeling based on non-equilibrium Green's function (NEGF). DFT can compute useful quantities like possible bond-rearrangements, binding energy, charge transfer, and changes to the electronic structure, while NEGF can predict changes in electronic transport behavior and contact resistance. Effects of surrounding medium and intrinsic structural defects can also be taken into account. In this work we review some recent DFT and transport investigations on (1) CNT-based nano-electromechanical sensors (NEMS) and (2) gas-sensing properties of CNTs and metal-oxide nanowires. We also briefly discuss our current understanding of CNT-metal contacts which, depending upon the metal, the deposition technique, and the masking method can have a significant effect on device performance.

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

Effect of structural distortion on the electronic band structure of NaOsO3 studied within density functional theory and a three-orbital model

NASA Astrophysics Data System (ADS)

Mohapatra, Shubhajyoti; Bhandari, Churna; Satpathy, Sashi; Singh, Avinash

2018-04-01

Effects of the structural distortion associated with the OsO6 octahedral rotation and tilting on the electronic band structure and magnetic anisotropy energy for the 5 d3 compound NaOsO3 are investigated using the density functional theory (DFT) and within a three-orbital model. Comparison of the essential features of the DFT band structures with the three-orbital model for both the undistorted and distorted structures provides insight into the orbital and directional asymmetry in the electron hopping terms resulting from the structural distortion. The orbital mixing terms obtained in the transformed hopping Hamiltonian resulting from the octahedral rotations are shown to account for the fine features in the DFT band structure. Staggered magnetization and the magnetic character of states near the Fermi energy indicate weak coupling behavior.

Synthesis and spectroscopical study of rhodanine derivative using DFT approaches

NASA Astrophysics Data System (ADS)

Anbarasan, R.; Dhandapani, A.; Manivarman, S.; Subashchandrabose, S.; Saleem, H.

2015-07-01

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of (E)-5-benzylidene-2-thioxothiazolidine-4-one (E5BTTO) have been investigated experimentally and theoretically based on Density Functional Theory (DFT) approach. The FT-Raman and FT-IR spectra of E5BTTO were recorded in solid phase. Theoretical calculations were performed at the DFT level using the Gaussian 03 program. The experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumber by their Total Energy Distribution (TED). The results of the calculation were applied to simulate infrared and raman spectra of the title compound which showed good agreement with the observed spectra. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Stability arising from hyperconjugative interactions leading to its NLO activity and charge delocalization were analyzed using Natural Bond Orbital (NBO) analysis.

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide

NASA Astrophysics Data System (ADS)

Saravanan, R. R.; Seshadri, S.; Gunasekaran, S.; Mendoza-Meroño, R.; Garcia-Granda, S.

2015-03-01

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.

Determination and interpretation of the optical constants for solar cell materials

NASA Astrophysics Data System (ADS)

Fujiwara, Hiroyuki; Fujimoto, Shohei; Tamakoshi, Masato; Kato, Masato; Kadowaki, Hideyuki; Miyadera, Tetsuhiko; Tampo, Hitoshi; Chikamatsu, Masayuki; Shibata, Hajime

2017-11-01

Solar cell materials in thin film form often exhibit quite rough surface, which makes the accurate determination of the optical constants using spectroscopic ellipsometry (SE) quite difficult. In this study, we investigate the effect of the rough surface on the SE analysis and establish an analysis procedure, which is quite helpful for the correction of the underestimated roughness contribution. As examples, the roughness analyses for CuInSe2 and CH3NH3PbI3 hybrid-perovskite thin films are presented. Moreover, to interpret the dielectric functions of emerging solar cell materials, such as CH3NH3PbI3 and Cu2ZnSnSe4, the optical transition analyses are performed based on density functional theory (DFT). The excellent agreement observed between the experimental and DFT results allows the detailed assignment of the transition peaks, confirming the importance of DFT for revealing fundamental optical characteristics.

Predicting the properties of the lead alloys from DFT calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buimaga-Iarinca, L., E-mail: luiza.iarinca@itim-cj.ro; Calborean, A.

2015-12-23

We provide qualitative results for the physical properties of the lead alloys at atomic scale by using DFT calculations. Our approach is based on the two assumptions: (i) the geometric structure of lead atoms provides a matrix where the alloying elements can take their positions in the structure as substitutions and (ii) there is a small probability of a direct interaction between the alloying elements, thus the interactions of each alloying element may be approximated by the interactions to the lead matrix. DFT calculations are used to investigate the interaction between several types of impurities and the lead matrix formore » low concentrations of the alloying element. We report results such as the enthalpy of formation, charge transfer and mechanical stress induced by the impurities in the lead matrix; these results can be used as qualitative guide in tuning the physico-chemical properties of the lead alloys.« less

Structure-activity relations of 2-(methylthio)benzimidazole by FTIR, FT-Raman, NMR, DFT and conceptual DFT methods.

PubMed

Arjunan, V; Raj, Arushma; Ravindran, P; Mohan, S

2014-01-24

The vibrational fundamental modes of 2-(methylthio)benzimidazole (2MTBI) have been analysed by combining FTIR, FT-Raman and quantum chemical calculations. The structural parameters of the compound are determined from the optimised geometry by B3LYP with 6-31G(∗∗), 6-311++G(∗∗) and cc-pVTZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra have been analysed and (1)H and (13)C nuclear magnetic resonance chemical shifts are calculated using the gauge independent atomic orbital (GIAO) method. The structure-activity relationship of the compound is also investigated by conceptual DFT methods. The chemical reactivity and site selectivity of the molecule has been determined with the help of global and local reactivity descriptors. Copyright © 2013 Elsevier B.V. All rights reserved.

Segregation formation, thermal and electronic properties of ternary cubic CdZnTe clusters: MD simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Kurban, Mustafa; Erkoç, Şakir

2017-04-01

Surface and core formation, thermal and electronic properties of ternary cubic CdZnTe clusters are investigated by using classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations. In this work, MD simulations of the CdZnTe clusters are performed by means of LAMMPS by using bond order potential (BOP). MD simulations are carried out at different temperatures to study the segregation phenomena of Cd, Zn and Te atoms, and deviation of clusters and heat capacity. After that, using optimized geometries obtained, excess charge on atoms, dipole moments, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, HOMO-LUMO gaps (Eg) , total energies, spin density and the density of states (DOS) have been calculated with DFT. Simulation results such as heat capacity and segregation formation are compared with experimental bulk and theoretical results.

Ethane and Xenon mixing: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, Rudolph; Root, Seth; Mattsson, Thomas; Cochrane, Kyle

2012-02-01

The combination of ethane and xenon is one of the simplest binary mixtures in which bond breaking is expected to play a role under shock conditions. At cryogenic conditions, xenon is often understood to mix with alkanes such as Ethane as if it were also an alkane, but this model is expected to break down at higher temperatures and pressures. To investigate the breakdown, we have performed density functional theory (DFT) calculations on several xenon/ethane mixtures. Additionally, we have performed shock compression experiments on Xenon-Ethane using the Sandia Z - accelerator. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

GW quasiparticle bandgaps of anatase TiO2 starting from DFT + U.

PubMed

Patrick, Christopher E; Giustino, Feliciano

2012-05-23

We investigate the quasiparticle band structure of anatase TiO(2), a wide gap semiconductor widely employed in photovoltaics and photocatalysis. We obtain GW quasiparticle energies starting from density-functional theory (DFT) calculations including Hubbard U corrections. Using a simple iterative procedure we determine the value of the Hubbard parameter yielding a vanishing quasiparticle correction to the fundamental bandgap of anatase TiO(2). The bandgap (3.3 eV) calculated using this optimal Hubbard parameter is smaller than the value obtained by applying many-body perturbation theory to standard DFT eigenstates and eigenvalues (3.7 eV). We extend our analysis to the rutile polymorph of TiO(2) and reach similar conclusions. Our work highlights the role of the starting non-interacting Hamiltonian in the calculation of GW quasiparticle energies in TiO(2) and suggests an optimal Hubbard parameter for future calculations.

Comparison of outcomes in patients undergoing defibrillation threshold testing at the time of implantable cardioverter-defibrillator implantation versus no defibrillation threshold testing.

PubMed

Hall, Burr; Jeevanantham, Vinodh; Levine, Ethan; Daubert, James; McNitt, Scott; Hall, Freburr; Jeevanantham, Vinodh; Levine, Ethan; Daubert, James; McNitt, Scott; Hall, Fred Morady And Frank Pelosiburr; Jeevanantham, Vinodh; Levine, Ethan; Daubert, James; McNitt, Scott; Morady, Fred Morady And Frank Pelosid; Pelosi, Frank

2007-01-01

Inability to perform defibrillation threshold (DFT) testing during implantable cardioverter defibrillator (ICD) implantation due to co-morbidities may influence long-term survival. Retrospective review at The University of Michigan (1999-2004) identified 55 patients undergoing ICD implantation without DFT testing ("No-DFT group"). A randomly selected sample of patients (n = 57) undergoing standard DFT testing ("DFT group") was compared in terms of appropriate shocks, clinical shock efficacy and all-cause mortality. DFT testing was withheld due to hypotension, atrial fibrillation with inability to exclude left atrial thrombus, left ventricular thrombus, CHF and/or ischemia. The No-DFT group had a similar appropriate shock rate, but lower total survival (69.1% vs. 91.2%, p = 0.004) than the DFT group. The No-DFT group had a higher incidence of ventricular fibrillation (VF) episodes (9.1% vs. 3.1%, p = 0.037), and deaths attributable to VF (3 of 17 deaths vs. 0 of 5 deaths) compared to the DFT group. Multivariate analysis found a trend toward increased risk of death in the No-DFT group (HR 3.18, 95% CI 0.82-12.41, p = 0.095) after adjusting for baseline differences in gender distribution, NYHA class and prior CABG. In summary, overall mortality was higher in the No-DFT group. More deaths attributable to VF occurred in the No-DFT group. Thus, DFT testing should therefore remain the standard of care. Nevertheless, ICD therapy should not be withheld in patients who meet appropriate implant criteria simply on the basis of clinical scenarios that preclude routine DFT testing. (Cardiol J 2007; 14: 463-469).

Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation.

PubMed

Casida, Mark E; Huix-Rotllant, Miquel

2016-01-01

In their famous paper, Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of N interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays, however, the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very similar to what the local density approximation (LDA) is to conventional ground-state DFT. Although some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this chapter focuses on many-body corrections to LR-TD-DFT as one way to build hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.

Surface atomic structure characterization of SnSe and black phosphorus using selected area uLEED-IV via LEEM

NASA Astrophysics Data System (ADS)

Dai, Zhongwei; Grady, Maxwell; Yu, Jiexiang; Zang, Jiadong; Pohl, Karsten; Jin, Wencan; Kim, Young Duck; Hone, James; Dadap, Jerry; Osgood, Richard; Sadowski, Jerzy; Vishwanath, Suresh; Xing, Huili

Selected area diffraction intensity-voltage (μLEED-IV) analysis via low energy electron microscopy (LEEM) has the combined functionality of atomic surface structure determination and μm area selectivity, making it ideal for structural investigations of 2-D materials. SnSe thin films have been predicted and observed to be topological crystalline insulators. Previous studies suggested that SnSe has a preferred Se-terminated surface configuration. Using μLEED-IV, we determined that SnSe has, on the contrary, a stable Sn termination. This surface is stabilized through an oscillatory interlayer relaxation, which agrees with previous DFT predictions. Black phosphorus (BP) has an intrinsic layer-dependent bandgap ranging from 0.3 eV to 2 eV. Previous STM and DFT studies suggested BP surfaces have a buckling of 0.02 Å to 0.06 Å. We experimentally determined that the surface buckling of BP to be near 0.2 Å. We further propose, using DFT calculations, that this large surface buckling is induced by the presence of surface defects. The influence of this surface buckling on the electronic structures of BP is under investigation.

Droplets and the three-phase contact line at the nano-scale. Statics and dynamics

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Sibley, David; Savva, Nikos; Kalliadasis, Serafim

2014-11-01

Understanding the behaviour of the solid-liquid-vapour contact line at the scale of several tens of molecular diameters is important in wetting hydrodynamics with applications in micro- and nano-fluidics, including the design of lab-on-a-chip devices and surfaces with specific wetting properties. Due to the fluid inhomogeneity at the nano-scale, the application of continuum-mechanical approaches is limited, and a natural way to remedy this is to seek descriptions accounting for the non-local molecular-level interactions. Density Functional Theory (DFT) for fluids offers a statistical-mechanical framework based on expressing the free energy of the fluid-solid pair as a functional of the spatially varying fluid density. DFT allows us to investigate small drops deposited on planar substrates whilst keeping track of the microscopic structural details of the fluid. Starting from a model of intermolecular forces, we systematically obtain interfaces, surface tensions, and the microscopic contact angle. Using a dynamic extension of equilibrium DFT, we investigate the diffusion-driven evolution of the three-phase contact line to gain insight into the dynamic behaviour of the microscopic contact angle, which is still under debate.

Synthesis, theoretical studies and molecular docking of a novel chlorinated tetracyclic: (Z/E)-3-(1,8-dichloro-9,10-dihydro-9,10-ethanoanthracen-11-yl)acrylaldehyde

NASA Astrophysics Data System (ADS)

Sultan, Mujeeb A.; Almansour, Abdulrahman I.; Pillai, Renjith Raveendran; Kumar, Raju Suresh; Arumugam, Natarajan; Armaković, Stevan; Armaković, Sanja J.; Soliman, Saied M.

2017-12-01

(Z/E)-3-(1,8-Dichloro-9,10-dihydro-9,10-ethanoanthracen-11-yl)acrylaldehyde 2 has been investigated experimentally and theoretically. The Wittig reaction of 1,8-dichloro-9,10-dihydro-9,10-ethanoanthracene-11-carbaldehyde 1 and (triphenylphosphoranylidene) acetaldehyde in toluene under reflux conditions resulted in compound 2. Spectroscopic characterization of compound 2 was performed by the Fourier-transform infrared spectroscopy, nuclear magnetic resonance, and high-resolution mass spectroscopy techniques. Density functional theory (DFT) calculations were conducted to study various global and local reactive properties. The spectra were also obtained by DFT calculations and corresponding comparisons were performed to validate the level of theory. Using DFT calculations, reactivity has been studied based on frontier molecular orbitals, charge distribution, average local ionization energies, Fukui functions, and bond dissociation energies for hydrogen abstraction. Molecular dynamics simulations have been used to investigate the influence of water as a solvent for compound 2. Finally, compound 2 was docked into the central and allosteric binding sites of the serotonin transporter enzyme and was found to be a good candidate as an antidepressant-like compound.

Modeling of a Tröger’s tweezer and its complexation properties

NASA Astrophysics Data System (ADS)

Parchaňský, Václav; Matějka, Pavel; Dolenský, Bohumil; Havlík, Martin; Bouř, Petr

2009-09-01

Molecular tweezers attracted attention because of their potential to selectively bind important chemicals, which can be utilized in medicine or in pollution treatment. In this study, the aromatic binding properties of a recently synthesized tweezer based on the Tröger's base and its complex with nitrobenzene are investigated ab initio, using the DFT and MP2 computations. The predicted geometries and energies of the complex with nitrobenzene are well comparable with the experimental data. The B3LYP and BPW91 functionals did not provide a stable binding, in contrast to the observation. Only addition of the empirical Grimme correction for the van der Waals forces, not present in conventional DFT, yielded results consistent with the experiment, MP2 computations, and similar benchmark models. The correction also caused minor improvements of the Raman and infrared spectra, but not in the entire region of vibrational frequencies. The results suggest that the role of the electrostatic interaction in the investigated complex is minor and the interaction stabilization is driven by the contact area between the polarizable aromatic systems. The vdW-DFT method thus provides an efficient tool for the rational synthesis of the complexes.

Experimental investigation and DFT calculation of different amine/ammonium salts adsorption on kaolinite

NASA Astrophysics Data System (ADS)

Chen, Jun; Min, Fan-fei; Liu, Lingyun; Liu, Chunfu; Lu, Fangqin

2017-10-01

The adsorption of four different amine/ammonium salts of DDA (Dodecyl amine), MDA (N-methyldodecyl amine), DMDA (N,N-dimethyldodecyl amine) and DTAC (Dodecyl trimethyl ammonium chloride) on kaolinite particles was investigated in the study through the measurement of contact angles, zeta potentials, aggregation observation, adsorption and sedimentation. The results show that different amine/ammonium salts can adsorb on the kaolinite surface to enhance the hydrophobicity and reduce the electronegativity of kaolinite particle surface, and thus induce a strong hydrophobic aggregation of kaolinite particles which promotes the settlement of kaolinite. To explore the adsorption mechanism of these four amine/ammonium salts on kaolinite surfaces, the adsorptions of DDA+, MDA+, DMDA+ and DTAC+ on kaolinite (001) surface and (00 1 bar) surface are calculated with DFT (Density functional theory). The DFT calculation results indicate that different amine/ammonium cations can strongly adsorbed on kaolinite (001) surface and (00 1 bar) surface by forming Nsbnd H⋯O strong hydrogen bonds or Csbnd H⋯O weak hydrogen bonds, and there are strongly electrostatic attractions between different amine/ammonium cations and kaolinite surfaces. The main adsorption mechanism of amine/ammonium cations on kaolinite is hydrogen-bond interaction and electrostatic attraction.

Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

2018-04-01

Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schober, Christoph; Reuter, Karsten; Oberhofer, Harald, E-mail: harald.oberhofer@ch.tum.de

2016-02-07

We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer),more » we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.« less

DFT and TD-DFT calculations of metallotetraphenylporphyrin and metallotetraphenylporphyrin fullerene complexes as potential dye sensitizers for solar cells

NASA Astrophysics Data System (ADS)

El Mahdy, A. M.; Halim, Shimaa Abdel; Taha, H. O.

2018-05-01

Density functional theory (DFT) and time-dependent DFT calculations have been employed to model metallotetraphenylporphyrin dyes and metallotetraphenylporphyrin -fullerene complexes in order to investigate the geometries, electronic structures, the density of states, non-linear optical properties (NLO), IR-vis spectra, molecular electrostatic potential contours, and electrophilicity. To calculate the excited states of the tetraphenyl porphyrin analogs, time-dependent density functional theory (TD-DFT) are used. Their UV-vis spectra were also obtained and a comparison with available experimental and theoretical results is included. The results reveal that the metal and the tertiary butyl groups of the dyes are electron donors, and the tetraphenylporphyrin rings are electron acceptors. The HOMOs of the dyes fall within the (TiO2)60 and Ti38O76 band gaps and support the issue of typical interfacial electron transfer reaction. The resulting potential drop of Mn-TPP-C60 increased by ca. 3.50% under the effect of the tertiary butyl groups. The increase in the potential drop indicates that the tertiary butyl complexes could be a better choice for the strong operation of the molecular rectifiers. The introduction of metal atom and tertiary butyl groups to the tetraphenyl porphyrin moiety leads to a stronger response to the external electric field and induces higher photo-to-current conversion efficiency. This also shifts the absorption in the dyes and makes them potential candidates for harvesting light in the entire visible and near IR region for photovoltaic applications.

Theoretical and spectroscopic studies of a tricyclic antidepressant, imipramine hydrochloride

NASA Astrophysics Data System (ADS)

Sagdinc, S. G.; Azkeskin, Caner; Eşme, A.

2018-06-01

Imipramine hydrochloride ([H-IMI]Cl), C19H24N2.HCl, is the prototypic tricyclic antidepressant (TCA) inhibitor of norepinephrine and serotonin neuronal reuptake. The molecular structure, molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis, linear and non-linear optical (NLO) properties of [H-IMI]Cl have been investigated using the density functional theory (DFT) calculations with the B3LYP level at the 6‒311++G(d,p) basis set. The UV-Vis spectra for [H-IMI]Cl were experimentally studied in water and methanol. TD‒DFT calculations in water and methanol were employed to investigate the absorption wavelengths (λ), excitation energies (E), and oscillator strengths (f) for the UV-Vis analysis and the major contributions to the electronic transitions. From NBO analysis, the orbitals with the stabilization energy E(2) of 192.15 kcal/mol are π*(C5sbnd C18) as donor NBO and π*(C19sbnd C20) as acceptor NBO. The FT‒IR (4000‒400 cm-1) and FT‒Raman (3500-50 cm-1) spectra have been measured and analyzed. The assignment of bands observed vibrational spectra have been made by comparison of its calculated theoretical vibrational frequencies obtained using the DFT/B3LYP/6‒311++G(d,p) method. The detailed vibrational assignments were performed with the DFT calculation, and the potential energy distribution (PED) of [H-IMI]Cl was obtained by the Vibrational Energy Distribution Analysis 4 (VEDA4) program. The scaled frequencies resulted in good agreement with the observed spectral patterns.

DFT computations on: Crystal structure, vibrational studies and optical investigations of a luminescent self-assembled material

NASA Astrophysics Data System (ADS)

Kessentini, A.; Ben Ahmed, A.; Dammak, T.; Belhouchet, M.

2018-02-01

The current work undertakes the growth and the physicochemical properties of a novel green-yellow luminescence semi-organic material, the 3-picolylammonium bromide abbreviated (Pico-Br). In this paper, we report the X-ray diffraction measurements which show that the crystal lattice consists of distinct 3-picolylammonium cations and free bromide anions connected via Nsbnd H ⋯ Br and Nsbnd H ⋯ N hydrogen bonds leading to form a two dimensional frameworks. Molecular geometry compared with its optimized counterpart shows that the quantum chemical calculations carried out with density functional method (DFT) well produce the perceived structure by X-ray resolution of the studied material. To provide further insight into the spectroscopic properties, additional characterization of this material have been performed with Raman and infrared studies at room temperature. Theoretical computations have been computed using the (DFT) method at B3LYP/LanL2DZ level of theory implemented within Gaussian 03 program to study the vibrational spectra of the investigated molecule in the ground state. Optical absorption spectrum inspected by UV-visible absorption reveals the appearance of sharp optical gap of 280 nm (4.42 eV) as well as a strong green photoluminescence emission at 550 nm (2.25 eV) is detected on the photoluminescence (PL) spectrum at room temperature. Using the TD/DFT method, HOMO-LUMO energy gap and the Mulliken atomic charges were calculated in order to get an insight into the material. Good agreement between the theoretical results and the experimental ones was predicted.

The N2O activation by Rh5 clusters. A quantum chemistry study.

PubMed

Olvera-Neria, Oscar; Avilés, Roberto; Francisco-Rodríguez, Héctor; Bertin, Virineya; García-Cruz, Raúl; González-Torres, Julio César; Poulain, Enrique

2015-04-01

Nitrous oxide (N2O) is a by-product of exhaust pipe gases treatment produced by motor vehicles. Therefore, the N2O reduction to N2 is necessary to meet the actual environmental legislation. The N2O adsorption and dissociation assisted by the square-based pyramidal Rh5 cluster was investigated using the density functional theory and the zero-order regular approximation (ZORA). The Rh5 sextet ground state is the most active in N2O dissociation, though the quartet and octet states are also active because they are degenerate. The Rh5 cluster spontaneously activates the N2─O cleavage, and the reaction is highly exothermic ca. -75 kcal mol(-1). The N2─O breaking is obtained for the geometrical arrangement that maximizes the overlap and electron transfers between the N2O and Rh5 frontier orbitals. The Rh5 high activity is due to the Rh 3d orbitals are located between the N2O HOMO and LUMO orbitals, which makes possible the interactions between them. In particular, the O 2p states strongly interact with Rh 3d orbitals, which finally weaken the N2─O bond. The electron transfer is from the Rh5 HOMO orbital to the N2O antibonding orbital.

Synthesis and corrosion inhibition application of NATN on mild steel surface in acidic media complemented with DFT studies

NASA Astrophysics Data System (ADS)

Al-Baghdadi, Shaimaa B.; Hashim, Fanar G.; Salam, Ahmed Q.; Abed, Talib K.; Gaaz, Tayser Sumer; Al-Amiery, Ahmed A.; Kadhum, Abdul Amir H.; Reda, Khalid S.; Ahmed, Wahab K.

2018-03-01

The corrosion inhibition effectiveness of thiosemicarbazide compound, namely 3-nitro-5-(2-amino-1,3,4-thiadiazolyl)nitrobenzene (NATN), on mild steel in 1 M hydrochloric acid media has been investigated by weight loss technique. The results exhibit that the corrosion ratio of mild steel was reduced regarding to adding NATN. The corrosion inhibition rate for the NATN was 92.3% at the highest investigated NATN concentration. From the weight loss results it could be concluded that NATN with sulfur, nitrogen and oxygen atoms has clarified best corrosion inhibition achievement comparing to 3,5-dinitrobenzoic acid. Regarding to theoretical studies, DFT was employee to figured geometrical structure and electronic characteristics on NATN. The investigation have been extensive to the HOMO and LUMO analysis to evaluate the energy gap, Ionization potential, Electron Affinity, Global Hardness, Chemical Potential, Electrophilicity, Electronegativity and Polarizability.

Adsorption properties of the molecule resveratrol on CNT(8,0-10) nanotube: Geometry optimization, molecular structure, spectroscopic (NMR, UV/Vis, excited state), FMO, MEP and HOMO-LUMO investigations

NASA Astrophysics Data System (ADS)

Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Hajikolaee, Fatemeh Haji; Balakhanava, Iryna; Alnajjar, Radwan

2018-05-01

In the present work the adsorption properties of the molecule Resveratrol (RSV) (trans-3,5,4‧-Trihydroxystilbene) on CNT(8,0-10) nanotube was investigated by Density Functional Theory (DFT) in the gaseous phase for the first time. The non-bonded interaction effects of compounds RSV and CNT(8,0-10) nanotube on the electronic properties, chemical shift tensors and natural charge were determined and discussed. The electronic spectra of the RSV and the complex CNT(8,0-10)/RSV in the gaseous phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for investigation of the maximum wavelength value of the RSV before and after the non-bonded interaction with the CNT(8,0-10) nanotube and molecular orbitals involved in the formation of absorption spectrum of the complex RSV at maximum wavelength.

DFT based vibrational spectroscopic investigations and biological activity of toxic material monocrotophos

NASA Astrophysics Data System (ADS)

Nimmi, D. E.; Sam, S. P. Chandhini; Praveen, S. G.; Binoy, J.

2018-05-01

Many organophosphate compounds exhibiting toxicity are widely used as pesticides and insecticides whose structural features can be explained excellently using geometric simulation using density functional theory and vibrational spectrum. In this work, the molecular structural parameters and vibrational frequencies of the fundamental modes of Monocrotophoshave been obtained using Density functional theory (DFT), using B3LYP functional with 6-311++G(d, p) basis sets and the detailed vibrational analysis of FT-IR and FT-Ramanspectral bands have been carried out using potential energy distribution (PED). The deviation from the resonance structure of phosphate group due to `bridging of oxygen' and π-resonance of amides has been investigated based on the spectral and geometric data. The molecular docking simulation of Monocrotophos with BSA and DNA has been performed to find the mode of binding and the interactions with BSA has been investigated with UV-Visible spectroscopic method, to assess the strength of binding.

Understanding the NMR properties and conformational behavior of indole vs. azaindole group in protoberberines: NICS and NCS analysis

NASA Astrophysics Data System (ADS)

Kadam, Shivaji S.; Toušek, Jaromír; Maier, Lukáš; Pipíška, Matej; Sklenář, Vladimír; Marek, Radek

2012-11-01

We report here the preparation and the structural investigation into a series of 8-(indol-1-yl)-7,8-dihydroprotoberberine derivatives derived from berberine, palmatine, and coptisine. Structures of these new compounds were characterized mainly by 2D NMR spectroscopy and the conformational behavior was investigated by using methods of density-functional theory (DFT). PBE0/6-311+G** calculated NMR chemical shifts for selected derivatives correlate excellently with the experimental NMR data and support the structural conclusions drawn from the NMR experiments. An interesting role of the nitrogen atom in position N7' of the indole moiety in 8-(7-azaindol-1-yl)-7,8-dihydroprotoberberines as compared to other 8-indolyl derivatives is investigated in detail. The experimentally observed trends in NMR chemical shifts are rationalized by DFT calculations and analysis based on the nucleus-independent chemical shifts (NICS) and natural localized molecular orbitals (NLMOs).

Investigation of dissociative electron attachment to 2'-deoxycytidine-3'-monophosphate using DFT method and time dependent wave packet approach

NASA Astrophysics Data System (ADS)

Bhowmick, Somnath; B, Renjith; Mishra, Manoj K.; Sarma, Manabendra

2012-08-01

Effect of electron correlation on single strand breaks (SSBs) induced by low energy electron (LEE) has been investigated in a fragment excised from a DNA, viz., 2'-deoxycytidine-3'-monophosphate [3'-dCMPH] molecule in gas phase at DFT-B3LYP/6-31+G(d) accuracy level and using local complex potential based time dependent wave packet (LCP-TDWP) approach. The results obtained, in conjunction with our earlier investigation, show the possibility of SSB at very low energy (0.15 eV) where the LEE transfers from π* to σ* resonance state which resembles a SN2 type mechanism. In addition, for the first time, an indication of quantum mechanical tunneling in strand breaking is seen from the highest anionic bound vibrational state (χ5), which may have a substantial role during DNA damage.

Relativistic DFT investigation of electronic structure effects arising from doping the Au25 nanocluster with transition metals.

PubMed

Alkan, Fahri; Muñoz-Castro, Alvaro; Aikens, Christine M

2017-10-26

We perform a theoretical investigation using density functional theory (DFT) and time-dependent DFT (TDDFT) on the doping of the Au 25 (SR) 18 -1 nanocluster with group IX transition metals (M = cobalt, rhodium and iridium). Different doping motifs, charge states and spin multiplicities were considered for the single-atom doped nanoclusters. Our results show that the interaction (or the lack of interaction) between the d-type energy levels that mainly originate from the dopant atom and the super-atomic levels plays an important role in the energetics, the electronic structure and the optical properties of the doped systems. The evaluated MAu 24 (SR) 18 q (q = -1, -3) systems favor an endohedral disposition of the doping atom typically in a singlet ground state, with either a 6- or 8-valence electron icosahedral core. For the sake of comparison, the role of the d energy levels in the electronic structure of a variety of doped Au 25 (SR) 18 -1 nanoclusters was investigated for dopant atoms from other families such as Cd, Ag and Pd. Finally, the effect of spin-orbit coupling (SOC) on the electronic structure and absorption spectra was determined. The information in this study regarding the relative energetics of the d-based and super-atom energy levels can be useful to extend our understanding of the preferred doping modes of different transition metals in protected gold nanoclusters.

A first principles investigation of the oxygen adsorption on Zr(0001) surface using cluster expansions

NASA Astrophysics Data System (ADS)

Samin, Adib J.; Taylor, Christopher D.

2017-11-01

The design of corrosion resistant zircalloys is important for a variety of technological applications ranging from medicine to the nuclear industry. Since corrosion resistance is mainly attributed to the formation of a surface oxide layer, developing a detailed understanding of this process may assist in future corrosion resistance design. In this work, we conduct a systematic multi-scale investigation of the early stages of oxide formation. This was accomplished by first using a database of fully relaxed DFT calculations to build a cluster-expansion description of the potential function. The developed potential was reasonably good at predicting DFT energies as evidenced by the cross-validation score of 4.4 meV/site. The effective cluster expansion parameters were indicative of repulsive adsorbate interactions in the adlayer in agreement with the literature. The potential then allowed for a systematic investigation of the oxygen configurations on the Zr(0001) surface via Monte Carlo simulations. The adsorption energy was recorded as a function of coverage and an increasing trend was observed in agreement with DFT predictions and the repulsive nature of interactions in the adlayer. The convex hull diagram was recorded indicating the most stable configuration to occur around a coverage of 0.6 ML. The adsorption isotherm was also recorded and contrasted for two temperatures relevant for different applications.

Molecular adsorption on metal surfaces with van der Waals density functionals

NASA Astrophysics Data System (ADS)

Li, Guo; Tamblyn, Isaac; Cooper, Valentino R.; Gao, Hong-Jun; Neaton, Jeffrey B.

2012-03-01

The adsorption of 1,4-benzenediamine (BDA) on Au(111) and azobenzene on Ag(111) is investigated using density functional theory (DFT) with the nonlocal van der Waals density functional (vdW-DF) and the semilocal Perdew-Burke-Ernzerhof functional. For BDA on Au(111), the inclusion of London dispersion interactions not only dramatically enhances the molecule-substrate binding, resulting in adsorption energies consistent with experimental results, but also significantly alters the BDA binding geometry. For azobenzene on Ag(111), vdW-DFs produce superior adsorption energies compared to those obtained with other dispersion-corrected DFT approaches. These results provide evidence for the applicability of the vdW-DF approach and serve as practical benchmarks for the investigation of molecules adsorbed on noble-metal surfaces.

Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods

NASA Astrophysics Data System (ADS)

Ramesh, Gaddam; Reddy, Byru Venkatram

2018-05-01

In this investigation, the monomeric structure is determined for picolinic and isonicotinic acids based on geometry optimization for one of the four possible conformers and intramolecular hydrogen bond of Osbnd H⋯O using density functional theory (DFT) employing B3LYP functional supplemented with 6-311++G(d,p) basis set. Using this optimized monomeric form, the dimer structure is determined based on minimum energy and length of hydrogen bonds obtained for two possible dimeric forms yielded due to head-to-tail intermolecular Osbnd H⋯N hydrogen bond (dimer 1) linkage and tail-to -tail intermolecular Osbnd H⋯O hydrogen bond (dimer 2) linkage between pyridine ring and carboxyl group. The structure parameters obtained for monomer and dimer forms are in good agreement with the experimental literature values. The vibrational assignments have been made unambiguously for all the vibrations from FTIR and FT-Raman spectra based on the potential energy distribution (PED) and eigen vectors obtained in DFT and inverse vibrational problem (IVP) computations. The rms error between the observed and scaled frequencies is 7.7 and 9.4 cm-1 for PIA and INA, respectively. A 74-element modified valence force field is derived by Wilson's GF matrix method using 58 experimental frequencies of the two molecules in overlay least-squares technique. The average error between observed and computed frequencies by this method is calculated to be 10.39 cm-1. The results of both DFT and IVP computations yielded good agreement between observed and calculated frequencies. The NLO behaviour using hyperpolarizability values; and HOMO and LUMO energies; of the two molecules are investigated by DFT. Charge density distribution and site of chemical reactivity of the molecules are studied by molecular electrostatic surface potential (MESP). Stability of the molecules arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The 13C and 1H NMR chemical shifts of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-visible (UV-Vis) spectra of the compounds are also recorded in the region 200-400 nm. Thermodynamic parameters and rotational constants are also determined and found that they are comparable with experimental literature values for these molecules.

Theoretical Investigation of the Electronic Structure of Fe(II) Complexes at Spin-State Transitions

PubMed Central

2013-01-01

The electronic structure relevant to low spin (LS)↔high spin (HS) transitions in Fe(II) coordination compounds with a FeN6 core are studied. The selected [Fe(tz)6]2+ (1) (tz = 1H-tetrazole), [Fe(bipy)3]2+ (2) (bipy = 2,2′-bipyridine), and [Fe(terpy)2]2+ (3) (terpy = 2,2′:6′,2″-terpyridine) complexes have been actively studied experimentally, and with their respective mono-, bi-, and tridentate ligands, they constitute a comprehensive set for theoretical case studies. The methods in this work include density functional theory (DFT), time-dependent DFT (TD-DFT), and multiconfigurational second order perturbation theory (CASPT2). We determine the structural parameters as well as the energy splitting of the LS–HS states (ΔEHL) applying the above methods and comparing their performance. We also determine the potential energy curves representing the ground and low-energy excited singlet, triplet, and quintet d6 states along the mode(s) that connect the LS and HS states. The results indicate that while DFT is well suited for the prediction of structural parameters, an accurate multiconfigurational approach is essential for the quantitative determination of ΔEHL. In addition, a good qualitative agreement is found between the TD-DFT and CASPT2 potential energy curves. Although the TD-DFT results might differ in some respect (in our case, we found a discrepancy at the triplet states), our results suggest that this approach, with due care, is very promising as an alternative for the very expensive CASPT2 method. Finally, the two-dimensional (2D) potential energy surfaces above the plane spanned by the two relevant configuration coordinates in [Fe(terpy)2]2+ were computed at both the DFT and CASPT2 levels. These 2D surfaces indicate that the singlet–triplet and triplet–quintet states are separated along different coordinates, i.e., different vibration modes. Our results confirm that in contrast to the case of complexes with mono- and bidentate ligands, the singlet–quintet transitions in [Fe(terpy)2]2+ cannot be described using a single configuration coordinate. PMID:25821416

To bend or not to bend: electronic structural analysis of linear versus bent M-H-M interactions in dinickel bis(dialkylphosphino)methane complexes.

PubMed

Wilson, Zakiya S; Stanley, George G; Vicic, David A

2010-06-21

The M-H-M bonding in the dinuclear complexes Ni(2)(mu-H)(mu-P(2))(2)X(2) (P(2) = R(2)PCH(2)PR(2), R = iPr, Cy; X = Cl, Br) has been investigated. These dinickel A-frames were studied via density functional theory (DFT) calculations to analyze the factors that influence linear and bent M-H-M bonding. The DFT calculations indicate that the bent geometry is favored electronically, with ligand steric effects driving the formation of the linear M-H-M structures.

Van der Waals corrected DFT study of adsorption of groups VA and VIA hydrides on graphene monoxide

NASA Astrophysics Data System (ADS)

Notash, M. Yaghoobi; Ebrahimzadeh, A. Rastkar

2016-06-01

Adsorption properties of H2O, H2S, NH3 and PH3 on graphene monoxide (GMO) nano flack are investigated using density functional theory (DFT). Calculations were carried out by van der Waals correction and general gradient approximation. The adsorption energies and charge transfer between species are obtained and discussed for the considered positions of adsorbate molecules. Charge transfer analysis show that the gas molecules act as an electron acceptor in all cases. The analysis of the adsorption energies suggest GMO can be a good candidate for the adsorption of these molecules.

Molecular properties via a subsystem density functional theory formulation: a common framework for electronic embedding.

PubMed

Höfener, Sebastian; Gomes, André Severo Pereira; Visscher, Lucas

2012-01-28

In this article, we present a consistent derivation of a density functional theory (DFT) based embedding method which encompasses wave-function theory-in-DFT (WFT-in-DFT) and the DFT-based subsystem formulation of response theory (DFT-in-DFT) by Neugebauer [J. Neugebauer, J. Chem. Phys. 131, 084104 (2009)] as special cases. This formulation, which is based on the time-averaged quasi-energy formalism, makes use of the variation Lagrangian techniques to allow the use of non-variational (in particular: coupled cluster) wave-function-based methods. We show how, in the time-independent limit, we naturally obtain expressions for the ground-state DFT-in-DFT and WFT-in-DFT embedding via a local potential. We furthermore provide working equations for the special case in which coupled cluster theory is used to obtain the density and excitation energies of the active subsystem. A sample application is given to demonstrate the method. © 2012 American Institute of Physics

Comparison of discrete Fourier transform (DFT) and principal component analysis/DFT as forecasting tools for absorbance time series received by UV-visible probes installed in urban sewer systems.

PubMed

Plazas-Nossa, Leonardo; Torres, Andrés

2014-01-01

The objective of this work is to introduce a forecasting method for UV-Vis spectrometry time series that combines principal component analysis (PCA) and discrete Fourier transform (DFT), and to compare the results obtained with those obtained by using DFT. Three time series for three different study sites were used: (i) Salitre wastewater treatment plant (WWTP) in Bogotá; (ii) Gibraltar pumping station in Bogotá; and (iii) San Fernando WWTP in Itagüí (in the south part of Medellín). Each of these time series had an equal number of samples (1051). In general terms, the results obtained are hardly generalizable, as they seem to be highly dependent on specific water system dynamics; however, some trends can be outlined: (i) for UV range, DFT and PCA/DFT forecasting accuracy were almost the same; (ii) for visible range, the PCA/DFT forecasting procedure proposed gives systematically lower forecasting errors and variability than those obtained with the DFT procedure; and (iii) for short forecasting times the PCA/DFT procedure proposed is more suitable than the DFT procedure, according to processing times obtained.

Modeling Excited States in TiO2 Nanoparticles: On the Accuracy of a TD-DFT Based Description

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berardo, Enrico; Hu, Hanshi; Shevlin, S. A.

2014-03-11

We have investigated the suitability of Time-Dependent Density Functional Theory (TD-DFT) to describe vertical low-energy excitations in naked and hydrated titanium dioxide nanoparticles through a comparison with results from Equation-of-Motion Coupled Cluster (EOM-CC) quantum chemistry methods. We demonstrate that for most TiO2 nanoparticles TD-DFT calculations with commonly used exchange-correlation (XC-)potentials (e.g. B3LYP) and EOM-CC methods give qualitatively similar results. Importantly, however, we also show that for an important subset of structures, TD-DFT gives qualitatively different results depending upon the XC-potential used and that in this case only TD-CAM-B3LYP and TD-BHLYP calculations yield results that are consistent with those obtained usingmore » EOM-CC theory. Moreover, we demonstrate that the discrepancies for such structures arise from a particular combination of defects, excitations involving which are charge-transfer excitations and hence are poorly described by XC-potentials that contain no or low fractions of Hartree-Fock like exchange. Finally, we discuss that such defects are readily healed in the presence of ubiquitously present water and that as a result the description of vertical low-energy excitations for hydrated TiO2 nanoparticles is hence non-problematic.« less

Dispersion interactions in Density Functional Theory

NASA Astrophysics Data System (ADS)

Andrinopoulos, Lampros; Hine, Nicholas; Mostofi, Arash

2012-02-01

Semilocal functionals in Density Functional Theory (DFT) achieve high accuracy simulating a wide range of systems, but miss the effect of dispersion (vdW) interactions, important in weakly bound systems. We study two different methods to include vdW in DFT: First, we investigate a recent approach [1] to evaluate the vdW contribution to the total energy using maximally-localized Wannier functions. Using a set of simple dimers, we show that it has a number of shortcomings that hamper its predictive power; we then develop and implement a series of improvements [2] and obtain binding energies and equilibrium geometries in closer agreement to quantum-chemical coupled-cluster calculations. Second, we implement the vdW-DF functional [3], using Soler's method [4], within ONETEP [5], a linear-scaling DFT code, and apply it to a range of systems. This method within a linear-scaling DFT code allows the simulation of weakly bound systems of larger scale, such as organic/inorganic interfaces, biological systems and implicit solvation models. [1] P. Silvestrelli, JPC A 113, 5224 (2009). [2] L. Andrinopoulos et al, JCP 135, 154105 (2011). [3] M. Dion et al, PRL 92, 246401 (2004). [4] G. Rom'an-P'erez, J.M. Soler, PRL 103, 096102 (2009). [5] C. Skylaris et al, JCP 122, 084119 (2005).

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model.

PubMed

Wang, Ke; Yu, Yang-Xin; Gao, Guang-Hua

2008-05-14

A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion around a uniform fluid. The electroneutrality in the cell leads to a variational equation with a constraint. Since the reference fluid is selected to be a bulk phase, the Lagrange multiplier proves to be the potential drop across the cell boundary (Donnan potential). The ion profiles and electrostatic potential profiles in the cell are calculated from the present DFT-cell model. Our DFT-cell model gives better prediction of ion profiles than the Poisson-Boltzmann (PB)- or modified PB-cell models when compared to the molecular simulation data. The effects of polyelectrolyte concentration, ion size, and added-salt concentration on the electrostatic potential difference between the DNA surface and the cell boundary are investigated. The expression of osmotic coefficient is derived from the general formula of grand potential. The osmotic coefficients predicted by the DFT are lower than the PB results and are closer to the simulation results and experimental data.

Absorption and fluorescence spectra of heterocyclic isomers from long-range-corrected density functional theory in polarizable continuum approach.

PubMed

Kityk, Andriy V

2012-03-22

Long-range-corrected (LC) DFT/TDDFT methods may provide adequate description of ground and excited state properties; however, accuracy of such an approach depends much on a range separation (exchange screening) representing adjustable model parameter. Its relation to a size or specific of molecular systems has been explored in numerous studies, whereas the effect of solvent environment is usually ignored during the evaluation of state properties. To benchmark and assess the quality of the LC-DFT/TDDFT formalism, we report the optical absorption and fluorescence emission energies of organic heterocyclic isomers, DPIPQ and PTNA, calculated by LC-BLYP DFT/TDDFT method in the polarizable continuum (PCM) approach. The calculations are compared with the optical absorption and fluorescence spectra measured in organic solvents of different polarity. Despite a considerable structural difference, both dyes exhibit quite similar range separations being somewhat different for the optical absorption and fluorescence emission processes. Properly parametrized LC-BLYP xc-potential well reproduces basic features of the optical absorption spectra including the electronic transitions to higher excited states. The DFT/TDDFT/PCM analysis correctly predicts the solvation trends although solvatochromic shifts of the electronic transition energies appear to be evidently underestimated in most cases, especially for the fluorescence emission. Considering the discrepancy between the experiment and theory, evaluated state dipole moments and solvation corrections to the exchange screening are analyzed. The results of the present study emphasize the importance of a solvent-dependent range separation in DFT/TDDFT/PCM calculations for investigating excited state properties. © 2012 American Chemical Society

The structure of N2 adsorbed on the rumpled NaCl(100) surface—A combined LEED and DFT-D study

NASA Astrophysics Data System (ADS)

Vogt, Jochen

2012-11-01

The structure of N2 physisorbed on the NaCl(100) single crystal surface is investigated by means of quantitative low-energy electron diffraction (LEED) in combination with dispersion corrected density functional theory (DFT-D). In the temperature range between 20 K and 45 K, a p(1 × 1) structure is observed in the LEED experiment. According to the structure analysis based on the measured diffraction spot intensity profiles, the N2 molecules are adsorbed over the topmost Na+ ions. The experimental distance of the lower nitrogen to the Na+ ion underneath is (2.55 ± 0.07) Å; the corresponding DFT-D value is 2.65 Å. The axes of the molecules are tilted (26 ± 3)° with respect to the surface normal, while in the zero Kelvin optimum structure from DFT-D, the molecules have a perpendicular orientation. The experimental monolayer heat of adsorption, deduced from a Fowler-Guggenheim kinetic model of adsorption is -(13.6 ± 1.6) kJ mol-1, including a lateral molecule-molecule interaction energy of -(2.0 ± 0.4) kJ mol-1. The zero Kelvin adsorption energy from DFT-D, including zero point energy correction, is -15.6 kJ mol-1; the molecule-molecule interaction is -2.4 kJ mol-1. While the rumpling of the NaCl(100) surface is unchanged upon adsorption of nitrogen, the best-fit root mean square thermal displacements of the ions in the topmost substrate layer are significantly reduced.

Polyphase-discrete Fourier transform spectrum analysis for the Search for Extraterrestrial Intelligence sky survey

NASA Technical Reports Server (NTRS)

Zimmerman, G. A.; Gulkis, S.

1991-01-01

The sensitivity of a matched filter-detection system to a finite-duration continuous wave (CW) tone is compared with the sensitivities of a windowed discrete Fourier transform (DFT) system and an ideal bandpass filter-bank system. These comparisons are made in the context of the NASA Search for Extraterrestrial Intelligence (SETI) microwave observing project (MOP) sky survey. A review of the theory of polyphase-DFT filter banks and its relationship to the well-known windowed-DFT process is presented. The polyphase-DFT system approximates the ideal bandpass filter bank by using as few as eight filter taps per polyphase branch. An improvement in sensitivity of approx. 3 dB over a windowed-DFT system can be obtained by using the polyphase-DFT approach. Sidelobe rejection of the polyphase-DFT system is vastly superior to the windowed-DFT system, thereby improving its performance in the presence of radio frequency interference (RFI).

DFT and TD-DFT insights, photolysis and photocatalysis investigation of three dyes with similar structure under UV irradiation with and without TiO2 as a catalyst: Effect of adsorption, pH and light intensity

NASA Astrophysics Data System (ADS)

Bendjabeur, Seyfeddine; Zouaghi, Razika; Zouchoune, Bachir; Sehili, Tahar

2018-02-01

TiO2-mediated photocatalytic degradation of three triphenylmethane dyes (basic fuchsin, acid fuchsin and Gentian violet), was investigated in aqueous suspensions in the presence and the absence of titanium dioxide P25 Degussa as photocatalyst. The photodegradation process was investigated using UV-A (365 nm) and UV-C (254 nm) light alone and UV-A in the presence of TiO2·The effects of various operational parameters were investigated such as: the effect of adsorption in the dark, the influence of pH, the influence of irradiation wavelength and the effect of light intensity. The study of the effect of various parameters reveals that the photolysis of dyes increases with the increase of light intensity, the degradation rate under UV-C (254 nm) was found better than under UV-A 365 nm. The photocatalytic degradation was found to follow the same order of adsorption. The decolorization and the degradation kinetics were found to follow the pseudo-first-order kinetics. The mineralization of dye was found to follow the same order of disappearance as the photocatalytic degradation and depended directly to its functional groups and its number of carbons. Additionally, density functional theory (DFT) was applied for calculations of both electronic structure and spectroscopic properties of the studied compounds, where the obtained results of the three dyes show that the theoretical electronic spectra and the experimental UV-visible ones are similar in shapes, positions and intensities.

Effect of defibrillation threshold testing on effectiveness of the subcutaneous implantable cardioverter defibrillator.

PubMed

Peddareddy, Lakshmi; Merchant, Faisal M; Leon, Angel R; Smith, Paige; Patel, Akshar; El-Chami, Mikhael F

2018-06-12

Defibrillation threshold (DFT) testing is recommended with the subcutaneous ICD (SICD). To describe first shock efficacy for appropriate SICD therapies stratified by the presence of implant DFT testing. We reviewed all patients receiving SICDs at our institution and stratified them based on whether implant DFT testing was performed. Appropriate shocks were reviewed to see if ventricular tachycardia/ventricular fibrillation (VT/VF) terminated with a single shock. First shock efficacy was stratified by implant DFT status. 178 patients implanted with SICDs and followed in our center were included in this study. Of these, 135 (76 %) underwent DFT testing (DFT (+) group). In the DFT (+) 80 appropriate shocks were needed to treat 69 episodes of VT/VF. The first shock was effective in 61 out of 69 episodes (88.4 %), whereas multiple shocks were required to terminate VT/VF in the remaining 8 episodes. Among 43 patients without implant DFT testing (DFT (-) group), 20 appropriate shocks to treat 17 episodes of VT/VF occurred in 7 patients. VT/VF was successfully terminated with the first shock in 16 out of 17 episodes (first shock efficacy 94.1 %). There was no significant difference in first shock effectiveness between those with and without implant DFT testing (p = 0.97). A strategy that omits DFT testing at implant did not appear to compromise the effictiveness of the SICD. These data suggest that routine DFT testing at SICD implant might not be necessary. Randomized trials are needed to confirm this finding. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A combined spectroscopic and TDDFT study of natural dyes extracted from fruit peels of Citrus reticulata and Musa acuminata for dye-sensitized solar cells.

PubMed

Prima, Eka Cahya; Hidayat, Novianto Nur; Yuliarto, Brian; Suyatman; Dipojono, Hermawan Kresno

2017-01-15

This study reports the novel spectroscopic investigations and enhanced the electron transfers of Citrus reticulata and Musa acuminata fruit peels as the photosensitizers for the dye-sensitized solar cells. The calculated TD-DFT-UB3LYP/6-31+G(d,p)-IEFPCM(UAKS), experiment spectra of ultra-violet-visible spectroscopy, and Fourier transform infrared spectroscopy studies indicate the main flavonoid (hesperidin and gallocatechin) structures of the dye extracts. The optimized flavonoid structures are calculated using Density functional theory (DFT) at 6-31+G(d,p) level. The rutinosyl group of the hesperidin pigment (Citrus reticulata) will be further investigated compared to the gallocatechin (Musa acuminata) pigment. The acidity of the dye extract is treated by adding 2% acetic acid. The energy levels of the HOMO-LUMO dyes are measured by a combined Tauc plot and cyclic voltammetry contrasted with the DFT data. The electrochemical impedance spectroscopy will be performed to model the dye electron transfer. As for the rutinosyl group presence and the acidic treatment, the acidified Citrus reticulata cell under continuous light exposure of 100mW·cm -2 yields a short-circuit current density (J sc ) of 3.23mA/cm 2 , a photovoltage (V oc ) of 0.48V, and a fill factor of 0.45 corresponding to an energy conversion efficiency (η) of 0.71% because the shifting down HOMO-LUMO edges and the broadening dye's absorbance evaluated by a combined spectroscopic and TD-DFT method. The result also leads to the longest diffusion length of 32.2μm, the fastest electron transit of 0.22ms, and the longest electron lifetime of 4.29ms. Copyright © 2016 Elsevier B.V. All rights reserved.

A combined spectroscopic and TDDFT study of natural dyes extracted from fruit peels of Citrus reticulata and Musa acuminata for dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Prima, Eka Cahya; Hidayat, Novianto Nur; Yuliarto, Brian; Suyatman; Dipojono, Hermawan Kresno

2017-01-01

This study reports the novel spectroscopic investigations and enhanced the electron transfers of Citrus reticulata and Musa acuminata fruit peels as the photosensitizers for the dye-sensitized solar cells. The calculated TD-DFT-UB3LYP/6-31 + G(d,p)-IEFPCM(UAKS), experiment spectra of ultra-violet-visible spectroscopy, and Fourier transform infrared spectroscopy studies indicate the main flavonoid (hesperidin and gallocatechin) structures of the dye extracts. The optimized flavonoid structures are calculated using Density functional theory (DFT) at 6-31 + G(d,p) level. The rutinosyl group of the hesperidin pigment (Citrus reticulata) will be further investigated compared to the gallocatechin (Musa acuminata) pigment. The acidity of the dye extract is treated by adding 2% acetic acid. The energy levels of the HOMO-LUMO dyes are measured by a combined Tauc plot and cyclic voltammetry contrasted with the DFT data. The electrochemical impedance spectroscopy will be performed to model the dye electron transfer. As for the rutinosyl group presence and the acidic treatment, the acidified Citrus reticulata cell under continuous light exposure of 100 mW·cm- 2 yields a short-circuit current density (Jsc) of 3.23 mA/cm2, a photovoltage (Voc) of 0.48 V, and a fill factor of 0.45 corresponding to an energy conversion efficiency (η) of 0.71% because the shifting down HOMO-LUMO edges and the broadening dye's absorbance evaluated by a combined spectroscopic and TD-DFT method. The result also leads to the longest diffusion length of 32.2 μm, the fastest electron transit of 0.22 ms, and the longest electron lifetime of 4.29 ms.

Spectroscopic (FT-IR, FT-Raman, UV and NMR) investigation and NLO, HOMO-LUMO, NBO analysis of organic 2,4,5-trichloroaniline.

PubMed

Govindarajan, M; Karabacak, M; Periandy, S; Tanuja, D

2012-11-01

In this work, the experimental and theoretical study on the molecular structure and vibrational spectra of 2,4,5-trichloroaniline (C(6)H(4)NCl(3), abbreviated as 2,4,5-TClA) were studied. The FT-IR and FT-Raman spectra were recorded. The molecular geometry and vibrational frequencies in the ground state were calculated by using the Hartree-Fock (HF) and density functional theory (DFT) methods (B3LYP) with 6-311++G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of 2,4,5-TClA with calculated results by HF and DFT indicates that B3LYP is superior to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4,5-TClA molecule may have microscopic nonlinear optical (NLO) behavior with non-zero values. Mulliken atomic charges of 2,4,5-TClA was calculated and compared with aniline and chlorobenzene molecules. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. Copyright © 2012 Elsevier B.V. All rights reserved.

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Dental caries prevalence and its association with fluoride level in drinking water in Sana'a, Yemen

PubMed Central

Al-Akwa, Ameen Abdullah; Al-Maweri, Sadeq Ali

2018-01-01

Objectives: Dental caries is the most prevalent chronic condition affecting schoolchildren worldwide. This study is aimed to assess the prevalence of dental caries among schoolchildren in urban and rural districts of Sana'a governorate, Yemen, and to investigate the correlation between caries experience and level of fluoride in drinking water, age, gender, and residence. Materials and Methods: This school-based survey involved 17,599 schoolchildren (aged 6–12 years), of whom 9623 were boys and 7976 were girls. We used decay-missing-filled teeth/decay-filled teeth (DMFT/dft) indices to evaluate dental caries experience. In addition, fluoride concentration in drinking water was investigated. Results: Around 67.6% of children had dental caries. Children residing in urban districts had significantly higher mean scores of DMFT/dft than those in rural areas (P < 0.05). A significant negative correlation between caries experience and fluoride level was found (P < 0.05), with the lowest dft/DMFT scores at the optimum fluoride level of 0.61–2 ppm and the highest at two extremes, 0.0–0.4 ppm and >2 ppm. Conclusion: This survey found a very high prevalence of caries among schoolchildren in Yemen. There was also an inverse relation between dental caries experience and fluoride levels. PMID:29657520

Adsorption of various types of amino acids on the graphene and boron-nitride nano-sheet, a DFT-D3 study

NASA Astrophysics Data System (ADS)

Zhiani, Rahele

2017-07-01

The binding properties of the adsorption of five different classes of amino acids, namely, alanine (Ala), arginine (Arg), asparagine (Asn), histidine (His) and cysteine (Cys) on the surface of the graphene (Gra) and the born-nitride (BN) nano-sheet structures were studied from molecular viewpoint using quantum mechanics methods. Density functional theory (DFT) and DFT-D3 calculations were carried out to investigate the electronic properties and the dispersion interaction of the amino acid/adsorbent complexes. Several parameters affecting the interactions between the amino acids and the adsorbent surfaces such as solvent effect, adsorption energy and separation distance were investigated. Findings show that Arg forms the most stable complexes with the graphene and the BN nano-sheet compare to the other amino acids used in this study. The observed frequency results which were related to the band gap energies were consistent with the above statement. Results exhibit that adsorption of the amino acids on the surface of the BN nano-sheet and the graphene accompanied with the release of the energy. Calculations show that there are no bonded interactions between the amino acids and adsorbent surfaces. The polarity of the BN nano-sheet provides the more affinity towards the amino acids. These results were proved by the quantum chemistry studies.

Mechanical and magneto-opto-electronic investigation of transition metal based fluoro-perovskites: An ab-initio DFT study

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2017-09-01

Detailed ab-initio calculations are performed to investigate structural, elastic, mechanical, magneto-electronic and optical properties of the KXF3 (X = V, Fe, Co, Ni) fluoro-perovskites using Full Potential Linearized Augmented Plane Wave (FP-LAPW) method within the framework of density functional theory (DFT). The calculated structural parameters by DFT and analytical methods are found consistent with the experimental results. From the elastic and mechanical properties, it can be inferred that these compounds are elastically stable and anisotropic while KCoF3 is harder than rest of the compounds. Furthermore, thermal behavior of these compounds is analyzed by calculating Debye temperature (θD). The calculated spin dependent magneto-electronic properties in these compounds reveal that exchange splitting is dominated by N-3d orbital. The stable magnetic phase optimizations verify the experimental observations at low temperature. Type of chemical bonding is analyzed with the help of variations in electron density difference distribution that is induced due to changes of the second cation. The linear optical properties are also discussed in terms of optical spectra. The present methodology represents an influential approach to calculate the whole set of mechanical and magneto-opto-electronic parameters, which would support to understand various physical phenomena and empower device engineers for implementing these materials in spintronic applications.

FTIR, FT-Raman, FT-NMR, UV-visible and quantum chemical investigations of 2-amino-4-methylbenzothiazole.

PubMed

Arjunan, V; Sakiladevi, S; Rani, T; Mythili, C V; Mohan, S

2012-03-01

The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectral measurements and complete assignments of the observed spectra of 2-amino-4-methylbenzothiazole (2A4MBT) have been proposed. Ab initio and DFT calculations have been performed and the structural parameters of the compound were determined from the optimised geometry with 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO, LUMO and band gap energies were measured by time-dependent DFT (TD-DFT) approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman activities chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. The influences of methyl and amino groups on the skeletal modes and on the proton chemical shifts have been investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach.

PubMed

Sert, Yusuf; Sreenivasa, S; Doğan, H; Manojkumar, K E; Suchetan, P A; Ucun, Fatih

2014-06-05

In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations. Copyright © 2014 Elsevier B.V. All rights reserved.

FT-IR, Laser-Raman spectra and quantum chemical calculations of methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate-A DFT approach

NASA Astrophysics Data System (ADS)

Sert, Yusuf; Sreenivasa, S.; Doğan, H.; Manojkumar, K. E.; Suchetan, P. A.; Ucun, Fatih

2014-06-01

In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor and anti-inflammatory agent namely, methyl 4-(trifluoromethyl)-1H-pyrrole-3-carboxylate have been investigated. The experimental FT-IR (4000-400 cm-1) and Laser-Raman spectra (4000-100 cm-1) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parameterized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

Experimental (FT-IR, NMR and UV) and theoretical (M06-2X and DFT) investigation, and frequency estimation analyses on (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile

NASA Astrophysics Data System (ADS)

Sert, Yusuf; Balakit, Asim A.; Öztürk, Nuri; Ucun, Fatih; El-Hiti, Gamal A.

2014-10-01

The spectroscopic properties of (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile have been investigated by FT-IR, UV, 1H and 13C NMR techniques. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been carried out by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies were in good agreement with the corresponding experimental data, and with the results in the literature. 1H and 13C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength wavelengths were performed by B3LYP methods. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.

Vibrational and electronic investigations, thermodynamic parameters, HOMO and LUMO analysis on Lornoxicam by density functional theory

NASA Astrophysics Data System (ADS)

Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

2015-11-01

The Fourier transform infrared (FT-IR) and FT-Raman spectra of Lornoxicam were recorded in the region 4000-450 cm-1 and 4000-50 cm-1 respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameters, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p) and 6-31++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the Vibrational modes calculated using Vibrational Energy Distribution Analysis (VEDA 4) program. The oscillator's strength calculated by TD-DFT and Lornoxicam is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis and the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like Entropy, Enthalpy, Specific heat capacity and zero vibrational energy have been calculated. Besides, molecular electrostatic potential (MEP) was investigated using theoretical calculations.

DENSITY FUNCTIONAL THEORY (DFT) AND MICROCALORIMETRIC INVESTIGATIONS OF CO ADSORPTION ON PT CLUSTERS. (R825370C056)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost

NASA Astrophysics Data System (ADS)

Bajaj, Akash; Janet, Jon Paul; Kulik, Heather J.

2017-11-01

The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and molecules. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such physically intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT.

Carbon dioxide capture using covalent organic frameworks (COFs) type material-a theoretical investigation.

PubMed

Dash, Bibek

2018-04-26

The present work deals with a density functional theory (DFT) study of porous organic framework materials containing - groups for CO 2 capture. In this study, first principle calculations were performed for CO 2 adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO 2 and nitrogen gas. Binding energies (BEs) of CO 2 and N 2 molecules with the polymer framework were calculated with DFT methods. Hybrid B3LYP and second order MP2 methods combined with of Pople 6-31G(d,p) and correlation consistent basis sets cc-pVDZ, cc-pVTZ and aug-ccVDZ were used to calculate BEs. The effect of linker groups in the designed covalent organic framework model system on the CO 2 and N 2 interactions was studied using quantum calculations.

Phenothiazine-anthraquinone donor-acceptor molecules: synthesis, electronic properties and DFT-TDDFT computational study.

PubMed

Zhang, Wen-Wei; Mao, Wei-Li; Hu, Yun-Xia; Tian, Zi-Qi; Wang, Zhi-Lin; Meng, Qing-Jin

2009-09-17

Two donor-acceptor molecules with different pi-electron conjugative units, 1-((10-methyl-10H-phenothiazin-3-yl)ethynyl)anthracene-9,10-dione (AqMp) and 1,1'-(10-methyl-10H-phenothiazine-3,7-diyl)bis(ethyne-2,1-diyl)dianthracene-9,10-dione (Aq2Mp), have been synthesized and investigated for their photochemical and electrochemical properties. Density functional theory (DFT) calculations provide insights into their molecular geometry, electronic structures, and properties. These studies satisfactorily explain the electrochemistry of the two compounds and indicate that larger conjugative effect leads to smaller HOMO-LUMO gap (Eg) in Aq2Mp. Both compounds show ICT and pi --> pi* transitions in the UV-visible range in solution, and Aq2Mp has a bathochromic shift and shows higher oscillator strength of the absorption, which has been verified by time-dependent DFT (TDDFT) calculations. The differences between AqMp and Aq2Mp indicate that the structural and conjugative effects have great influence on the electronic properties of the molecules.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

Spectral investigations and DFT studies of 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine) interaction and recognition by single amino acid derived self-assembled nanostructures

NASA Astrophysics Data System (ADS)

Govindhan, R.; Karthikeyan, B.

2018-03-01

Recognition of xanthine alkaloid caffeine with 3,5-bis(trifluoromethyl)benzylamine derived peptide nanotubes (BTTPNTs) through chemical interaction have been achieved through the host-guest like interaction. DFT simulation is carried out for caffeine interacted with BTTPNTs system and also experimentally characterized by ultraviolet-visible (UV-vis) absorbance, confocal Raman spectra (CRS) with microscopic imaging (CRM), FT-Raman, surface enhanced Raman scattering (SERS), UV-diffuse reflectance spectra (UV-DRS), high resolution transmission electron microscopy (HR-TEM) and cyclic voltammetry (CV) studies. The results are used to examine the morphologies, size of the nanostructure and study of its interaction with the caffeine molecule. The results show that BTTPNTs is having potential for sensing the caffeine molecules through the binding occurred from the NH2 of tyrosine moiety of the BTTPNTs. This intermolecular association through face-to-face stacking of BTTPNTs is explained by detailed DFT calculations.

Structure and gas phase stability of complexes L . .. M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

NASA Astrophysics Data System (ADS)

Remko, Milan

Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+ , Na+ and Mg2+ . Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li+ > Na+ . The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

Chemisorption of Hydroxide on 2D Materials from DFT Calculations: Graphene versus Hexagonal Boron Nitride.

PubMed

Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lydéric; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

2016-11-17

Recent nanofluidic experiments revealed strongly different surface charge measurements for boron-nitride (BN) and graphitic nanotubes when in contact with saline and alkaline water (Nature 2013, 494, 455-458; Phys. Rev. Lett. 2016, 116, 154501). These observations contrast with the similar reactivity of a graphene layer and its BN counterpart, using density functional theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials-chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values, resulting in a favorable (nonfavorable) adsorption on BN (graphene). We also calculate a pK a ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echo the weaker surface charge measurements but point to an alternative scenario.

Chemisorption of Hydroxide on 2D Materials From DFT Calculations: Graphene Versus Hexagonal Boron Nitride

PubMed Central

Grosjean, Benoit; Pean, Clarisse; Siria, Alessandro; Bocquet, Lyderic; Vuilleumier, Rodolphe; Bocquet, Marie-Laure

2017-01-01

Recent nanofluidic measurements revealed strongly different surface charge measurements for boron-nitride and graphitic nanotubes when in contact with saline and alkaline water. 1,2 These observations contrast with the similar reactivity of a graphene layer and its boron nitride counterpart, using Density Functional Theory (DFT) framework, for intact and dissociative adsorption of gaseous water molecules. Here, we investigate, by DFT in implicit water, single and multiple adsorption of anionic hydroxide on single layers. A differential adsorption strength is found in vacuum for the first ionic adsorption on the two materials – chemisorbed on BN while physisorbed on graphene. The effect of implicit solvation reduces all adsorption values resulting in a favorable (non-favorable) adsorption on BN (graphene). We also calculate a pKa ≃ 6 for BN in water, in good agreement with experiments. Comparatively, the unfavorable results for graphene in water echoes the weaker surface charge measurements, but points to an alternative scenario. PMID:27809540

Design of donor-acceptor copolymers for organic photovoltaic materials: a computational study.

PubMed

Turan, Haydar Taylan; Kucur, Oğuzhan; Kahraman, Birce; Salman, Seyhan; Aviyente, Viktorya

2018-01-31

80 different push-pull type organic chromophores which possess Donor-Acceptor (D-A) and Donor-Thiophene-Acceptor-Thiophene (D-T-A-T) structures have been systematically investigated by means of density functional theory (DFT) and time-dependent DFT (TD-DFT) at the B3LYP/6-311G* level. The introduction of thiophene (T) in the chain has allowed us to monitor the effect of π-spacers. Benchmark studies on the methodology have been carried out to predict the HOMO and LUMO energies and optical band gaps of the D-A systems accurately. The HOMO and LUMO energies and transition dipoles are seen to converge for tetrameric oligomers, and the latter have been used as optimal chain length to evaluate various geometrical and optoelectronic properties such as bond length alternations, distortion energies, frontier molecular orbital energies, reorganization energies and excited-state vertical transition of the oligomers. Careful analysis of our findings has allowed us to propose potential donor-acceptor couples to be used in organic photovoltaic cells.

Theoretical Study of Effect of Introducing π-Conjugation on Efficiency of Dye-Sensitized Solar Cell.

PubMed

Lee, Geon Hyeong; Kim, Young Sik

2018-09-01

In this study, phenoxazine (PXZ)-based dye sensitizers with triphenylamine (TPA) as a dual-electron donor and thiophen and benzothiadiazole (BTD) or 4,7-diethynylbenzo[c][1,2,5]thiadiazole (DEBT) as an electron acceptor (dye1, dye2, and dye3) were designed and investigated. dye3 can significantly stabilize the lowest unoccupied molecular orbital (LUMO) energy level of an organic dye. We used density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations to better understand the factors responsible for the photovoltaic performance. The absorption spectrum of the dyes showed different forms because of the different energy levels of the molecular orbital (MO) of each dye and the intramolecular energy transfer (EnT). Among the three dyes, dye3 showed greater red-shift, broader absorption spectra, and higher molar extinction coefficient. These results indicate that adding a withdrawing unit and π-conjugation to a dye can result in good photovoltaic properties for dye-sensitized solar cells (DSSCs).

The effect of Pd ensemble structure on the O2 dissociation and CO oxidation mechanisms on Au—Pd(100) surface alloys

NASA Astrophysics Data System (ADS)

Oǧuz, Ismail-Can; Mineva, Tzonka; Guesmi, Hazar

2018-01-01

The reactivity of various Pd ensembles on the Au—Pd(100) alloy catalyst toward CO oxidation was investigated by using density functional theory (DFT). This study was prompted by the search for efficient catalysts operating at low temperature for the CO oxidation reaction that is of primary environmental importance. To this aim, we considered Pd modified Au(100) surfaces including Pd monomers, Pd dimers, second neighboring Pd atoms, and Pd chains in a comparative study of the minimum energy reaction pathways. The effect of dispersion interactions was included in the calculations of the O2 dissociation reaction pathway by using the DFT-D3 scheme. The addition of the dispersion interaction strongly improves the adsorption ability of O2 on the Au—Pd surface but does not affect the activation energy barriers of the Transitions States (TSs). As for O2 to dissociate, it is imperative that the TS has lower activation energy than the O2 desorption energy. DFT-D3 is found to favor, in some cases, O2 dissociation on configurations being identified from uncorrected DFT calculations as inactive. This is the case of the second neighboring Pd configuration for which uncorrected DFT predicts positive Gibbs free energy (ΔG) of the O2 adsorption, therefore an endergonic reaction. With the addition of D3 correction, ΔG becomes negative that reveals a spontaneous O2 adsorption. Among the investigated Au—Pd (100) ensembles, the Pd chain dissociates most easily O2 and highly stabilizes the dissociated O atoms; however, it has an inferior reactivity toward CO oxidation and CO2 formation. Indeed, CO strongly adsorbs on the palladium bridge sites and therefore poisoning the surface Pd chain. By contrast, the second neighboring Pd configuration that shows somewhat lower ability to dissociate O2 turns out to be more reactive in the CO2 formation step. These results evidence the complex effect of Pd ensembles on the CO oxidation reaction. Associative CO oxidation proceeds with high energy barriers on all the considered Pd ensembles and should be excluded, in agreement with experimental observations.

Comparative study of DFT+U functionals for non-collinear magnetism

NASA Astrophysics Data System (ADS)

Ryee, Siheon; Han, Myung Joon

2018-07-01

We performed comparative analysis for DFT+U functionals to better understand their applicability to non-collinear magnetism. Taking LiNiPO4 and Sr2IrO4 as examples, we investigated the results out of two formalisms based on charge-only density and spin density functional plus U calculations. Our results show that the ground state spin order in terms of tilting angle is strongly dependent on Hund J. In particular, the opposite behavior of canting angles as a function of J is found for LiNiPO4. The dependence on the other physical parameters such as Hubbard U and Slater parameterization is investigated. We also discuss the formal aspects of these functional dependences as well as parameter dependences. The current study provides useful information and important intuition for the first-principles calculation of non-collinear magnetic materials.

Chemical shielding properties for BN, BP, AlN, and AlP nanocones: DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Mahmoud; Yousefi, Mohammad; Meskinfam, Masoumeh

2012-06-01

The properties of boron nitride (BN), boron phosphide (BP), aluminum nitride (AlN), and aluminum phosphide (AlP) nanocones were investigated by density functional theory (DFT) calculations. The investigated structures were optimized and chemical shielding (CS) properties including isotropic and anisotropic CS parameters were calculated for the atoms of the optimized structures. The magnitudes of CS parameters were observed to be mainly dependent on the bond lengths of considered atoms. The results indicated that the atoms could be divided into atomic layers due to the similarities of their CS properties for the atoms of each layer. The trend means that the atoms of each layer detect almost similar electronic environments. Moreover, the atoms at the apex and mouth of nanocones exhibit different properties with respect to the other atomic layers.

Signatures of spin-orbital states of t2g 2 system in optical conductivity: R VO3 (R =Y and La)

NASA Astrophysics Data System (ADS)

Kim, Minjae

2018-04-01

We investigate signatures of the spin and orbital states of R VO3 (R =Y and La) in optical conductivity using density functional theory plus dynamical mean-field theory (DFT+DMFT). From the assignment of multiplet state configurations to optical transitions, the DFT+DMFT reproduces experimental temperature-dependent evolutions of optical conductivity for both YVO3 and LaVO3. We also show that the optical conductivity is a useful quantity to probe the evolution of the orbital state even in the absence of spin order. The result provides a reference to investigate the spin and orbital states of t2g 2 vanadate systems, which is an important issue for both fundamental physics on spin and orbital states and applications of vanadates by means of orbital state control.

A microscopic study investigating the structure of SnSe surfaces

NASA Astrophysics Data System (ADS)

Kim, Sang-ui; Duong, Anh-Tuan; Cho, Sunglae; Rhim, S. H.; Kim, Jungdae

2016-09-01

SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. Herein, for the first time, the atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM) and density functional theory (DFT) calculations. The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by DFT calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms.

Elastic and Photoelastic Properties of M(NO3)2, MO (M = Mg, Ca, Sr, Ba)

NASA Astrophysics Data System (ADS)

Zhuravlev, Yu. N.; Korabel'nikov, D. V.

2017-05-01

The paper deals with ab initio investigations of elastic and photoelastic properties of oxides and nitrates of alkaline-earth metals. In gradient approximation of the density functional theory (DFT), these properties are studied with the use of the linear combination of the atomic orbital technique. DFT calculations are done with the CRYSTAL 14 software package. The paper introduces the elastic and photoelastic constants, anisotropy parameters for single-crystalline phases and the elastic modules, hardness, Poisson ratio for polycrystalline phases. Such parameters as sonic speed, Debye temperature, thermal conductivity, and Gruneisen parameter are estimated herein. For the fist time, mechanical stability, anisotropy of elastic and photoelastic properties and their dependences are investigated ab initio in this paper. Experimental results on elastic and photoelastic properties of oxides and nitrates are in good agreement with theoretical calculations.

Adsorption of CGA on colloidal silver particles: DFT and SERS study

NASA Astrophysics Data System (ADS)

Biswas, Nandita; Kapoor, Sudhir; Mahal, Harbir S.; Mukherjee, Tulsi

2007-08-01

Raman and surface-enhanced Raman scattering (SERS) of chlorogenic acid (CGA) have been investigated. CGA is an important plant metabolite with anti-viral and anti-bacterial properties and thus, it is useful to study its surface adsorption characteristics. The experimental Raman data is supported with DFT calculations using B3LYP functional with 6-31G ∗ and LANL2DZ basis set. This is the first report on the vibrational analysis of CGA and its silver complex. From the SERS spectra as well as theoretical calculations, it has been inferred that the molecule is chemisorbed to the silver surface through the oxygen atoms of the carboxylate group.

Synthesis and DFT calculations of some 2-aminothiazoles

NASA Astrophysics Data System (ADS)

Rezania, Jafar; Behzadi, Hadi; Shockravi, Abbas; Ehsani, Morteza; Akbarzadeh, Elahe

2018-04-01

A series of 2-aminothiazole derivatives have been synthesized by the reaction of acetyl compounds with thiourea and iodine as catalyst under solvent-free condition, a green chemistry method. The quantum chemical calculations at the DFT/B3LYP level of theory in gas phase were carried out for starting acetyl derivatives. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and related reactivity descriptor of acetyl derivatives, as well as, enthalpy of reactions are calculated in order to investigate the reaction properties of acetyl compounds and yields of the reactions. The calculated reactivity descriptors are well correlated to activity of different acetyl derivatives.

Highly efficient regioselective synthesis, spectroscopic characterizations and DFT calculations of novel hydroxymethylated 1,4-disubstituted-1,2,3-triazole-based sulfonamides

NASA Astrophysics Data System (ADS)

Taheri, Elmira; Mirjafary, Zohreh; Saeidian, Hamid

2018-04-01

The novel hydroxymethylated 1,4-disubstituted-1,2,3-triazole-based sulfonamides were synthesized in excellent yields and high regioselectivity via a one-pot, two-step, three-component reaction of N-propargylsulfonamides, sodium azide, and epoxide derivatives under green conditions. Green and mild reaction condition, commercially readily available and inexpensive starting materials, wide scope and easy work-up are the key features of the present method. The Li+ and Na+ ion affinities of the model structure have been also investigated by density functional theory (DFT) studies to find the applicability of these products as ligand in coordination chemistry.

DFT investigation of the interaction of gold nanoclusters with poly(amidoamine) PAMAM G0 dendrimer

NASA Astrophysics Data System (ADS)

Camarada, M. B.

2016-06-01

The interaction between PAMAM G0 and gold nanoclusters Aun (n = 2, 4, 6, and 8) was studied theoretically at DFT level. Different coordination sites were explored, including internal and superficial coordination. All stable complexes exhibited external interaction with the amine or carbonyl site, while the core site coordination was not favored. The more stable binding of Aun was registered with the terminal amine group, while the binding at the amide site was relatively weaker. The vertical first ionization potential, electron affinity, Fermi level, and the HOMO-LUMO gap of PAMAM and Aun-PAMAM G0 complexes were also analyzed.

DFT investigation on the adsorption behavior of dimethyl and trimethyl amine molecules on borophene nanotube

NASA Astrophysics Data System (ADS)

Bhuvaneswari, R.; Chandiramouli, R.

2018-06-01

The electronic properties of borophene nanotube (BNT) are witnessed and the adsorption properties of dimethyl amine (DMA) and trimethyl amine (TMA) molecules on borophene nanotube are explored through non-equilibrium Green's function (NEGF) and density functional theory (DFT) method. The device density of states spectrum interprets the change in peak maxima, thus indicating the electron transition between DMA, TMA molecules and BNT base material. I-V characteristics strengthen the adsorption property of DMA and TMA on BNT by pointing out the variation in the current. The present work assures that borophene nanotube (BNT) can be employed as DMA and TMA sensor.

Phase transition in conjugated oligomers suspended in chloroform

NASA Astrophysics Data System (ADS)

Dwivedi, Shikha; Kumar, Anupam; Yadav, S. N. S.; Mishra, Pankaj

2015-08-01

Density functional theory (DFT) has been used to investigate the isotropic-nematic (I-N) phase transition in a system of high aspect ratio conjugated oligomers suspended in chloroform. The interaction between the oligomers is modeled using Gay-Berne potential in which effect of solvent is implicit. Percus-Yevick integral equation theory has been used to evaluate the pair correlation functions of the fluid phase at several temperatures and densities. These pair correlation function has been used in the DFT to evaluate the I-N freezing parameters. Highly oriented nematic is found to stabilize at low density. The results obtained are in qualitative agreement with the simulation and are verifiable.

Doping of the step-edge Si chain: Ag on a Si(557)-Au surface

NASA Astrophysics Data System (ADS)

Krawiec, M.; Jałochowski, M.

2010-11-01

Structural and electronic properties of monatomic Ag chains on the Au-induced, highly ordered Si(557) surface are investigated by scanning tunneling microscopy (STM)/spectroscopy and first-principles density functional theory (DFT) calculations. The STM topography data show that a small amount of Ag (0.25 ML) very weakly modifies the one-dimensional structure induced by Au atoms. However, the bias-dependent STM topography and spectroscopy point to the importance of the electronic effects in this system, which are further corroborated by the DFT calculations. The obtained results suggest that Ag atoms act as electron donors leaving the geometry of the surface almost unchanged.

Scanning tunneling microscopy current from localized basis orbital density functional theory

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Paulsson, Magnus

2016-03-01

We present a method capable of calculating elastic scanning tunneling microscopy (STM) currents from localized atomic orbital density functional theory (DFT). To overcome the poor accuracy of the localized orbital description of the wave functions far away from the atoms, we propagate the wave functions, using the total DFT potential. From the propagated wave functions, the Bardeen's perturbative approach provides the tunneling current. To illustrate the method we investigate carbon monoxide adsorbed on a Cu(111) surface and recover the depression/protrusion observed experimentally with normal/CO-functionalized STM tips. The theory furthermore allows us to discuss the significance of s - and p -wave tips.

Extent of tooth decay in the mouth and increased need for replacement of dental restorations: the New England Children's Amalgam Trial.

PubMed

Trachtenberg, Felicia; Maserejian, Nancy Nairi; Tavares, Mary; Soncini, Jennifer Ann; Hayes, Catherine

2008-01-01

The purpose of this study was to assess the relationship between baseline caries experience and the restoration replacement rate in children. The 5-year New England Children's Amalgam Trial recruited 534 6- to 10-year-old children with 2 or more carious posterior teeth. The association between decoy and longevity of restorations was assessed. Restorations with no follow-up (N = 391) were excluded from analysis. The average follow-up was 3.0 +/- 1.6 years in 489 children. Restorations with follow-up (N = 3,604) were placed in mouths with a median of 15 dfs/DFS and 8 dft/DFT. The need for replacement increased significantly (P < or = .001) with increasing numbers of dfs/DFS and dft/DFT. After 5 years of follow-up, at least 15% of restorations in a mouth with > or = 14 dfs/DFS needed replacement, compared to 9% for 2 to 5 dfs/DFS. Comparing dft/DFT after 5 years of follow-up, there was a 23% replacement rate for > or = 12 dft/DFT compared to 10% for 2 to 3 dft/DFT. Decoy in the mouth had a greater association with the need for replacement due to new caries compared to replacement due to recurrent caries. Children with more decoy at the time of restoration placement were at higher risk for replacement of restorations.

ERBB3: A potential serum biomarker for early detection and therapeutic target for devil facial tumour 1 (DFT1)

PubMed Central

Kunde, Dale A.; Taylor, Robyn L.; Pyecroft, Stephen B.; Sohal, Sukhwinder Singh; Snow, Elizabeth T.

2017-01-01

Devil Facial Tumour 1 (DFT1) is one of two transmissible neoplasms of Tasmanian devils (Sarcophilus harrisii) predominantly affecting their facial regions. DFT1’s cellular origin is that of Schwann cell lineage where lesions are evident macroscopically late in the disease. Conversely, the pre-clinical timeframe from cellular transmission to appearance of DFT1 remains uncertain demonstrating the importance of an effective pre-clinical biomarker. We show that ERBB3, a marker expressed normally by the developing neural crest and Schwann cells, is immunohistohemically expressed by DFT1, therefore the potential of ERBB3 as a biomarker was explored. Under the hypothesis that serum ERBB3 levels may increase as DFT1 invades local and distant tissues our pilot study determined serum ERBB3 levels in normal Tasmanian devils and Tasmanian devils with DFT1. Compared to the baseline serum ERBB3 levels in unaffected Tasmanian devils, Tasmanian devils with DFT1 showed significant elevation of serum ERBB3 levels. Interestingly Tasmanian devils with cutaneous lymphoma (CL) also showed elevation of serum ERBB3 levels when compared to the baseline serum levels of Tasmanian devils without DFT1. Thus, elevated serum ERBB3 levels in otherwise healthy looking devils could predict possible DFT1 or CL in captive or wild devil populations and would have implications on the management, welfare and survival of Tasmanian devils. ERBB3 is also a therapeutic target and therefore the potential exists to consider modes of administration that may eradicate DFT1 from the wild. PMID:28591206

Surface vacancies concentration of CeO2(1 1 1) using kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Mattiello, S.; Kolling, S.; Heiliger, C.

2016-01-01

Kinetic Monte Carlo simulations (kMC) are useful tools for the investigation of the dynamics of surface properties. Within this method we investigate the oxygen vacancy concentration of \\text{Ce}{{\\text{O}}2}(1 1 1) at ultra high vacuum conditions (UHV). In order to achieve first principles calculations the input for the simulations, i.e. energy barriers for the microscopic processes, we use density functional theory (DFT) results from literature. We investigate the possibility of ad- and desorption of oxygen on ceria as well as the diffusion of oxygen vacancies to and from the subsurface. In particular, we focus on the vacancy surface concentration as well as on the ratio of the number of subsurface vacancies to the number of vacancies at the surface. The comparison of our dynamically obtained results to the experimental findings leads to several issues. In conclusion, we can claim a substantial incompatibility of the experimental results and the dynamical calculation using DFT inputs.

A new look into the quantum chemical and spectroscopic investigations of 5-chloro-1-methyl-4-nitroimidazole.

PubMed

Arjunan, V; Raj, Arushma; Anitha, R; Mohan, S

2014-05-05

Optimised geometrical structural parameters, harmonic vibrational frequencies, natural bonding orbital analysis and frontier molecular orbitals are determined by B3LYP and B3PW91 methods. The exact geometry of 5-chloro-1-methyl-4-nitroimidazole is determined through conformational analysis. The experimentally observed infrared and Raman bands have been assigned and analysed. The (13)C and (1)H NMR chemical shifts of the compound are investigated. The total electron density and molecular electrostatic potentials are determined. The electrostatic potential (electron+nuclei) distribution, molecular shape, size and dipole moments of the molecule have been displayed. The energies of the frontier molecular orbitals and LUMO-HOMO energy gap are measured. The possible electronic transitions of the molecule are studied by TD-DFT method along with the UV-Visible spectrum. The structure-activity relationship of the compound is also investigated by conceptual DFT methods. Copyright © 2014 Elsevier B.V. All rights reserved.

The role of the [CpM(CO)2](-) chromophore in the optical properties of the [Cp2ThMCp(CO)2](+) complexes, where M = Fe, Ru and Os. A theoretical view.

PubMed

Cantero-López, Plinio; Le Bras, Laura; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

2015-12-14

The chemical bond between actinide and the transition metal unsupported by bridging ligands is not well characterized. In this paper we study the electronic properties, bonding nature and optical spectra in a family of [Cp2ThMCp(CO)2](+) complexes where M = Fe, Ru, Os, based on the relativistic two component density functional theory calculations. The Morokuma-Ziegler energy decomposition analysis shows an important ionic contribution in the Th-M interaction with around 25% of covalent character. Clearly, charge transfer occurs on Th-M bond formation, however the orbital term most likely represents a strong charge rearrangement in the fragments due to the interaction. Finally the spin-orbit-ZORA calculation shows the possible NIR emission induced by the [FeCp(CO)2](-) chromophore accomplishing the antenna effect that justifies the sensitization of the actinide complexes.

X2Y2 isomers: tuning structure and relative stability through electronegativity differences (X = H, Li, Na, F, Cl, Br, I; Y = O, S, Se, Te).

PubMed

El-Hamdi, Majid; Poater, Jordi; Bickelhaupt, F Matthias; Solà, Miquel

2013-03-04

We have studied the XYYX and X2YY isomers of the X2Y2 species (X = H, Li, Na, F, Cl, Br, I; Y = O, S, Se, Te) using density functional theory at the ZORA-BP86/QZ4P level. Our computations show that, over the entire range of our model systems, the XYYX isomers are more stable than the X2YY forms except for X = F and Y = S and Te, for which the F2SS and F2TeTe isomers are slightly more stable. Our results also point out that the Y-Y bond length can be tuned quite generally through the X-Y electronegativity difference. The mechanism behind this electronic tuning is the population or depopulation of the π* in the YY fragment.

Solid-state (55)Mn NMR spectroscopy of bis(μ-oxo)dimanganese(IV) [Mn(2)O(2)(salpn)(2)], a model for the oxygen evolving complex in photosystem II.

PubMed

Ellis, Paul D; Sears, Jesse A; Yang, Ping; Dupuis, Michel; Boron, Thaddeus T; Pecoraro, Vincent L; Stich, Troy A; Britt, R David; Lipton, Andrew S

2010-12-01

We have examined the antiferromagneticly coupled bis(μ-oxo)dimanganese(IV) complex [Mn(2)O(2)(salpn)(2)] (1) with (55)Mn solid-state NMR at cryogenic temperatures and first-principle theory. The extracted values of the (55)Mn quadrupole coupling constant, C(Q), and its asymmetry parameter, η(Q), for 1 are 24.7 MHz and 0.43, respectively. Further, there was a large anisotropic contribution to the shielding of each Mn(4+), i.e. a Δσ of 3375 ppm. Utilizing broken symmetry density functional theory, the predicted values of the electric field gradient (EFG) or equivalently the C(Q) and η(Q) at ZORA, PBE QZ4P all electron level of theory are 23.4 MHz and 0.68, respectively, in good agreement with experimental observations.

Quantum Simulations of Solvated Biomolecules Using Hybrid Methods

NASA Astrophysics Data System (ADS)

Hodak, Miroslav

2009-03-01

One of the most important challenges in quantum simulations on biomolecules is efficient and accurate inclusion of the solvent, because the solvent atoms usually outnumber those in the biomolecule of interest. We have developed a hybrid method that allows for explicit quantum-mechanical treatment of the solvent at low computational cost. In this method, Kohn-Sham (KS) density functional theory (DFT) is combined with an orbital-free (OF) DFT. Kohn-Sham (KS) DFT is used to describe the biomolecule and its first solvation shells, while the orbital-free (OF) DFT is employed for the rest of the solvent. The OF part is fully O(N) and capable of handling 10^5 solvent molecules on current parallel supercomputers, while taking only ˜ 10 % of the total time. The compatibility between the KS and OF DFT methods enables seamless integration between the two. In particular, the flow of solvent molecules across the KS/OF interface is allowed and the total energy is conserved. As the first large-scale applications, the hybrid method has been used to investigate the binding of copper ions to proteins involved in prion (PrP) and Parkinson's diseases. Our results for the PrP, which causes mad cow disease when misfolded, resolve a contradiction found in experiments, in which a stronger binding mode is replaced by a weaker one when concentration of copper ions is increased, and show how it can act as a copper buffer. Furthermore, incorporation of copper stabilizes the structure of the full-length PrP, suggesting its protective role in prion diseases. For alpha-synuclein, a Parkinson's disease (PD) protein, we show that Cu binding modifies the protein structurally, making it more susceptible to misfolding -- an initial step in the onset of PD. In collaboration with W. Lu, F. Rose and J. Bernholc.

Local and average structure of Mn- and La-substituted BiFeO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Bo; Selbach, Sverre M., E-mail: selbach@ntnu.no

2017-06-15

The local and average structure of solid solutions of the multiferroic perovskite BiFeO{sub 3} is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO{sub 3}. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions. - Graphical abstract: The experimental and simulated partial pair distribution functions (PDF) for BiFeO{sub 3}, BiFe{sub 0.875}Mn{sub 0.125}O{sub 3}, BiFe{sub 0.75}Mn{sub 0.25}O{sub 3} and Bi{sub 0.9}La{sub 0.1}FeO{sub 3}.« less

Direct Production of Propene from the Thermolysis of Poly(β-hydroxybutyrate) (PHB). An Experimental and DFT Investigation.

PubMed

Clark, Jared M; Pilath, Heidi M; Mittal, Ashutosh; Michener, William E; Robichaud, David J; Johnson, David K

2016-01-28

We demonstrate a synthetic route toward the production of propene directly from poly(β-hydroxybutyrate) (PHB), the most common of a wide range of high-molecular-mass microbial polyhydroxyalkanoates. Propene, a major commercial hydrocarbon, was obtained from the depolymerization of PHB and subsequent decarboxylation of the crotonic acid monomer in good yields (up to 75 mol %). The energetics of PHB depolymerization and the gas-phase decarboxylation of crotonic acid were also studied using density functional theory (DFT). The average activation energy for the cleavage of the R'C(O)O-R linkage is calculated to be 163.9 ± 7.0 kJ mol(-1). Intramolecular, autoacceleration effects regarding the depolymerization of PHB, as suggested in some literature accounts, arising from the formation of crotonyl and carboxyl functional groups in the products could not be confirmed by the results of DFT and microkinetic modeling. DFT results, however, suggest that intermolecular catalysis involving terminal carboxyl groups may accelerate PHB depolymerization. Activation energies for this process were estimated to be about 20 kJ mol(-1) lower than that for the noncatalyzed ester cleavage, 144.3 ± 6.4 kJ mol(-1). DFT calculations predict the decarboxylation of crotonic acid to follow second-order kinetics with an activation energy of 147.5 ± 6.3 kJ mol(-1), consistent with that measured experimentally, 146.9 kJ mol(-1). Microkinetic modeling of the PHB to propene overall reaction predicts decarboxylation of crotonic acid to be the rate-limiting step, consistent with experimental observations. The results also indicate that improvements made to enhance the isomerization of crotonic acid to vinylacetic acid will improve the direct conversion of PHB to propene.

Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT

NASA Astrophysics Data System (ADS)

Bardak, F.; Karaca, C.; Bilgili, S.; Atac, A.; Mavis, T.; Asiri, A. M.; Karabacak, M.; Kose, E.

2016-08-01

Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, 1H and 13C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm- 1 and 3500-50 cm- 1, respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The 13C and 1H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained.

Vibrational investigation on FT-IR and FT-Raman spectra, IR intensity, Raman activity, peak resemblance, ideal estimation, standard deviation of computed frequencies analyses and electronic structure on 3-methyl-1,2-butadiene using HF and DFT (LSDA/B3LYP/B3PW91) calculations.

PubMed

Ramalingam, S; Jayaprakash, A; Mohan, S; Karabacak, M

2011-11-01

FT-IR and FT-Raman (4000-100 cm(-1)) spectral measurements of 3-methyl-1,2-butadiene (3M12B) have been attempted in the present work. Ab-initio HF and DFT (LSDA/B3LYP/B3PW91) calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, IR intensities and Raman activities. Complete vibrational assignments on the observed spectra are made with vibrational frequencies obtained by HF and DFT (LSDA/B3LYP/B3PW91) at 6-31G(d,p) and 6-311G(d,p) basis sets. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The potential energy distribution (PED) corresponding to each of the observed frequencies are calculated which confirms the reliability and precision of the assignment and analysis of the vibrational fundamentals modes. The oscillation of vibrational frequencies of butadiene due to the couple of methyl group is also discussed. A study on the electronic properties such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties of the title compound at different temperatures reveal the correlations between standard heat capacities (C) standard entropies (S), and standard enthalpy changes (H). Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

FT-IR, FT-Raman, UV spectra and DFT calculations on monomeric and dimeric structure of 2-amino-5-bromobenzoic acid.

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-02-01

In this work, the molecular conformation, vibrational and electronic transition analysis of 2-amino-5-bromobenzoic acid (2A5BrBA) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000 cm(-1) and 50-4000 cm(-1), respectively. There are four conformers, C1, C2, C3 and C4 for this molecule. The geometrical parameters, energies and wavenumbers have been obtained for all four conformers. The computational results diagnose the most stable conformer of 2A5BrBA as the C1 form. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. The UV spectra of investigated compound were recorded in the region of 200-400 nm for ethanol and water solutions. The electronic properties were evaluated with help of time-dependent DFT (TD-DFT) theoretically and results were compared with experimental observations. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. The observed and the calculated geometric parameters, vibrational wavenumbers and electronic transitions were compared with observed data and found to be in good agreement. Copyright © 2011 Elsevier B.V. All rights reserved.

Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Zainuri, D. Alwani; Arshad, Suhana; Khalib, N. Che; Razak, I. Abdul; Pillai, Renjith Raveendran; Sulaiman, S. Fariza; Hashim, N. Shafiqah; Ooi, K. Leong; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-01-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

Investigation of different physical aspects such as structural, mechanical, optical properties and Debye temperature of Fe2ScM (M=P and As) semiconductors: A DFT-based first principles study

NASA Astrophysics Data System (ADS)

Ali, Md. Lokman; Rahaman, Md. Zahidur

2018-04-01

By using first principles calculation dependent on the density functional theory (DFT), we have investigated the mechanical, structural properties and the Debye temperature of Fe2ScM (M=P and As) compounds under various pressures up to 60 GPa. The optical properties have been investigated under zero pressure. Our calculated optimized structural parameters of both the materials are in good agreement with other theoretical predictions. The calculated elastic constants show that Fe2ScM (M=P and As) compounds are mechanically stable under external pressure below 60 GPa. From the elastic constants, the shear modulus G, the bulk modulus B, Young’s modulus E, anisotropy factor A and Poisson’s ratio ν are calculated by using the Voigt-Reuss-Hill approximation. The Debye temperature and average sound velocities are also investigated from the obtained elastic constants. The detailed analysis of all optical functions reveals that both compounds are good dielectric material.

Quantum Mechanical Simulations of Complex Nanostructures for Photovoltaic Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Zhigang

A quantitative understanding of the electronic excitations in nanostructures, especially complex nanostructures, is crucial for making new-generation photovoltaic (PV) cells based on nanotechnology, which have high efficiency and low cost. Yet current quantum mechanical simulation methods are either computationally too expensive or not accurate and reliable enough, hindering the rational design of the nanoscale PV cells. The PI seeks to develop new methodologies to overcome the challenges in this very difficult and long-lasting problem, pushing the field forward so that electronic excitations can be accurately predicted for systems involving thousands of atoms. The primary objective of this project is tomore » develop new approaches for electronic excitation calculations that are more accurate than traditional density functional theory (DFT) and are applicable to systems larger than what current beyond-DFT methods can treat. In this proposal, the PI will first address the excited-state problem within the DFT framework to obtain quasiparticle energies from both Kohn-Sham (KS) eigenvalues and orbitals; and the electron-hole binding energy will be computed based on screened Coulomb interaction of corresponding DFT orbitals. The accuracy of these approaches will be examined against many-body methods of GW/BSE and quantum Monte Carlo (QMC). The PI will also work on improving the accuracy and efficiency of the GW/BSE and QMC methods in electronic excitation computations by using better KS orbitals obtained from orbital-dependent DFT as inputs. Then an extended QMC database of ground- and excited-state properties will be developed, and this will be spot checked and supplemented with data from GW/BSE calculations. The investigation will subsequently focus on the development of an improved exchange-correlation (XC) density functional beyond the current generalized gradient approximation (GGA) level of parameterization, with parameters fitted to the QMC database. This will allow the ground-state properties of focus systems to be more precisely predicted using DFT. These new developments will then be applied to investigate a chosen set of complex nanostructures that have great potential for opening new routes in designing materials with improved transport, electronic, and optical properties for PV and other optoelectronic usages: (1) Hybrid interfaces between materials with distinct electronic and optical properties, such as organic molecules (conjugated polymers, e.g. P3HT) and inorganic semiconducting materials (Si and ZnO). Complicated interface structures, including interface bonding configurations, compositional and geometrical blending patterns, interfacial defects, and various sizes and shapes of inorganic nanomaterials, will be considered for the purpose of understanding the working mechanisms of present organic/nano PV systems and designing optimum interface structures for fast charge separation and injection. (2) Complex-structured semiconducting nanomaterials that could induce charge separation without pn- or hetero-junctions. The new methodology will allow the PI to investigate the performance of realistic semiconducting nanomaterials of internal (impurities, defects, etc.) and external (uneven surface, mechanical twisting and bending, surface chemistry, etc.) complexities on optical absorption and charge transport against charge trapping and recombination. Of particular interest is whether such structural complexity in a single material could even be beneficial for PV usage, for example, charge separation through morphology control. Successful completion of the proposed DFT methodology would have a far-reaching impact on our ability to study and exploit the nature of electronic excitations in complex materials, advancing the design of next-generation electronic and optoelectronic devices in all facets of renewable energy conversion and storage, including photovoltaics, thermoelectricity, photochemistry, etc.« less

Optical characterization of shock-induced chemistry in the explosive nitromethane using DFT and time-dependent DFT

NASA Astrophysics Data System (ADS)

Pellouchoud, Lenson; Reed, Evan

2014-03-01

With continual improvements in ultrafast optical spectroscopy and new multi-scale methods for simulating chemistry for hundreds of picoseconds, the opportunity is beginning to exist to connect experiments with simulations on the same timescale. We compute the optical properties of the liquid phase energetic material nitromethane (CH3NO2) for the first 100 picoseconds behind the front of a simulated shock at 6.5km/s, close to the experimentally observed detonation shock speed. We utilize molecular dynamics trajectories computed using the multi-scale shock technique (MSST) for time-resolved optical spectrum calculations based on both linear response time-dependent DFT (TDDFT) and the Kubo-Greenwood (KG) formula within Kohn-Sham DFT. We find that TDDFT predicts optical conductivities 25-35% lower than KG-based values and provides better agreement with the experimentally measured index of refraction of unreacted nitromethane. We investigate the influence of electronic temperature on the KG spectra and find no significant effect at optical wavelengths. With all methods, the spectra evolve non-monotonically in time as shock-induced chemistry takes place. We attribute the time-resolved absorption at optical wavelengths to time-dependent populations of molecular decomposition products, including NO, CNO, CNOH, H2O, and larger molecules. Supported by NASA Space Technology Research Fellowship (NSTRF) #NNX12AM48H.

Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

2018-03-01

The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

Structures, mechanical properties, equations of state, and electronic properties of β-HMX under hydrostatic pressures: a DFT-D2 study.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; De, Suvranu

2014-10-07

We report the hydrostatic compression studies of the β-polymorph of a cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using DFT-D2, a first-principles calculation based on density functional theory (DFT) with van der Waals (vdW) corrections. The molecular structure, mechanical properties, electronic properties, and equations of state of β-HMX are investigated. For the first time, we predict the elastic constants of β-HMX using DFT-D2 studies. The equations of state under hydrostatic compression are studied for pressures up to 100 GPa. We found that the N-N bonds along the minor axis are responsible for the sensitivity of β-HMX. The analysis of the charge distribution shows that the electronic charge is transferred from hydrogen atoms to nitro groups with the amount of 0.131 and 0.064e for the nitro groups along the minor axis and major axis, respectively, when pressure changes from 0 GPa to 100 GPa. The electronic energy band gap changes from direct at a pressure of 0 GPa to indirect at a pressure of 50 GPa and higher. The band gap decreases with respect to an increase in pressure, implying that the impact sensitivity increases with compression. Our study suggests that the van der Waals interactions are critically important in modeling the mechanical properties of this molecular crystal.

DFT and TD-DFT insights, photolysis and photocatalysis investigation of three dyes with similar structure under UV irradiation with and without TiO2 as a catalyst: Effect of adsorption, pH and light intensity.

PubMed

Bendjabeur, Seyfeddine; Zouaghi, Razika; Zouchoune, Bachir; Sehili, Tahar

2018-02-05

TiO 2 -mediated photocatalytic degradation of three triphenylmethane dyes (basic fuchsin, acid fuchsin and Gentian violet), was investigated in aqueous suspensions in the presence and the absence of titanium dioxide P25 Degussa as photocatalyst. The photodegradation process was investigated using UV-A (365nm) and UV-C (254nm) light alone and UV-A in the presence of TiO 2 ·The effects of various operational parameters were investigated such as: the effect of adsorption in the dark, the influence of pH, the influence of irradiation wavelength and the effect of light intensity. The study of the effect of various parameters reveals that the photolysis of dyes increases with the increase of light intensity, the degradation rate under UV-C (254nm) was found better than under UV-A 365nm. The photocatalytic degradation was found to follow the same order of adsorption. The decolorization and the degradation kinetics were found to follow the pseudo-first-order kinetics. The mineralization of dye was found to follow the same order of disappearance as the photocatalytic degradation and depended directly to its functional groups and its number of carbons. Additionally, density functional theory (DFT) was applied for calculations of both electronic structure and spectroscopic properties of the studied compounds, where the obtained results of the three dyes show that the theoretical electronic spectra and the experimental UV-visible ones are similar in shapes, positions and intensities. Copyright © 2017. Published by Elsevier B.V.

Applicability of DFT model in reactive distillation

NASA Astrophysics Data System (ADS)

Staszak, Maciej

2017-11-01

The density functional theory (DFT) applicability to reactive distillation is discussed. Brief modeling techniques description of distillation and rectification with chemical reaction is provided as a background for quantum method usage description. The equilibrium and nonequilibrium distillation models are described for that purpose. The DFT quantum theory is concisely described. The usage of DFT in the modeling of reactive distillation is described in two parts. One of the fundamental and very important component of distillation modeling is vapor-liquid equilibrium description for which the DFT quantum approach can be used. The representative DFT models, namely COSMO-RS (Conductor like Screening Model for Real Solvents), COSMOSPACE (COSMO Surface Pair Activity Coefficient) and COSMO-SAC (SAC - segment activity coefficient) approaches are described. The second part treats the way in which the chemical reaction is described by means of quantum DFT method. The intrinsic reaction coordinate (IRC) method is described which is used to find minimum energy path of substrates to products transition. The DFT is one of the methods which can be used for that purpose. The literature data examples are provided which proves that IRC method is applicable for chemical reaction kinetics description.

Role of exact exchange in thermally-assisted-occupation density functional theory: A proposal of new hybrid schemes.

PubMed

Chai, Jeng-Da

2017-01-28

We propose hybrid schemes incorporating exact exchange into thermally assisted-occupation-density functional theory (TAO-DFT) [J.-D. Chai, J. Chem. Phys. 136, 154104 (2012)] for an improved description of nonlocal exchange effects. With a few simple modifications, global and range-separated hybrid functionals in Kohn-Sham density functional theory (KS-DFT) can be combined seamlessly with TAO-DFT. In comparison with global hybrid functionals in KS-DFT, the resulting global hybrid functionals in TAO-DFT yield promising performance for systems with strong static correlation effects (e.g., the dissociation of H 2 and N 2 , twisted ethylene, and electronic properties of linear acenes), while maintaining similar performance for systems without strong static correlation effects. Besides, a reasonably accurate description of noncovalent interactions can be efficiently achieved through the inclusion of dispersion corrections in hybrid TAO-DFT. Relative to semilocal density functionals in TAO-DFT, global hybrid functionals in TAO-DFT are generally superior in performance for a wide range of applications, such as thermochemistry, kinetics, reaction energies, and optimized geometries.

Search For a Consistent Mean-Field Treatment of Magnetic Properties of Yittrium-Cobalt-5 Under Moderate Hydrostatic Stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benedict, Lorin X.; Aberg, Daniel; Soderlind, Per

2015-10-26

We explore the use of particular variants of DFT + U and DFT + orbital polarization (OP) to calculate the electronic structure and magnetic properties of YCo5 under hydrostatic pressures up to 600 kbar. While the speci c DFT + U (with U= 0.75 eV) and DFT + OP schemes we employ produce magneto-crystalline anisotropy energies for YCo5 in good agreement with experiments performed in ambient conditions, our DFT + U results are shown to greatly overestimate the pressure at which a high-spin to low-spin (HS-LS) transition is known to occur. In contrast, our DFT + OP results predict themore » HS-LS transition to occur at the same stress as DFT, and in better agreement with experiment. This sensitivity suggests that care should be taken when attempting to model magnetic properties with self-interaction and/or correlation corrections to DFT for this and related materials, and highlights the usefulness of moderate pressure as an additional parameter to vary when discriminating between candidate theoretical schemes.« less

Mono- and tri-ester hydrogenolysis using tandem catalysis. Scope and mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lohr, Tracy L.; Li, Zhi; Assary, Rajeev S.

The scope and mechanism of thermodynamically leveraged ester RC(O)O–R' bond hydrogenolysis by tandem metal triflate + supported Pd catalysts are investigated both experimentally and theoretically by DFT and energy span analysis.

Mono- and tri-ester hydrogenolysis using tandem catalysis. Scope and mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lohr, Tracy L.; Li, Zhi; Assary, Rajeev S.

2016-01-01

The scope and mechanism of thermodynamically leveraged ester RC(O)O–R' bond hydrogenolysis by tandem metal triflate + supported Pd catalysts are investigated both experimentally and theoretically by DFT and energy span analysis.

Density Functional Theory (DFT) Study of Molecularly Imprinted Polymer (MIP) Methacrylic Acid (MAA) with D-Glucose

NASA Astrophysics Data System (ADS)

Wungu, T. D. K.; Marsha, S. E.; Widayani; Suprijadi

2017-07-01

In order to find an alternative biosensor material which enables to detect the glucose level, therefore in this study, the interaction between Methacrylic Acid (MAA) based Molecularly Imprinted Polymer (MIP) with D-Glucose is investigated using the Density Functional Theory (DFT). The aim of this study is to determine whether a molecule of the MAA can be functioned as a bio-sensing of glucose. In this calculation, the Gaussian 09 with B3LYP and 631+G(d) basis sets is used to calculate all electronic properties. It is found that the interaction between a molecule of MAA and a molecule of D-Glucose was observed through the shortened distance between the two molecules. The binding energy of MAA/D-glucose and the Mulliken population analysis are investigated for checking possible interaction. From analysis, the MAA based MIP can be used as a bio-sensing material.

Structural, dynamic and photophysical properties of a fluorescent dye incorporated in an amorphous hydrophobic polymer bundle.

PubMed

De Mitri, N; Prampolini, G; Monti, S; Barone, V

2014-08-21

The properties of a low molecular weight organic dye, namely 4-naphthyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine, covalently bound to an apolar polyolefin were investigated by means of a multi-level approach, combining classical molecular dynamics simulations, based on purposely parameterized force fields, and quantum mechanical calculations based on density functional theory (DFT) and its time-dependent extension (TD-DFT). The structure and dynamics of the dye in its embedding medium were analyzed and discussed taking the entangling effect of the surrounding polymer into account, and also by comparing the results to those obtained for a different environment, i.e. toluene solution. Finally, the influence was investigated of long lived cages found in the polymeric embedding on photophysical properties, in terms of the slow and fast dye's internal dynamics, by comparing computed IR and UV spectra with their experimental counterparts.

Assessing the role of Hartree-Fock exchange, correlation energy and long range corrections in evaluating ionization potential, and electron affinity in density functional theory.

PubMed

Vikramaditya, Talapunur; Lin, Shiang-Tai

2017-06-05

Accurate determination of ionization potentials (IPs), electron affinities (EAs), fundamental gaps (FGs), and HOMO, LUMO energy levels of organic molecules play an important role in modeling and predicting the efficiencies of organic photovoltaics, OLEDs etc. In this work, we investigate the effects of Hartree Fock (HF) Exchange, correlation energy, and long range corrections in predicting IP and EA in Hybrid Functionals. We observe increase in percentage of HF exchange results in increase of IPs and decrease in EAs. Contrary to the general expectations inclusion of both HF exchange and correlation energy (from the second order perturbation theory MP2) leads to poor prediction. Range separated Hybrid Functionals are found to be more reliable among various DFT Functionals investigated. DFT Functionals predict accurate IPs whereas post HF methods predict accurate EAs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

DFT investigation of electronic structures and magnetic properties of halides family MeHal3 (Me=Ti, Mo,Zr,Nb, Ru, Hal=Cl,Br,I) one dimensional structures

NASA Astrophysics Data System (ADS)

Kuzubov, A. A.; Kovaleva, E. A.; Popova, M. I.; Kholtobina, A. S.; Mikhaleva, N. S.; Visotin, M. A.; Fedorov, A. S.

2017-10-01

Using DFT GGA calculations, electronic structure and magnetic properties of wide family of transition metal trihalides (TMHal3) (Zr, Ti and Nb iodides, Mo, Ru, Ti and Zr bromides and Ti or Zr chlorides) are investigated. These structures consist of transition metal atoms chains surrounded by halides atoms. Chains are connected to each other by weak interactions. All TMHal3 compounds were found to be conductive along chain axis except of MoBr3 which is indirect gap semiconductor. It was shown that NbI3 and MoBr3 have large magnetic moments on metal atoms (1.17 and 1.81 μB, respectively) but other TMHal3 materials have small or zero magnetic moments. For all structures ferromagnetic and anti-ferromagnetic phases have almost the same energies. The causes of these properties are debated.

High-resolution molybdenum K-edge X-ray absorption spectroscopy analyzed with time-dependent density functional theory.

PubMed

Lima, Frederico A; Bjornsson, Ragnar; Weyhermüller, Thomas; Chandrasekaran, Perumalreddy; Glatzel, Pieter; Neese, Frank; DeBeer, Serena

2013-12-28

X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems.

Calculation of exchange coupling constants in triply-bridged dinuclear Cu(II) compounds based on spin-flip constricted variational density functional theory.

PubMed

Seidu, Issaka; Zhekova, Hristina R; Seth, Michael; Ziegler, Tom

2012-03-08

The performance of the second-order spin-flip constricted variational density functional theory (SF-CV(2)-DFT) for the calculation of the exchange coupling constant (J) is assessed by application to a series of triply bridged Cu(II) dinuclear complexes. A comparison of the J values based on SF-CV(2)-DFT with those obtained by the broken symmetry (BS) DFT method and experiment is provided. It is demonstrated that our methodology constitutes a viable alternative to the BS-DFT method. The strong dependence of the calculated exchange coupling constants on the applied functionals is demonstrated. Both SF-CV(2)-DFT and BS-DFT affords the best agreement with experiment for hybrid functionals.

Experimental and theoretical investigation of [Al(PCr)(H2O)] complex in aqueous solution

NASA Astrophysics Data System (ADS)

Tenório, Thaís; Lopes, Damiana C. N.; Silva, Andréa M.; Ramos, Joanna Maria; Buarque, Camilla D.

2014-01-01

Phosphocreatine is a phosphorylated creatine molecule synthesized in the liver and transported to muscle cells where it is used for the temporary storage of energy. In Alzheimer's disease, the capture of glucose by cells is impaired, which negatively affects the Krebs cycle, leading to problems with the generation of phosphocreatine. Furthermore, the creatine-phosphocreatine system, regulated by creatine kinase, is affected in the brains of Alzheimer's disease patients. Aluminum ions are associated with Alzheimer's disease. Al(III) decreases cell viability and increases the fluidity of the plasma membrane, profoundly altering cell morphology. In this study, one of the complexes formed by Al(III) and phosphocreatine in aqueous solution was investigated by potentiometry, 31P and 27Al NMR, Raman spectroscopy and density functional theory (DFT) calculations. The log KAlPCr value was 11.37 ± 0.03. Phosphocreatine should act as a tridentate ligand in this complex. The 27Al NMR peak at 48.92 ppm indicated a tetrahedral molecule. The fourth position in the arrangement was occupied by a coordinated water molecule. Raman spectroscopy, 31P NMR and DFT calculations (DFT:B3LYP/6-311++G**) indicated that the donor atoms are oxygen in the phosphate group, the nitrogen of the guanidine group and the oxygen of the carboxylate group. Mulliken charges, NBO charges, frontier molecular orbitals, electrostatic potential contour surfaces and mapped electrostatic potential were also examined.

Synthesis, X-ray diffraction method, spectroscopic characterization (FT-IR, 1H and 13C NMR), antimicrobial activity, Hirshfeld surface analysis and DFT computations of novel sulfonamide derivatives

NASA Astrophysics Data System (ADS)

Demircioğlu, Zeynep; Özdemir, Fethi Ahmet; Dayan, Osman; Şerbetçi, Zafer; Özdemir, Namık

2018-06-01

Synthesized compounds of N-(2-aminophenyl)benzenesulfonamide 1 and (Z)-N-(2-((2-nitrobenzylidene)amino)phenyl)benzenesulfonamide 2 were characterized by antimicrobial activity, FT-IR, 1H and 13C NMR. Two new Schiff base ligands containing aromatic sulfonamide fragment of (Z)-N-(2-((3-nitrobenzylidene)amino)phenyl)benzenesulfonamide 3 and (Z)-N-(2-((4-nitrobenzylidene)amino)phenyl)benzenesulfonamide 4 were synthesized and investigated by spectroscopic techniques including 1H and 13C NMR, FT-IR, single crystal X-ray diffraction, Hirshfeld surface, theoretical method analyses and by antimicrobial activity. The molecular geometry obtained from the X-ray structure determination was optimized Density Functional Theory (DFT/B3LYP) method with the 6-311++G(d,p) basis set in ground state. From the optimized geometry of the molecules of 3 and 4, the geometric parameters, vibrational wavenumbers and chemical shifts were computed. The optimized geometry results, which were well represented the X-ray data, were shown that the chosen of DFT/B3LYP 6-311G++(d,p) was a successful choice. After a successful optimization, frontier molecular orbitals, chemical activity, non-linear optical properties (NLO), molecular electrostatic mep (MEP), Mulliken population method, natural population analysis (NPA) and natural bond orbital analysis (NBO), which cannot be obtained experimentally, were calculated and investigated.

Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Venkatesan, Perumal; Rajakannan, Venkatachalam; Venkataramanan, Natarajan S.; Ilangovan, Andivelu; Sundius, Tom; Thamotharan, Subbiah

2016-09-01

The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular Nsbnd H⋯O and Osbnd H⋯O and intermolecular Nsbnd H⋯O and Csbnd H⋯O interactions along with carbonyl⋯carbonyl and Csbnd H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol-1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular Csbnd H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV-Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.

Experimental (FT-IR, NMR and UV) and theoretical (M06-2X and DFT) investigation, and frequency estimation analyses on (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile.

PubMed

Sert, Yusuf; Balakit, Asim A; Öztürk, Nuri; Ucun, Fatih; El-Hiti, Gamal A

2014-10-15

The spectroscopic properties of (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile have been investigated by FT-IR, UV, (1)H and (13)C NMR techniques. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been carried out by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies were in good agreement with the corresponding experimental data, and with the results in the literature. (1)H and (13)C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength wavelengths were performed by B3LYP methods. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted. Copyright © 2014 Elsevier B.V. All rights reserved.

Aqueous phase hydration and hydrate acidity of perfluoroalkyl and n:2 fluorotelomer aldehydes.

PubMed

Rayne, Sierra; Forest, Kaya

2016-01-01

The SPARC software program and comparative density functional theory (DFT) calculations were used to investigate the aqueous phase hydration equilibrium constants (Khyd) of perfluoroalkyl aldehydes (PFAlds) and n:2 fluorotelomer aldehydes (FTAlds). Both classes are degradation products of known industrial compounds and environmental contaminants such as fluorotelomer alcohols, iodides, acrylates, phosphate esters, and other derivatives, as well as hydrofluorocarbons and hydrochlorofluorocarbons. Prior studies have generally failed to consider the hydration, and subsequent potential hydrate acidity, of these compounds, resulting in incomplete and erroneous predictions as to their environmental behavior. In the current work, DFT calculations suggest that all PFAlds will be dominantly present as the hydrated form in aqueous solution. Both SPARC and DFT calculations suggest that FTAlds will not likely be substantially hydrated in aquatic systems or in vivo. PFAld hydrates are expected to have pKa values in the range of phenols (ca. 9 to 10), whereas n:2 FTAld hydrates are expected to have pKa values ca. 2 to 3 units higher (ca. 12 to 13). In order to avoid spurious modeling predictions and a fundamental misunderstanding of their fate, the molecular and/or dissociated hydrate forms of PFAlds and FTAlds need to be explicitly considered in environmental, toxicological, and waste treatment investigations. The results of the current study will facilitate a more complete examination of the environmental fate of PFAlds and FTAlds.

Molecular interactions of alcohols with zeolite BEA and MOR frameworks.

PubMed

Stückenschneider, Kai; Merz, Juliane; Schembecker, Gerhard

2013-12-01

Zeolites can adsorb small organic molecules such as alcohols from a fermentation broth. Also in the zeolite-catalyzed conversion of alcohols to biofuels, biochemicals, or gasoline, adsorption is the first step. Several studies have investigated the adsorption of alcohols in different zeolites experimentally, but computational investigations in this field have mostly been restricted to zeolite MFI. In this study, the adsorption of C1-C4 alcohols in BEA and MOR was investigated using density functional theory (DFT). Calculated adsorption geometries and the corresponding energies of the designed cluster models were comparable to periodic calculations, and the adsorption energies were in the same range as the corresponding computational and experimental values reported in the literature for zeolite MFI. Thus, BEA and MOR may be good adsorption materials for alcohols in the field of downstream processing and catalysis. Aside from the DFT calculations, adsorption isotherms were determined experimentally in this study from aqueous solutions. For BEA, the adsorption of significant amounts of alcohol from aqueous solution was observed experimentally. In contrast, MOR was loaded with only a very small amount of alcohol. Although differences were found between the affinities obtained from gas-phase DFT calculations and those observed experimentally in aqueous solution, the computational data presented here represent molecular level information on the geometries and energies of C1-C4 alcohols adsorbed in zeolites BEA and MOR. This knowledge should prove very useful in the design of zeolite materials intended for use in adsorption and catalytic processes, as it allows adsorption behavior to be predicted via judiciously designed computational models.

A second transmissible cancer in Tasmanian devils

PubMed Central

Pye, Ruth J.; Pemberton, David; Tovar, Cesar; Tubio, Jose M. C.; Dun, Karen A.; Fox, Samantha; Darby, Jocelyn; Hayes, Dane; Knowles, Graeme W.; Kreiss, Alexandre; Siddle, Hannah V. T.; Swift, Kate; Lyons, A. Bruce; Murchison, Elizabeth P.; Woods, Gregory M.

2016-01-01

Clonally transmissible cancers are somatic cell lineages that are spread between individuals via the transfer of living cancer cells. There are only three known naturally occurring transmissible cancers, and these affect dogs, soft-shell clams, and Tasmanian devils, respectively. The Tasmanian devil transmissible facial cancer was first observed in 1996, and is threatening its host species with extinction. Until now, this disease has been consistently associated with a single aneuploid cancer cell lineage that we refer to as DFT1. Here we describe a second transmissible cancer, DFT2, in five devils located in southern Tasmania in 2014 and 2015. DFT2 causes facial tumors that are grossly indistinguishable but histologically distinct from those caused by DFT1. DFT2 bears no detectable cytogenetic similarity to DFT1 and carries a Y chromosome, which contrasts with the female origin of DFT1. DFT2 shows different alleles to both its hosts and DFT1 at microsatellite, structural variant, and major histocompatibility complex (MHC) loci, confirming that it is a second cancer that can be transmitted between devils as an allogeneic, MHC-discordant graft. These findings indicate that Tasmanian devils have spawned at least two distinct transmissible cancer lineages and suggest that transmissible cancers may arise more frequently in nature than previously considered. The discovery of DFT2 presents important challenges for the conservation of Tasmanian devils and raises the possibility that this species is particularly prone to the emergence of transmissible cancers. More generally, our findings highlight the potential for cancer cells to depart from their hosts and become dangerous transmissible pathogens. PMID:26711993

A second transmissible cancer in Tasmanian devils.

PubMed

Pye, Ruth J; Pemberton, David; Tovar, Cesar; Tubio, Jose M C; Dun, Karen A; Fox, Samantha; Darby, Jocelyn; Hayes, Dane; Knowles, Graeme W; Kreiss, Alexandre; Siddle, Hannah V T; Swift, Kate; Lyons, A Bruce; Murchison, Elizabeth P; Woods, Gregory M

2016-01-12

Clonally transmissible cancers are somatic cell lineages that are spread between individuals via the transfer of living cancer cells. There are only three known naturally occurring transmissible cancers, and these affect dogs, soft-shell clams, and Tasmanian devils, respectively. The Tasmanian devil transmissible facial cancer was first observed in 1996, and is threatening its host species with extinction. Until now, this disease has been consistently associated with a single aneuploid cancer cell lineage that we refer to as DFT1. Here we describe a second transmissible cancer, DFT2, in five devils located in southern Tasmania in 2014 and 2015. DFT2 causes facial tumors that are grossly indistinguishable but histologically distinct from those caused by DFT1. DFT2 bears no detectable cytogenetic similarity to DFT1 and carries a Y chromosome, which contrasts with the female origin of DFT1. DFT2 shows different alleles to both its hosts and DFT1 at microsatellite, structural variant, and major histocompatibility complex (MHC) loci, confirming that it is a second cancer that can be transmitted between devils as an allogeneic, MHC-discordant graft. These findings indicate that Tasmanian devils have spawned at least two distinct transmissible cancer lineages and suggest that transmissible cancers may arise more frequently in nature than previously considered. The discovery of DFT2 presents important challenges for the conservation of Tasmanian devils and raises the possibility that this species is particularly prone to the emergence of transmissible cancers. More generally, our findings highlight the potential for cancer cells to depart from their hosts and become dangerous transmissible pathogens.

Acylation and deacylation mechanism of Helicobacter pylori AmiF formamidase: A computational DFT study

NASA Astrophysics Data System (ADS)

He, Rongxing; Yang, Qinlei; Li, Ming

2014-04-01

The acylation and deacylation mechanisms of Helicobacter pylori AmiF formamidase were investigated using DFT method. In the constructed active site, residues Glu60, Glu141 and His167 were taken into account besides Lys133 and Cys166. Calculations provided insight on the details of mechanism and explained crucial roles played by Glu60, Glu141 and His167. For acetylation, we proposed a new stepwise mechanism in which the thiol group first attacks the carbon atom of formamide and produces tetrahedral intermediate. In deacylation, Glu60 activates a water molecule to perform nucleophilic attack and then forms an intermediate, which is different from the usually suggested mechanism.

Absorption and emission spectroscopic characteristics of dipterex and its molecularly imprinted recognition: A TD-DFT investigation

NASA Astrophysics Data System (ADS)

Cheng, Xueli; Li, Liqing; Zhao, Yanyun; Wang, Chang'an

2016-05-01

By using G09 program package, the absorption and fluorescence/phosphorescence spectra of dipterex were explored, and its spectroscopic characters were altered by methacrylic acid (MAA) as the imprinted molecule. The TD-DFT results revealed that: (1) All absorption and emission excitations of dipterex are assigned to the nσ∗ transition; (2) without MAA as imprinted molecule, one of the dipterex Csbnd Cl bonds is extended significantly and dipterex is almost destroyed in transition states; (3) dipterex is connected to methacrylic acid via two hydrogen bonds; (4) for the dipterex-MAA complex, the electronic excitation (ππ∗ excitation) in absorption spectra is dominated by the configuration HOMO → LUMO.

Electronic transport properties of nano-scale Si films: an ab initio study

NASA Astrophysics Data System (ADS)

Maassen, Jesse; Ke, Youqi; Zahid, Ferdows; Guo, Hong

2010-03-01

Using a recently developed first principles transport package, we study the electronic transport properties of Si films contacted to heavily doped n-type Si leads. The quantum transport analysis is carried out using density functional theory (DFT) combined with nonequilibrium Green's functions (NEGF). This particular combination of NEGF-DFT allows the investigation of Si films with thicknesses in the range of a few nanometers and lengths up to tens of nanometers. We calculate the conductance, the momentum resolved transmission, the potential profile and the screening length as a function of length, thickness, orientation and surface structure. Moreover, we compare the properties of Si films with and without a top surface passivation by hydrogen.

A DFT investigation on interactions between asymmetric derivatives of cisplatin and nucleobase guanine

NASA Astrophysics Data System (ADS)

Tai, Truong Ba; Nhat, Pham Vu

2017-07-01

The interactions of hydrolysis products of cisplatin and its asymmetric derivatives cis- and trans-[PtCl2(iPram)(Mepz)] with guanine were studied using DFT methods. These interactions are dominated by electrostatic effects, namely hydrogen bond contributions and there exists a charge flow from H-atoms of ligands to the O-atoms of guanine. The replacement of NH3 moieties by larger functional groups accompanies with a moderate reaction between PtII and guanine molecule, diminishing the cytotoxicity of the drug. The asymmetric and symmetric NH2 stretching modes of complexes having strong hydrogen bond interactions are red shifted importantly as compared to complexes without presence of hydrogen bond interactions.

Thermal properties of black phosphorene and doped phosphorene (C, N & O): A DFT study

NASA Astrophysics Data System (ADS)

Devi, Anjna; Singh, Amarjeet

2018-04-01

In this work, we present the results from a DFT based computational study of pristine phosphorene and doped (C, N & O) phosphorene. We systematically investigated the lattice thermal properties of black phosphorene and the effect of doping on its thermal properties. We first determined the vibrational properties of pristine and doped phosphorene and from these results we calculated their thermal properties. We doped the phosphorene with C, N and O and observed that the structural stability of doped phosphorene decreases, while the thermal stability is increased as compared to pristine phosphorene. The presence of finite temperature effects in the doped system can contribute to acceleration of progress in future nano-scale technology.

Probing the adsorption mechanism in thiamazole bound to the silver surface with Surface-enhanced Raman Scattering and DFT

NASA Astrophysics Data System (ADS)

Biswas, Nandita; Thomas, Susy; Sarkar, Anjana; Mukherjee, Tulsi; Kapoor, Sudhir

2009-09-01

Surface-enhanced Raman scattering (SERS) of thiamazole have been investigated in aqueous solution. Thiamazole is an important anti-thyroid drug that is used in the treatment of hyperthyroidism (over activity of the thyroid gland). Due to its medicinal importance, the surface adsorption properties of thiamazole have been studied. The experimental Raman and SERS data are supported with DFT calculations using B3LYP functional with LANL2DZ basis set. From the SERS spectra as well as theoretical calculations, it has been inferred that thiamazole is chemisorbed to the silver surface directly through the sulphur atom and the ring N atom, with a tilted orientation.

The syntheses, molecular structure analyses and DFT studies on new benzil monohydrazone based Schiff bases

NASA Astrophysics Data System (ADS)

Elmacı, Gökhan; Duyar, Halil; Aydıner, Burcu; Seferoğlu, Nurgül; Naziri, Mir Abolfazl; Şahin, Ertan; Seferoğlu, Zeynel

2018-06-01

Benzil monohydrazone based Schiff bases were synthesized and characterized by 1H NMR, 13C NMR, HRMS as well as by single crystal X-ray diffraction. The geometries of the compounds was optimized by the DFT method and the results were compared with the X-ray diffraction data. The HOMO and LUMO energy gap and also related parameters (electronic chemical potential (μ) and global hardness (η), global electrophilicity index (ω) and softness (s)) were obtained from ground state calculations. In addition, the thermal properties of the compounds were investigated by DTA-TGA. The results showed that the compounds have good thermal properties for practical applications as optic dye.

Theoretical study of zeatin - A plant hormone and potential drug for neural diseases - On the basis of DFT, MP2 and target docking

NASA Astrophysics Data System (ADS)

Liu, Xueping; Bereźniak, Tomasz; Panek, Jarosław Jan; Jezierska-Mazzarello, Aneta

2013-02-01

Zeatin, a cytokinin of the adenine family, originally isolated from Zea mays L., exhibits also bioeffects towards human cells: it is a potent acetylcholinesterase inhibitor and can potentially inhibit amyloid β-protein formation. The role of zeatin in neural disease treatment is yet to be established. This computational study describes a hierarchy of interactions between zeatin and a receptor, a protein from the nodulin family. DFT in hybrid and dispersion-corrected form as well as MP2 approaches were used to derive interaction energies. Docking procedure was employed to investigate the role of selected interaction for anchoring the ligand.

Experimental approach to the anion problem in DFT calculation of the partial charge transfer during adsorption at electrochemical interfaces

NASA Astrophysics Data System (ADS)

Marichev, V. A.

2005-08-01

In DFT calculation of the charge transfer (Δ N), anions pose a special problem since their electron affinities are unknown. There is no method for calculating reasonable values of the absolute electronegativity ( χA) and chemical hardness ( ηA) for ions from data of species themselves. We propose a new approach to the experimental measurement of χA at the condition: Δ N = 0 at which η values may be neglected and χA = χMe. Electrochemical parameters corresponding to this condition may be obtained by the contact electric resistance method during in situ investigation of anion adsorption in the particular system anion-metal.

SbCl3-catalyzed one-pot synthesis of 4,4′-diaminotriarylmethanes under solvent-free conditions: Synthesis, characterization, and DFT studies

PubMed Central

2011-01-01

Summary A simple, efficient, and mild procedure for a solvent-free one-step synthesis of various 4,4′-diaminotriarylmethane derivatives in the presence of antimony trichloride as catalyst is described. Triarylmethane derivatives were prepared in good to excellent yields and characterized by elemental analysis, FTIR, 1H and 13C NMR spectroscopic techniques. The structural and vibrational analysis were investigated by performing theoretical calculations at the HF and DFT levels of theory by standard 6-31G*, 6-31G*/B3LYP, and B3LYP/cc-pVDZ methods and good agreement was obtained between experimental and theoretical results. PMID:21445373

Optimization of constrained density functional theory

NASA Astrophysics Data System (ADS)

O'Regan, David D.; Teobaldi, Gilberto

2016-07-01

Constrained density functional theory (cDFT) is a versatile electronic structure method that enables ground-state calculations to be performed subject to physical constraints. It thereby broadens their applicability and utility. Automated Lagrange multiplier optimization is necessary for multiple constraints to be applied efficiently in cDFT, for it to be used in tandem with geometry optimization, or with molecular dynamics. In order to facilitate this, we comprehensively develop the connection between cDFT energy derivatives and response functions, providing a rigorous assessment of the uniqueness and character of cDFT stationary points while accounting for electronic interactions and screening. In particular, we provide a nonperturbative proof that stable stationary points of linear density constraints occur only at energy maxima with respect to their Lagrange multipliers. We show that multiple solutions, hysteresis, and energy discontinuities may occur in cDFT. Expressions are derived, in terms of convenient by-products of cDFT optimization, for quantities such as the dielectric function and a condition number quantifying ill definition in multiple constraint cDFT.

Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach.

PubMed

Cecchet, F; Lis, D; Caudano, Y; Mani, A A; Peremans, A; Champagne, B; Guthmuller, J

2012-03-28

The knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular, DFT calculations have been carried out on three classes of models for the aliphatic chains. The first class of models consists of aliphatic chains, containing from 3 to 12 carbon atoms, in which only one methyl group can freely vibrate, while the rest of the chain is frozen by a strong overweight of its C and H atoms. This enables us to localize the probed vibrational modes on the methyl group. In the second class, only one methyl group is frozen, while the entire remaining chain is allowed to vibrate. This enables us to analyse the influence of the aliphatic chain on the methyl stretching vibrations. Finally, the dodecanethiol (DDT) molecule is considered, for which the effects of two dielectrics, i.e. n-hexane and n-dodecane, are investigated. Moreover, DDT calculations are also carried out by using different exchange-correlation (XC) functionals in order to assess the DFT approximations. Using the DFT IR vectors and Raman tensors, the SFG spectrum of DDT has been simulated and the orientation of the methyl group has then been deduced and compared with that obtained using an analytical approach based on a bond additivity model. This analysis shows that when using DFT molecular properties, the predicted orientation of the terminal methyl group tends to converge as a function of the alkyl chain length and that the effects of the chain as well as of the dielectric environment are small. Instead, a more significant difference is observed when comparing the DFT-based results with those obtained from the analytical approach, thus indicating the importance of a quantum chemical description of the hyperpolarizability tensor elements of the methyl group. © 2012 IOP Publishing Ltd

Quantifying confidence in density functional theory predictions of magnetic ground states

NASA Astrophysics Data System (ADS)

Houchins, Gregory; Viswanathan, Venkatasubramanian

2017-10-01

Density functional theory (DFT) simulations, at the generalized gradient approximation (GGA) level, are being routinely used for material discovery based on high-throughput descriptor-based searches. The success of descriptor-based material design relies on eliminating bad candidates and keeping good candidates for further investigation. While DFT has been widely successfully for the former, oftentimes good candidates are lost due to the uncertainty associated with the DFT-predicted material properties. Uncertainty associated with DFT predictions has gained prominence and has led to the development of exchange correlation functionals that have built-in error estimation capability. In this work, we demonstrate the use of built-in error estimation capabilities within the BEEF-vdW exchange correlation functional for quantifying the uncertainty associated with the magnetic ground state of solids. We demonstrate this approach by calculating the uncertainty estimate for the energy difference between the different magnetic states of solids and compare them against a range of GGA exchange correlation functionals as is done in many first-principles calculations of materials. We show that this estimate reasonably bounds the range of values obtained with the different GGA functionals. The estimate is determined as a postprocessing step and thus provides a computationally robust and systematic approach to estimating uncertainty associated with predictions of magnetic ground states. We define a confidence value (c-value) that incorporates all calculated magnetic states in order to quantify the concurrence of the prediction at the GGA level and argue that predictions of magnetic ground states from GGA level DFT is incomplete without an accompanying c-value. We demonstrate the utility of this method using a case study of Li-ion and Na-ion cathode materials and the c-value metric correctly identifies that GGA-level DFT will have low predictability for NaFePO4F . Further, there needs to be a systematic test of a collection of plausible magnetic states, especially in identifying antiferromagnetic (AFM) ground states. We believe that our approach of estimating uncertainty can be readily incorporated into all high-throughput computational material discovery efforts and this will lead to a dramatic increase in the likelihood of finding good candidate materials.

Is the Bethe–Salpeter Formalism Accurate for Excitation Energies? Comparisons with TD-DFT, CASPT2, and EOM-CCSD

PubMed Central

2017-01-01

Developing ab initio approaches able to provide accurate excited-state energies at a reasonable computational cost is one of the biggest challenges in theoretical chemistry. In that framework, the Bethe–Salpeter equation approach, combined with the GW exchange-correlation self-energy, which maintains the same scaling with system size as TD-DFT, has recently been the focus of a rapidly increasing number of applications in molecular chemistry. Using a recently proposed set encompassing excitation energies of many kinds [J. Phys. Chem. Lett.2016, 7, 586–591], we investigate here the performances of BSE/GW. We compare these results to CASPT2, EOM-CCSD, and TD-DFT data and show that BSE/GW provides an accuracy comparable to the two wave function methods. It is particularly remarkable that the BSE/GW is equally efficient for valence, Rydberg, and charge-transfer excitations. In contrast, it provides a poor description of triplet excited states, for which EOM-CCSD and CASPT2 clearly outperform BSE/GW. This contribution therefore supports the use of the Bethe–Salpeter approach for spin-conserving transitions. PMID:28301726

U(v) in metal uranates: A combined experimental and theoretical study of MgUO 4, CrUO 4, and FeUO 4

DOE PAGES

Guo, Xiaofeng; Tiferet, Eitan; Qi, Liang; ...

2016-01-01

Although pentavalent uranium can exist in aqueous solution, its presence in the solid state is uncommon. Metal monouranates, MgUO 4, CrUO 4 and FeUO 4 were synthesized for detailed structural and energetic investigations. Structural characteristics of these uranates used powder X-ray diffraction, synchrotron X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and 57Fe-Mossbauer spectroscopy. Enthalpies of formation were measured by high temperature oxide melt solution calorimetry. Density functional theory (DFT) calculations provided both structural and energetic information. The measured structural and thermodynamic properties show good consistency with those predicted from DFT. The presence of U 5+ has been solidly confirmed in CrUOmore » 4 and FeUO 4, which are thermodynamically stable compounds, and the origin and stability of U 5+ in the system was elaborated by DFT. Lastly, the structural and thermodynamic behaviour of U 5+ elucidated in this work is relevant to fundamental actinide redox chemistry and to applications in the nuclear industry and radioactive waste disposal.« less

Probing the (110)-Oriented plane of rutile ZnF2: A DFT investigation

NASA Astrophysics Data System (ADS)

Tamijani, Ali Abbaspour; Ebrahimiaqda, Elham

2017-12-01

For many years, rutile-like crystals have given rise to pronounced enthusiasm amongst mineralogists. In this context, rutile-type ZnF2 has found numerous applications across a variety of disciplines, ranging from material sciences to optoelectronics. Surprisingly, very limited literature is concerned with the molecular adsorption on ZnF2 surfaces and related energetics. Additionally, surface probing with small particles is a well-entrenched technique to analyze the interfacial properties. In this regard, small organic species are valuable picks. In the present work, we have employed electronic structure calculations to simulate the adsorption of methane, chloroform, pyrrole, benzene, naphthalene, anthracene, tetracene and pentacene at the (110) plane of rutile ZnF2. Dispersion-corrected DFT method was chosen to predict the binding energies and structures of molecule-adsorbed surfaces. Interestingly, a linear proportionality relationship was found between the binding energies of aromatic adsorbates and their respective molecular lengths. By applying this relationship, we were able to predict the adsorption energy of pentacene on ZnF2 to within 2% of our DFT-based result.

A comparative study of DFT calculated and experimental UV/Visible spectra for thirty carboline and carbazole based compounds

NASA Astrophysics Data System (ADS)

Zara, Zeenat; Iqbal, Javed; Ayub, Khurshid; Irfan, Muhammad; Mahmood, Athar; Khera, Rasheed Ahmad; Eliasson, Bertil

2017-12-01

A comparative study of UV/Visible spectra of carboline and carbazole derivatives was conducted by employing the Density Functional Theory (DFT) approach. In this study, the geometries of ground and excited states, excitation energy and absorption spectra were estimated by using seven different DFT functional; CAM-B3LYP, B3LYP, MPW1PW91, PBE, B3PW91, WB97XD and HSE06 with 6-31G basis set. Moreover, five different basis sets 3-21G, 6-31G, DGDZVP, DGTZVP and SDD were also investigated with the CAM-B3LYP and WB97XD functional to take out the best combination of functional and basis set. CAM-B3LYP/6-31G and WB97XD/DGDZVP combination were found to have closest agreement with the experimental values of β-carboline derivatives and carbazole derivatives, respectively. This study provided an insight about the electronic characteristics of the selected compounds and provided an effective tool for developing and designing the better UV absorber compounds.

Electronic structure of YbB 6 : Is it a topological insulator or not?

DOE PAGES

Kang, Chang -Jong; Denlinger, J. D.; Allen, J. W.; ...

2016-03-17

Here, to finally resolve the controversial issue of whether or not the electronic structure of YbB6 is nontrivially topological, we have made a combined study using angle-resolved photoemission spectroscopy (ARPES) of the nonpolar (110) surface and density functional theory (DFT). The flat-band conditions of the (110) ARPES avoid the strong band bending effects of the polar (001) surface and definitively show that YbB 6 has a topologically trivial B 2p–Yb 5d semiconductor band gap of ~0.3 eV. Accurate determination of the low energy band topology in DFT requires the use of a modified Becke-Johnson exchange potential incorporating spin-orbit coupling andmore » an on-site Yb 4f Coulomb interaction U as large as 7 eV. The DFT result, confirmed by a more precise GW band calculation, is similar to that of a small gap non-Kondo nontopological semiconductor. Additionally, the pressure-dependent electronic structure of YbB 6 is investigated theoretically and found to transform into a p–d overlap semimetal with small Yb mixed valency.« less

Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.

PubMed

Arjunan, V; Rani, T; Mythili, C V; Mohan, S

2011-08-01

A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Spectroscopic and vibrational analysis of the methoxypsoralen system: A comparative experimental and theoretical study

NASA Astrophysics Data System (ADS)

Liu, Y.; Yuan, H.; Vo-Dinh, T.

2013-03-01

Raman spectra measurements and density functional theory (DFT) calculations were performed to investigate three psoralens: 5-amino-8-methoxypsoralen (5-A-8-MOP), 5-methoxypsoralen (5-MOP) and 8-methoxypsoralen (8-MOP) with the aim of differentiating these similar bioactive molecules. The Raman spectra were recorded in the region 300-3500 cm-1. All three psoralens were found to have similar Raman spectrum in the region 1500-1650 cm-1. 5-A-8-MOP can be easily differentiated from 5-MOP or 8-MOP based on the Raman spectrum. The Raman spectrum differences at 651 and 795 cm-1 can be used to identify 5-MOP from 8-MOP. The theoretically computed vibrational frequencies and relative peak intensities were compared with experimental data. DFT calculations using the B3LYP method and 6-311++G(d,p) basis set were found to yield results that are very comparable to experimental Raman spectra. Detailed vibrational assignments were performed with DFT calculations and the potential energy distribution (PED) obtained from the Vibrational Energy Distribution Analysis (VEDA) program.

Vibrational frequency analysis, FT-IR, DFT and M06-2X studies on tert-Butyl N-(thiophen-2yl)carbamate

NASA Astrophysics Data System (ADS)

Sert, Yusuf; Singer, L. M.; Findlater, M.; Doğan, Hatice; Çırak, Ç.

2014-07-01

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized tert-Butyl N-(thiophen-2yl)carbamate have been investigated. The experimental FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with the 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The vibrational frequencies have been assigned using potential energy distribution (PED) analysis by using VEDA 4 software. The computational optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with related literature results. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and are depicted.

Optimization of Robotic Spray Painting process Parameters using Taguchi Method

NASA Astrophysics Data System (ADS)

Chidhambara, K. V.; Latha Shankar, B.; Vijaykumar

2018-02-01

Automated spray painting process is gaining interest in industry and research recently due to extensive application of spray painting in automobile industries. Automating spray painting process has advantages of improved quality, productivity, reduced labor, clean environment and particularly cost effectiveness. This study investigates the performance characteristics of an industrial robot Fanuc 250ib for an automated painting process using statistical tool Taguchi’s Design of Experiment technique. The experiment is designed using Taguchi’s L25 orthogonal array by considering three factors and five levels for each factor. The objective of this work is to explore the major control parameters and to optimize the same for the improved quality of the paint coating measured in terms of Dry Film thickness(DFT), which also results in reduced rejection. Further Analysis of Variance (ANOVA) is performed to know the influence of individual factors on DFT. It is observed that shaping air and paint flow are the most influencing parameters. Multiple regression model is formulated for estimating predicted values of DFT. Confirmation test is then conducted and comparison results show that error is within acceptable level.

Ammonia-water cation and ammonia dimer cation.

PubMed

Kim, Hahn; Lee, Han Myoung

2009-06-25

We have investigated the structure, interaction energy, electronic properties, and IR spectra of the ammonia-water cation (NH(3)H(2)O)(+) using density functional theory (DFT) and high-level ab initio theory. The ammonia-water cation has three minimum-energy structures of (a) H(2)NH(+)...OH(2), (b) H(3)N(+)...OH(2), and (c) H(3)NH(+)...OH. The lowest-energy structure is (a), followed by (c) and (b). The ammonia dimer cation has two minimum-energy structures [the lowest H(3)NH(+)...NH(2) structure and the second lowest (H(3)N...NH(3))(+) structure]. The minimum transition barrier for the interconversion between (a), (b), and (c) is approximately 6 kcal/mol. Most DFT calculations with various functionals, except a few cases, overstabilize the N...O and N...N binding, predicting different structures from Moller-Plesset second-order perturbation (MP2) theory and the most reliable complete basis set (CBS) limit of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. Thus, the validity test of the DFT functionals for these ionized molecular systems would be of importance.

Genetic algorithm based approach to investigate doped metal oxide materials: Application to lanthanide-doped ceria

NASA Astrophysics Data System (ADS)

Hooper, James; Ismail, Arif; Giorgi, Javier B.; Woo, Tom K.

2010-06-01

A genetic algorithm (GA)-inspired method to effectively map out low-energy configurations of doped metal oxide materials is presented. Specialized mating and mutation operations that do not alter the identity of the parent metal oxide have been incorporated to efficiently sample the metal dopant and oxygen vacancy sites. The search algorithms have been tested on lanthanide-doped ceria (L=Sm,Gd,Lu) with various dopant concentrations. Using both classical and first-principles density-functional-theory (DFT) potentials, we have shown the methodology reproduces the results of recent systematic searches of doped ceria at low concentrations (3.2% L2O3 ) and identifies low-energy structures of concentrated samarium-doped ceria (3.8% and 6.6% L2O3 ) which relate to the experimental and theoretical findings published thus far. We introduce a tandem classical/DFT GA algorithm in which an inexpensive classical potential is first used to generate a fit gene pool of structures to enhance the overall efficiency of the computationally demanding DFT-based GA search.

A density functional theory study of the correlation between analyte basicity, ZnPc adsorption strength, and sensor response.

PubMed

Tran, N L; Bohrer, F I; Trogler, W C; Kummel, A C

2009-05-28

Density functional theory (DFT) simulations were used to determine the binding strength of 12 electron-donating analytes to the zinc metal center of a zinc phthalocyanine molecule (ZnPc monomer). The analyte binding strengths were compared to the analytes' enthalpies of complex formation with boron trifluoride (BF(3)), which is a direct measure of their electron donating ability or Lewis basicity. With the exception of the most basic analyte investigated, the ZnPc binding energies were found to correlate linearly with analyte basicities. Based on natural population analysis calculations, analyte complexation to the Zn metal of the ZnPc monomer resulted in limited charge transfer from the analyte to the ZnPc molecule, which increased with analyte-ZnPc binding energy. The experimental analyte sensitivities from chemiresistor ZnPc sensor data were proportional to an exponential of the binding energies from DFT calculations consistent with sensitivity being proportional to analyte coverage and binding strength. The good correlation observed suggests DFT is a reliable method for the prediction of chemiresistor metallophthalocyanine binding strengths and response sensitivities.

Expedient and click synthesis, spectroscopic characterizations and DFT calculations of novel 1,5-bis(N-substituted 1,2,3‒triazole) benzodiazepinedione scaffolds

NASA Astrophysics Data System (ADS)

Paghandeh, Hossein; Saeidian, Hamid

2018-04-01

A practically reliable procedure for synthesis of new 1,5-bis(N-substituted 1,2,3‒triazole) benzodiazepinedione derivatives was reported by sequential amidation, propargylation and a click azide‒alkyne [3 + 2] cycloaddition reaction in a one pot fashion. The desired products were characterized by CHN analysis, 1H and 13C NMR and ESI-MS spectroscopy. Short reaction time, good yields (55-91%), mild reaction conditions and easily available and less expensive starting materials are advantages of this protocol. Natural bond orbital charge distribution and HOMO-LUMO analysis of the characterized structure of 4e have been also calculated by density functional theory (DFT) calculations. The Li+ and Na+ ion affinities of 4e have been also investigated by DFT studies to find the applicability of these products as ligand in coordination chemistry. Sodium ion affinity of 4e was determined as 60 kJ mol-1 is less than its lithium ion affinity, indicating that the lithiation of 4e is more exothermic than the sodiation.

Structural characterization, surface characteristics and non covalent interactions of a heterocyclic Schiff base: Evaluation of antioxidant potential by UV-visible spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Chithiraikumar, S.; Gandhimathi, S.; Neelakantan, M. A.

2017-06-01

A heterocyclic Schiff base, (E)-4-(1-((pyridin-2-ylmethyl)imino)ethyl)benzene-1,3-diol (L) was synthesized and isolated as single crystals. Its structure was characterized by FT-IR, UV, 1H and 13C NMR, and further confirmed by X-ray crystallography. Qualitatively and quantitatively the various interactions in the crystal structure of L has been analyzed by Hirshfeld surfaces and 2D fingerprint plots. Non covalent interactions have been studied by electron localization function (ELF) and mapped with reduced density gradient (RDG) analysis. The molecular structure was studied computationally by DFT-B3LYP/6-311G(d,p) calculations. HOMO-LUMO energy levels, chemical reactivity descriptors and thermodynamic parameters have been investigated at the same level of theory. The antioxidant potential of L was evaluated experimentally by measuring DPPH free radical scavenging effect using UV-visible spectroscopy and theoretically by DFT. Theoretical parameters, such as bond dissociation enthalpy (BDE) and spin density calculated suggests that antioxidant potential of L is due to H atom abstraction from the sbnd OH group.

Dynamics of two-phase interfaces and surface tensions: A density-functional theory perspective

NASA Astrophysics Data System (ADS)

Yatsyshin, Petr; Sibley, David N.; Duran-Olivencia, Miguel A.; Kalliadasis, Serafim

2016-11-01

Classical density functional theory (DFT) is a statistical mechanical framework for the description of fluids at the nanoscale, where the inhomogeneity of the fluid structure needs to be carefully accounted for. By expressing the grand free-energy of the fluid as a functional of the one-body density, DFT offers a theoretically consistent and computationally accessible way to obtain two-phase interfaces and respective interfacial tensions in a ternary solid-liquid-gas system. The dynamic version of DFT (DDFT) can be rigorously derived from the Smoluchowsky picture of the dynamics of colloidal particles in a solvent. It is generally agreed that DDFT can capture the diffusion-driven evolution of many soft-matter systems. In this context, we use DDFT to investigate the dynamic behaviour of two-phase interfaces in both equilibrium and dynamic wetting and discuss the possibility of defining a time-dependent surface tension, which still remains in debate. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031 and from the Engineering and Physical Sciences Research Council of the UK via Grants No. EP/L027186 and EP/L020564.

Exploring two-dimensional electron gases with two-dimensional Fourier transform spectroscopy

DOE PAGES

Paul, J.; Dey, P.; Tokumoto, T.; ...

2014-10-07

The dephasing of excitons in a modulation doped single quantum well was carefully measured using time integrated four-wave mixing (FWM) and two-dimensional Fourier transform (2DFT) spectroscopy. These are the first 2DFT measurements performed on a modulation doped single quantum well. The inhomogeneous and homogeneous excitonic line widths were obtained from the diagonal and cross-diagonal profiles of the 2DFT spectra. The laser excitation density and temperature were varied and 2DFT spectra were collected. A very rapid increase of the dephasing decay, and as a result, an increase in the cross-diagonal 2DFT linewidths with temperature was observed. Furthermore, the lineshapes of themore » 2DFT spectra suggest the presence of excitation induced dephasing and excitation induced shift.« less

Thermal density functional theory, ensemble density functional theory, and potential functional theory for warm dense matter

NASA Astrophysics Data System (ADS)

Pribram-Jones, Aurora

Warm dense matter (WDM) is a high energy phase between solids and plasmas, with characteristics of both. It is present in the centers of giant planets, within the earth's core, and on the path to ignition of inertial confinement fusion. The high temperatures and pressures of warm dense matter lead to complications in its simulation, as both classical and quantum effects must be included. One of the most successful simulation methods is density functional theory-molecular dynamics (DFT-MD). Despite great success in a diverse array of applications, DFT-MD remains computationally expensive and it neglects the explicit temperature dependence of electron-electron interactions known to exist within exact DFT. Finite-temperature density functional theory (FT DFT) is an extension of the wildly successful ground-state DFT formalism via thermal ensembles, broadening its quantum mechanical treatment of electrons to include systems at non-zero temperatures. Exact mathematical conditions have been used to predict the behavior of approximations in limiting conditions and to connect FT DFT to the ground-state theory. An introduction to FT DFT is given within the context of ensemble DFT and the larger field of DFT is discussed for context. Ensemble DFT is used to describe ensembles of ground-state and excited systems. Exact conditions in ensemble DFT and the performance of approximations depend on ensemble weights. Using an inversion method, exact Kohn-Sham ensemble potentials are found and compared to approximations. The symmetry eigenstate Hartree-exchange approximation is in good agreement with exact calculations because of its inclusion of an ensemble derivative discontinuity. Since ensemble weights in FT DFT are temperature-dependent Fermi weights, this insight may help develop approximations well-suited to both ground-state and FT DFT. A novel, highly efficient approach to free energy calculations, finite-temperature potential functional theory, is derived, which has the potential to transform the simulation of warm dense matter. As a semiclassical method, it connects the normally disparate regimes of cold condensed matter physics and hot plasma physics. This orbital-free approach captures the smooth classical density envelope and quantum density oscillations that are both crucial to accurate modeling of materials where temperature and pressure effects are influential.

On the number of multiplications necessary to compute a length-2 exp n DFT

NASA Technical Reports Server (NTRS)

Heideman, M. T.; Burrus, C. S.

1986-01-01

The number of multiplications necessary and sufficient to compute a length-2 exp n DFT is determined. The method of derivation is shown to apply to the multiplicative complexity results of Winograd (1980, 1981) for a length-p exp n DFT, for p an odd prime number. The multiplicative complexity of the one-dimensional DFT is summarized for many possible lengths.

A computational study of Na behavior on graphene

NASA Astrophysics Data System (ADS)

Malyi, Oleksandr I.; Sopiha, Kostiantyn; Kulish, Vadym V.; Tan, Teck L.; Manzhos, Sergei; Persson, Clas

2015-04-01

We present the first ab initio and molecular dynamics study of Na adsorption and diffusion on ideal graphene that considers Na-Na interaction and dispersion forces. From density functional theory (DFT) calculations using the generalized gradient approximation (GGA), the binding energy (vs. the vacuum reference state) of -0.75 eV is higher than the cohesive energy of Na metal (E

Density-functional theory molecular dynamics simulations of a-HfO2/Ge(100)(2 × 1) and a-ZrO2/Ge(100)(2 × 1) interface passivation.

PubMed

Chagarov, E A; Porter, L; Kummel, A C

2016-02-28

The structural properties of a-HfO2/Ge(2 × 1)-(001) and a-ZrO2/Ge(2 × 1)-(001) interfaces were investigated with and without a GeOx interface interlayer using density-functional theory (DFT) molecular dynamics (MD) simulations. Realistic a-HfO2 and a-ZrO2 samples were generated using a hybrid classical-DFT MD "melt-and-quench" approach and tested against experimental properties. The oxide/Ge stacks were annealed at 700 K, cooled to 0 K, and relaxed providing the system with enough freedom to form realistic interfaces. For each high-K/Ge stack type, two systems with single and double interfaces were investigated. All stacks were free of midgap states; however, stacks with a GeO(x) interlayer had band-edge states which decreased the band gaps by 0%-30%. These band-edge states were mainly produced by under-coordinated Ge atoms in GeO(x) layer or its vicinity due to deformation, intermixing, and bond-breaking. The DFT-MD simulations show that electronically passive interfaces can be formed either directly between high-K dielectrics and Ge or with a monolayer of GeO2 if the processing does not create or properly passivate under-coordinated Ge atoms and Ge's with significantly distorted bonding angles. Comparison to the charge states of the interfacial atoms from DFT to experimental x-ray photoelectron spectroscopy results shows that while most studies of gate oxide on Ge(001) have a GeO(x) interfacial layer, it is possible to form an oxide/Ge interface without a GeO(x) interfacial layer. Comparison to experiments is consistent with the dangling bonds in the suboxide being responsible for midgap state formation.

Synthesis, electronic structure investigation of 3-pentyl-2,6-di(furan-2-yl)piperidin-4-one by FT-IR, FT-Raman and UV-Visible spectral studies and ab initio/DFT calculations.

PubMed

Arockia Doss, M; Savithiri, S; Rajarajan, G; Thanikachalam, V; Anbuselvan, C

2015-12-05

FT-IR and FT-Raman spectra of 3-pentyl-2,6-di(furan-2-yl) piperidin-4-one (3-PFPO) were recorded in the solid phase. The structural and spectroscopic analyses of 3-PFPO were made by using B3LYP/HF level with 6-311++G(d, p) basis set. The fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Comparison of the observed fundamental vibrational frequencies of 3-PFPO with calculated results by HF and DFT methods indicates that B3LYP is superior to HF method for molecular vibrational problems. The electronic properties such as excitation energies, oscillator strength, wavelengths and HOMO-LUMO energies were obtained by time-dependent DFT (TD-DFT) approach. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The hyperconjugative interaction energy (E((2))) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. In addition, MEP and atomic charges of carbon, nitrogen, oxygen and hydrogen were calculated using B3LYP/6-311++G(d, p) level theory. Moreover, thermodynamic properties (heat capacities, entropy and enthalpy) of the title compound at different temperatures were calculated in gas phase. Copyright © 2015 Elsevier B.V. All rights reserved.

Mutual effects of copper and phosphate on their interaction with γ-Al2O3: combined batch macroscopic experiments with DFT calculations.

PubMed

Ren, Xuemei; Yang, Shitong; Tan, Xiaoli; Chen, Changlun; Sheng, Guodong; Wang, Xiangke

2012-10-30

The mutual effects of Cu(II) and phosphate on their interaction with γ-Al(2)O(3) are investigated by using batch experiments combined with density functional theory (DFT) calculations. The results of batch experiments show that coexisting phosphate promotes the retention of Cu(II) on γ-Al(2)O(3), whereas phosphate retention is not affected by coexisting Cu(II) at low initial phosphate concentrations (≤ 3.6 mg P/L). Cu-phosphate aqueous complexes control Cu(II) retention through the formation of type B ternary surface complexes (where phosphate bridges γ-Al(2)O(3) and Cu(II)) at pH 5.5. This deduction is further supported by the results of DFT calculations. More specifically, the DFT calculation results indicate that the type B ternary surface complexes prefer to form outer-sphere or monodentate inner-sphere binding mode under our experimental conditions. The enhancement of phosphate retention on γ-Al(2)O(3) in the presence of Cu(II) at high initial phosphate concentrations (>3.6 mg P/L) may be attributed to the formation of 1:2 Cu(II)-phosphate species and/or surface precipitates. Understanding the mutual effects of phosphate and Cu(II) on their mobility and transport in mineral/water environments is more realistic to design effective remediation strategies for reducing their negative impacts on aquatic/terrestrial environments. Copyright © 2012 Elsevier B.V. All rights reserved.

Methanol Synthesis from CO2 Hydrogenation over a Pd4/In2O3 Model Catalyst: A Combined DFT and Kinetic Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Jingyun; Liu, Changjun; Mei, Donghai

2014-08-01

Methanol synthesis from CO2 hydrogenation on Pd4/In2O3 has been investigated using density functional theory (DFT) and microkinetic modeling. In this study, three possible routes in the reaction network of CO2 + H2 → CH3OH + H2O have been examined. Our DFT results show that the HCOO route competes with the RWGS route whereas a high activation barrier kinetically blocks the HCOOH route. DFT results also suggest that H2COO* + H* ↔ H2CO* +OH* and cis-COOH* + H* ↔CO* + H2O* are the rate limiting steps in the HCOO route and the RWGS route, respectively. Microkinetic modeling results demonstrate that themore » HCOO route is the dominant reaction route for methanol synthesis from CO2 hydrogenation. We found that the activation of H adatom on the small Pd cluster and the presence of H2O on the In2O3 substrate play important roles in promoting the methanol synthesis. The hydroxyl adsorbed at the interface of Pd4/In2O3 induces the transformation of the supported Pd4 cluster from a butterfly structure into a tetrahedron structure. This important structure change not only indicates the dynamical nature of the supported nanoparticle catalyst structure during the reaction but also shifts the final hydrogenation step from H2COH to CH3O.« less

Molecular structure and vibrational assignments of 2,4-dichlorophenoxyacetic acid herbicide

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.

2010-09-01

The structural stability of 2,4-dichlorophenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G** basis set. From the calculations at both levels of theory the Cgcpp structure was predicted to be the lowest energy minimum for the acid. The DFT and the MP2 levels disagreed about the nature of the second stable structure of 2,4-dichlorophenoxyacetic acid. At the DFT-B3LYP level of calculation the planar Tttp ( transoid O dbnd C sbnd O sbnd H) and the non-planar Tgcpp ( cisoid O dbnd C sbnd O sbnd H) forms were predicted to be 0.7 and 1.5 kcal/mol, respectively higher in energy than the Cgcpp conformation. At the MP2 level the two high energy Tttp and Tgcpp forms were predicted to be 2.7 and 1.4 kcal/mol, respectively higher in energy than the ground state Cgcpp structure. The Tgcpp form was adopted as the second possible structure of 2,4-dichlorophenoxyacetic acid on the basis of the fact that the Møller-Plesset calculations account better than the DFT ones for the non-bonding O⋯H interactions. The vibrational frequencies of the lowest energy Cgcpp conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis and experimental infrared and Raman data.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

2006-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+n, MNO+, and MCO+2. The DFT works well for frequencies and geometries, even in case with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of successes as well as failures of DFT will be given.

Interaction Between New Anti-cancer Drug Syndros and CNT(6,6-6) Nanotube for Medical Applications: Geometry Optimization, Molecular Structure, Spectroscopic (NMR, UV/Vis, Excited state), FMO, MEP and HOMO-LUMO Investigation

NASA Astrophysics Data System (ADS)

Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Kumar, Rakesh

2018-03-01

In the present work, Density Functional Theory (DFT) was first time employed to investigate the interaction between new drug (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol (Syndros) and the CNT(6,6-6) Nanotube in the gaseous phase. The interaction effects of compounds Syndros and CNT (6,6-6) nanotube on the electronic properties, chemical shift tensors and natural charge was also determined and discussed. The electronic spectra of the Syndros and the complex CNT(6,6-6)/Syndros in the gas phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for the formation of adsorption effect on maximum wavelength of the Syndros. Nucleus-Independent Chemical Shifts (NICS) calculations have also been carried out for the compound Syndors and the complex CNT(6,6-6)/Syndros and the aromaticity of the compound Syndors before and after interaction with the CNT(6,6-6) Nanotube was investigated.

Adsorption of rare gases on the C20 nanocage: a theoretical investigation

NASA Astrophysics Data System (ADS)

Rahimi, Rezvan; Kamalinahad, Saeedeh; Solimannejad, Mohammad

2018-03-01

The adsorption of rare gases (Rg) on the external surface of pristine and Sc-doped C20 (ScC19) nanocage is investigated using density functional theory (DFT). Also, time-dependent density functional theory (TD-DFT) and natural bond orbital (NBO) calculations are performed at the CAM-B3LYP/6-31G (d) level. The NBO analyses indicate that the adsorption of Rg molecules with studied nanocage significantly alters its electronic nature. Theoretical results have shown that Rg is weakly adsorbed on the pristine C20, so this nanocage cannot be a proper sensor for detecting and sensing rare gases. In order to improve properties of the nanocage as a promising sensor, Sc-doping process was investigated. The more negative adsorption energies (Eads) of Rg/ScC19 means that adsorption of Rg on the surface of ScC19 is energetically more favored than C20 and other nano-structures as reported in previous studies. It is expected that significant changes in the electronic properties caused by Rg may be used for designing new sensors for detection of rare gases.

DFT/TDDFT investigation on the photophysical properties of a series of phosphorescent cyclometalated complexes based on the benchmark complex FIrpic

NASA Astrophysics Data System (ADS)

Han, Deming; Gong, Ping; Lv, Shuhui; Zhao, Lihui; Zhao, Henan

2018-05-01

The photophysical properties of four Ir(III) complexes have been investigated by means of the density functional theory/time-dependent density functional theory (DFT/TDDFT). The effect of the electron-withdrawing and electron-donating substituents on charge injection, transport, absorption and phosphorescent properties has been studied. The theoretical calculation shows that the lowest-lying singlet absorptions for complexes 1-4 are located at 387, 385, 418 and 386 nm, respectively. For 1-4, the phosphorescence at 465, 485, 494 and 478 nm is mainly attributed to the LUMO → HOMO and LUMO → HOMO-1 transition configurations characteristics. In addition, ionisation potential (IP), electron affinities (EAs) and reorganisation energy have been investigated to evaluate the charge transfer and balance properties between hole and electron. The balance of the reorganisation energies for complex 3 is better than others. The difference between hole transport and electron transport for complex 3 is the smallest among these complexes, which is beneficial to achieve the hole and electron transfer balance in emitting layer.

Conformational, spectroscopic and nonlinear optical investigations on 1-(4-chlorophenyl)-3-(4-chlorophenyl)-2-propen-1-one: a DFT study

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Boukabcha, Nourdine; Benhalima, Nadia; Tamer, Ömer; Chouaih, Abdelkader; Avcı, Davut; Atalay, Yusuf; Hamzaoui, Fodil

2017-05-01

The density functional theory calculations on 1-(4-chlorophenyl)-3-(4-chlorophenyl)-2-propen-1-one (CPCPP) are performed by using B3LYP and HSEh1PBE levels. These methods along with 6-311++G(d,p) basis set have been used to determine optimized molecular geometries, vibrational frequencies, electronic absorption wavelengths and bonding features of CPCPP. The solvent effect on the electronic absorption properties of CPCPP is examined at polar (ethanol and water) and nonpolar (toluene and n-hexane) solvents. In order to find the most stable conformers, conformational analysis is carried out by using B3LYP level. The computed small energy gaps between HOMO and LUMO energies show that the charge transfers occur within CPCPP. DFT calculations have been also performed to investigate the dipole moment (μ), mean polarizability (α), anisotropy of polarizability (Δα), first order static hyperpolarizability (β) for CPCPP. The obtained values show that CPCPP is an excellent candidate to nonlinear optical materials. NBO analysis has been used to investigate the bond strengths, molecular stability, hyperconjugative interactions and intramolecular charge transfer (ICT).

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2017-06-01

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

Assessing the density functional theory-based multireference configuration interaction (DFT/MRCI) method for transition metal complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Escudero, Daniel, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de; Thiel, Walter, E-mail: escudero@kofo.mpg.de, E-mail: thiel@kofo.mpg.de

2014-05-21

We report an assessment of the performance of density functional theory-based multireference configuration interaction (DFT/MRCI) calculations for a set of 3d- and 4d-transition metal (TM) complexes. The DFT/MRCI results are compared to published reference data from reliable high-level multi-configurational ab initio studies. The assessment covers the relative energies of different ground-state minima of the highly correlated CrF{sub 6} complex, the singlet and triplet electronically excited states of seven typical TM complexes (MnO{sub 4}{sup −}, Cr(CO){sub 6}, [Fe(CN){sub 6}]{sup 4−}, four larger Fe and Ru complexes), and the corresponding electronic spectra (vertical excitation energies and oscillator strengths). It includes comparisons withmore » results from different flavors of time-dependent DFT (TD-DFT) calculations using pure, hybrid, and long-range corrected functionals. The DFT/MRCI method is found to be superior to the tested TD-DFT approaches and is thus recommended for exploring the excited-state properties of TM complexes.« less

First-Principles Thermodynamics of Energetic Materials

DTIC Science & Technology

2012-01-01

thermal and zero-point energy ( ZPE ) effects on the crystalline environment [8]. By including vdW, thermal, and ZPE effects into DFT (DFT+vdW+T...by their relation to experiment (triangles) pure DFT over-predicts, while DFT+vdW under-predicts the EOSs. Only when temperature and ZPE effects...crystals with ZPE effects still included. To get a sense of how the vdW damping function might affect the calculation of the dynamical matrix, the

Density functional theory across chemistry, physics and biology.

PubMed

van Mourik, Tanja; Bühl, Michael; Gaigeot, Marie-Pierre

2014-03-13

The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT.

Molecular interactions investigated with DFT calculations of QTAIM and NBO analyses: An application to dimeric structures of rice α-amylase/subtilisin inhibitor

NASA Astrophysics Data System (ADS)

Astani, Elahe K.; Hadipour, Nasser L.; Chen, Chun-Jung

2017-03-01

Characterization of the dimer interactions at the dimeric interface of the crystal structure of rice α-amylase/subtilisin inhibitor (RASI) were performed using the quantum theory of atoms in molecules (QTAIM) and natural bonding orbital (NBO) analyses at the density-functional theory (DFT) level. The results revealed that Gly27 and Arg151 of chain A are the main residues involved in hydrogen bonds, dipole-dipole, and charge-dipole interactions with Gly64, Ala66, Ala67 and Arg81 of chain B at the dimeric interface. Calcium ion of chain A plays the significant role in the stability of the dimeric structure through a strong charge-charge interaction with Ala66.

Chlorophenol sorption on multi-walled carbon nanotubes: DFT modeling and structure-property relationship analysis.

PubMed

Watkins, Marquita; Sizochenko, Natalia; Moore, Quentarius; Golebiowski, Marek; Leszczynska, Danuta; Leszczynski, Jerzy

2017-02-01

The presence of chlorophenols in drinking water can be hazardous to human health. Understanding the mechanisms of adsorption under specific experimental conditions would be beneficial when developing methods to remove toxic substances from drinking water during water treatment in order to limit human exposure to these contaminants. In this study, we investigated the sorption of chlorophenols on multi-walled carbon nanotubes using a density functional theory (DFT) approach. This was applied to study selected interactions between six solvents, five types of nanotubes, and six chlorophenols. Experimental data were used to construct structure-adsorption relationship (SAR) models that describe the recovery process. Specific interactions between solvents and chlorophenols were taken into account in the calculations by using novel specific mixture descriptors.

Optical properties of LiGaS2: an ab initio study and spectroscopic ellipsometry measurement

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Lin, Z. S.; Isaenko, L. I.; Kesler, V. G.; Kruchinin, V. N.; Lobanov, S. I.

2009-11-01

Electronic and optical properties of lithium thiogallate crystal, LiGaS2, have been investigated by both experimental and theoretical methods. The plane-wave pseudopotential method based on DFT theory has been used for band structure calculations. The electronic parameters of Ga 3d orbitals have been corrected by the DFT+U methods to be consistent with those measured with x-ray photoemission spectroscopy. Evolution of optical constants of LiGaS2 over a wide spectral range was determined by developed first-principles theory and dispersion curves were compared with optical parameters defined by spectroscopic ellipsometry in the photon energy range 1.2-5.0 eV. Good agreement has been achieved between theoretical and experimental results.

DFT calculations of electronic and optical properties of SrS with LDA, GGA and mGGA functionals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Shatendra, E-mail: shatendra@gmai.com; Sharma, Jyotsna; Sharma, Yogita

2016-05-06

The theoretical investigations of electronic and optical properties of SrS are made using the first principle DFT calculations. The calculations are performed for the local-density approximation (LDA), generalized gradient approximation (GGA) and for an alternative form of GGA i.e. metaGGA for both rock salt type (B1, Fm3m) and cesium chloride (B2, Pm3m) structures. The band structure, density of states and optical spectra are calculated under various available functional. The calculations with LDA and GGA functional underestimate the values of band gaps with all functional, however the values with mGGA show reasonably good agreement with experimental and those calculated by usingmore » other methods.« less

Synthesis and antibacterial activity of sulfonamides. SAR and DFT studies

NASA Astrophysics Data System (ADS)

Boufas, Wahida; Dupont, Nathalie; Berredjem, Malika; Berrezag, Kamel; Becheker, Imène; Berredjem, Hajira; Aouf, Nour-Eddine

2014-09-01

A series of substituted sulfonamide derivatives were synthesized from chlorosulfonyl isocyanate (CSI) in tree steps (carbamoylation, sulfamoylation and deprotection). Antibacterial activity in vitro of some newly formed compounds investigated against clinical strains Gram-positive and Gram-negative: Escherichia coli and Staphylococcus aureus applying the method of dilution and minimal inhibition concentration (MIC) methods. These compounds have significant bacteriostatic activity with totalities of bacterial strains used. DFT calculations with B3LYP/6-31G(d) level have been used to analyze the electronic and geometric characteristics deduced for the stable structure of three compounds presenting conjugation between a nitrogen atom N through its lone pair and an aromatic ring next to it. The principal quantum chemical descriptors have been correlated with the antibacterial activity.

Efficient near-infrared emission of π-extended cyclometalated iridium complexes based on pyrene in solution-processed polymer light-emitting diode

NASA Astrophysics Data System (ADS)

Liu, Yu; Hao, Zhaoran; Meng, Fanyuan; Wang, Pu; Yang, Liang; Wang, Yafei; Pei, Yong; Su, Shijian

2018-05-01

A novel iridium complex grafting hole-transporting triphenylamine (TPA) unit onto cyclometalated ligand, namely t-BuPyrPyTPA)2Ir(acac), was successfully synthesized and characterized. The photophysical, electrochemical and DFT/TD-DFT calculation, as well as electroluminescence properties of this iridium complex were fully investigated. Meanwhile, the PLEDs employing (t-BuPyrPyTPA)2Ir(acac) as dopant presented stable NIR emission peaked at 697 nm and a shoulder at 764 nm with a highest external quantum efficiency (EQE) of 0.56% at 4 wt% dopant concentration. These results demonstrate that expanding the conjugation length of the ligand is an effective way to achieve NIR emission.

Electronic properties of Laves phase ZrFe{sub 2} using Compton spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatt, Samir, E-mail: sameerbhatto11@gmail.com; Kumar, Kishor; Ahuja, B. L.

First-ever experimental Compton profile of Laves phase ZrFe{sub 2}, using indigenous 20 Ci {sup 137}Cs Compton spectrometer, is presented. To analyze the experimental electron momentum density, we have deduced the theoretical Compton profiles using density functional theory (DFT) and hybridization of DFT and Hartree-Fock scheme within linear combination of atomic orbitals (LCAO) method. The energy bands and density of states are also calculated using LCAO prescription. The theoretical profile based on local density approximation gives a better agreement with the experimental profile than other reported schemes. The present investigations validate the inclusion of correlation potential of Perdew-Zunger in predicting themore » electronic properties of ZrFe{sub 2}.« less

Finite Size Effects in Submonolayer Catalysts Investigated by CO Electrosorption on PtsML/Pd(100).

PubMed

Yuan, Qiuyi; Doan, Hieu A; Grabow, Lars C; Brankovic, Stanko R

2017-10-04

A combination of scanning tunneling microscopy, subtractively normalized interfacial Fourier transform infrared spectroscopy (SNIFTIRS), and density functional theory (DFT) is used to quantify the local strain in 2D Pt clusters on the 100 facet of Pd and its effect on CO chemisorption. Good agreement between SNIFTIRS experiments and DFT simulations provide strong evidence that, in the absence of coherent strain between Pt and Pd, finite size effects introduce local compressive strain, which alters the chemisorption properties of the surface. Though this effect has been widely neglected in prior studies, our results suggest that accurate control over cluster sizes in submonolayer catalyst systems can be an effective approach to fine-tune their catalytic properties.

Arsenic incorporation into FeS 2 pyrite and its influence on dissolution: A DFT study

NASA Astrophysics Data System (ADS)

Blanchard, Marc; Alfredsson, Maria; Brodholt, John; Wright, Kate; Catlow, C. Richard A.

2007-02-01

FeS 2 pyrite can incorporate large amounts of arsenic (up to ca. 10 wt%) and hence has a strong impact on the mobility of this toxic metalloid. Focussing on the lowest arsenic concentrations for which the incorporation occurs in solid solution, the substitution mechanisms involved have been investigated by assuming simple incorporation reactions in both oxidising and reducing conditions. The solution energies were calculated by Density Functional Theory (DFT) calculations and we predict that the formation of AsS dianion groups is the most energetically favourable mechanism. The results also suggest that the presence of arsenic will accelerate the dissolution and thus the generation of acid drainage, when the crystal dissolves in oxidising conditions.

Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Roonasi, Payman; Assle taghipour, Khatoon; van der Spoel, David; Manzetti, Sergio

2015-07-01

The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including EHOMO, ELUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.

Structure of a zinc oxide ultra-thin film on Rh(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuhara, J.; Kato, D.; Matsui, T.

The structural parameters of ultra-thin zinc oxide films on Rh(100) are investigated using low-energy electron diffraction intensity (LEED I–V) curves, scanning tunneling microscopy (STM), and first-principles density functional theory (DFT) calculations. From the analysis of LEED I–V curves and DFT calculations, two optimized models A and B are determined. Their structures are basically similar to the planer h-BN ZnO(0001) structure, although some oxygen atoms protrude from the surface, associated with an in-plane shift of Zn atoms. From a comparison of experimental STM images and simulated STM images, majority and minority structures observed in the STM images represent the two optimizedmore » models A and B, respectively.« less

NTO-Picryl Constitutional Isomers—A DFT Study

NASA Astrophysics Data System (ADS)

Türker, Lemi; Çelik Bayar, Çağlar

2012-01-01

The quantum chemical properties and the detonation performance of some new explosives, 5-nitro-4-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class A) and 5-nitro-2-picryl-2,4-dihydro-3H-1,2,4-triazol-3-one (class B), and their constitutional isomers have been investigated theoretically using the density functional theory (DFT) 6-31G(d,p) method. All of the constitutional isomers were found to be more sensitive than 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) and TNT but more insensitive than RDX and HMX. Their detonation performance is higher than that of NTO and TNT and all except two had lower detonation performance than RDX and HMX.

Experimental (X-ray, FT-IR and UV-vis spectra) and theoretical methods (DFT study) of (E)-3-methoxy-2-[(p-tolylimino)methyl]phenol.

PubMed

Demircioğlu, Zeynep; Albayrak, Çiğdem; Büyükgüngör, Orhan

2014-07-15

A suitable single crystal of (E)-3-methoxy-2-[(p-tolylimino)methyl]phenol, formulated as C15H15N1O2, reveals that the structure is adopted to its E configuration about the azomethine C=N double bond. The compound adopts a enol-imine tautomeric form with a strong intramolecular O-H⋯N hydrogen bond. The single crystal X-ray diffraction analysis at 296K crystallizes in the monoclinic space group P21/c with a = 13.4791(11) Å, b = 6.8251(3) Å, c = 18.3561(15) Å, α = 90°, β = 129.296(5)°, γ = 90° and Z = 4. Comprehensive theoretical and experimental structural studies on the molecule have been carried out by FT-IR and UV-vis spectrometry. Optimized molecular structure and harmonic vibrational frequencies have been investigated by DFT/B3LYP method with 6-31G(d,p) basis set. Stability of the molecule, hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed by using natural bond orbital (NBO) analysis. Electronic structures were discussed by TD-DFT method and the relocation of the electron density were determined. The energetic behavior of the title compound has been examined in solvent media using polarizable continuum model (PCM). Molecular electrostatic potential (MEP), Mulliken population method and natural population analysis (NPA) have been studied. Nonlinear optical (NLO) properties were also investigated. In addition, frontier molecular orbitals analysis have been performed from the optimized geometry. An ionization potential (I), electron affinity (A), electrophilicity index (ω), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S), have been investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

The structural and spectroscopic investigation of 2-chloro-3-methylquinoline by DFT method and UV-Vis, NMR and vibrational spectral techniques combined with molecular docking analysis

NASA Astrophysics Data System (ADS)

Kose, Etem; Atac, Ahmet; Bardak, Fehmi

2018-07-01

This study comprises the structural and spectroscopic evaluation of a quinoline derivative, 2-chloro-3-methylquinoline (2Cl3MQ), via UV-Vis, 1H and 13C NMR, FT-IR and FT-Raman techniques experimentally, theoretically with DFT and TD-DFT quantum chemical calculations at B3LYP/6-311++G (d, p) level of theory, and investigation of the in silico pharmaceutical potent of 2Cl3MQ in comparison to 2ClnMQ (n = 3,4,7,8,9,10) substituted quinolines. The experimental measurements were recorded as follows; UV-vis spectra were obtained in the range of 200-400 nm in the water and ethanol solvents. 1H and 13C NMR spectra were recorded in CDCl3. Vibrational spectra were obtained in the region of 4000-400 cm-1 and 3500-10 cm-1 for FT-IR and FT-Raman spectra, respectively. Structural and spectroscopic features obtained through theoretical evaluations include: electrostatic features, atomic charges and molecular electrostatic potential surface, the frontier molecular orbital characteristics, the density of states and their overlapping nature, the electronic transition properties, thermodynamical and nonlinear optical characteristics, and predicted UV-Vis, 1H and 13C NMR, FT-IR and FT-Raman spectra. Ligand-enzyme interactions of 2ClnMQ (n = 3,4,7,8,9,10) substituted quinolines with Malate Synthase from Mycobacterium Tuberculosis (MtbMS) were investigated via molecular docking. The role of position of methyl substitution on the inhibitor character of the ligands was discussed on the basis of noncovalent interaction profiles.

Characterization of prepared In2O3 thin films: The FT-IR, FT-Raman, UV-Visible investigation and optical analysis.

PubMed

Panneerdoss, I Joseph; Jeyakumar, S Johnson; Ramalingam, S; Jothibas, M

2015-08-05

In this original work, the Indium oxide (In2O3) thin film is deposited cleanly on microscope glass substrate at different temperatures by spray pyrolysis technique. The physical properties of the films are characterized by XRD, SEM, AFM and AFM measurements. The spectroscopic investigation has been carried out on the results of FT-IR, FT-Raman and UV-Visible. XRD analysis exposed that the structural transformation of films from stoichiometric to non-stoichiometric orientation of the plane vice versa and also found that, the film is polycrystalline in nature having cubic crystal structure with a preferred grain orientation along (222) plane. SEM and AFM studies revealed that, the film with 0.1M at 500°C has spherical grains with uniform dimension. The complete vibrational analysis has been carried out and the optimized parameters are calculated using HF and DFT (CAM-B3LYP, B3LYP and B3PW91) methods with 3-21G(d,p) basis set. Furthermore, NMR chemical shifts are calculated by using the gauge independent atomic orbital (GIAO) technique. The molecular electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, molecular electrostatic potential energy (MEP) analysis and Polarizability first order hyperpolarizability calculations are performed by time dependent DFT (TD-DFT) approach. The energy excitation on electronic structure is investigated and the assignment of the absorption bands in the electronic spectra of steady compound is discussed. The calculated HOMO and LUMO energies showed the enhancement of energy gap by the addition of substitutions with the base molecule. The thermodynamic properties (heat capacity, entropy, and enthalpy) at different temperatures are calculated and interpreted in gas phase. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Secure Image Transmission over DFT-precoded OFDM-VLC systems based on Chebyshev Chaos scrambling

NASA Astrophysics Data System (ADS)

Wang, Zhongpeng; Qiu, Weiwei

2017-08-01

This paper proposes a physical layer image secure transmission scheme for discrete Fourier transform (DFT) precoded OFDM-based visible light communication systems by using Chebyshev chaos maps. In the proposed scheme, 256 subcarriers and QPSK modulation are employed. The transmitted digital signal of the image is encrypted with a Chebyshev chaos sequence. The encrypted signal is then transformed by a DFT precoding matrix to reduce the PAPR of the OFDM signal. After that, the encrypted and DFT-precoded OFDM are transmitted over a VLC channel. The simulation results show that the proposed image security transmission scheme can not only protect the DFT-precoded OFDM-based VLC from eavesdroppers but also improve BER performance.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

1997-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+(sub n), MNO+, and MCO+(sub 2). The DFT works well for frequencies and geometries, even in cases with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of the successes as well as failures of DFT will be given.

The spectroscopic properties of anticancer drug Apigenin investigated by using DFT calculations, FT-IR, FT-Raman and NMR analysis

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.; Manoharan, S.

2012-09-01

The FT-Raman and FT-Infrared spectra of solid Apigenin sample were measured in order to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm-1 and 4000-400 cm-1, respectively. The recorded FT-IR and FT-Raman spectral measurements favor the calculated (by B3LYP/6-31G(d,p) method) structural parameters which are further supported by spectral simulation. Additional support is given by the collected 1H and 13C NMR spectra recorded with the sample dissolved in DMSO. The predicted chemical shifts at the B3LYP/6-31G(d) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. The UV-visible absorption spectra of the compound that dissolved in Ethanol, Methanol and DMSO were recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and atomic charges of the title compound were investigated using theoretical calculations. The results are discussed herein and compared with similar molecules whenever appropriate.

A combined TD-DFT and spectroscopic investigation of the solute-solvent interactions of efavirenz

NASA Astrophysics Data System (ADS)

Jordaan, Maryam A.; Singh, Parvesh; Martincigh, Bice S.

2016-03-01

Efavirenz, commercially known as Sustiva® or Stocrin®, is a first-line antiretroviral treatment for HIV/AIDS. The clinical efficacy of efavirenz is, however, hindered by its solubility. We sought to investigate the solute-solvent effects of efavirenz by means of a combined qualitative study implementing UV-visible spectrophotometry, 1H NMR spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The UV spectrum displayed two main absorbance maxima, band I and band II at 246-260 and 291-295 nm, respectively. A general bathochromic shift was noticed from the non-polar solvent cyclohexane to the most polar solvent DMSO (≈ 13.69 nm) in band I and a smaller bathochromic (≈ 2.17 nm) and hyperchromic shift was observed in band II. We propose that these observations are due to the role of the amino (NH) and carbonyl (CO) functionalities which induce charge-transfer and intra- and inter-molecular hydrogen bonding. The aromatic and amine protons showed the most deshielded effects in the observed chemical shifts (δ) in the more polar DMSO-d6 solvent relative to CDCl3. The 1H NMR chemical shifts observed are due to the increased delocalization of the lone pair electrons of the amino nitrogen with increased polarity of the more polar DMSO solvent. The theoretical reproduction of the UV and 1H NMR spectra by means of TD-DFT is in good agreement with the experimental results.

Complexation of rhodium(II) tetracarboxylates with aliphatic diamines in solution: 1H and 13C NMR and DFT investigations.

PubMed

Jaźwiński, Jarosław; Sadlej, Agnieszka

2013-10-01

The complexation of rhodium(II) tetraacetate, tetrakistrifluoroaceate and tetrakisoctanoate with a set of diamines (ethane-1,diamine, propane-1,3-diamine and nonane-1,9-diamine) and their N,N'-dimethyl and N,N,N',N'-tetramethyl derivatives in chloroform solution has been investigated by (1) H and (13) C NMR spectroscopy and density functional theory (DFT) modelling. A combination of two bifunctional reagents, diamines and rhodium(II) tetracarboxylates, yielded insoluble coordination polymers as main products of complexation and various adducts in the solution, being in equilibrium with insoluble material. All diamines initially formed the 2 : 1 (blue), (1 : 1)n oligomeric (red) and 1 : 2 (red) axial adducts in solution, depending on the reagents' molar ratio. Adducts of primary and secondary diamines decomposed in the presence of ligand excess, the former via unstable equatorial complexes. The complexation of secondary diamines slowed down the inversion at nitrogen atoms in NH(CH3 ) functional groups and resulted in the formation of nitrogenous stereogenic centres, detectable by NMR. Axial adducts of tertiary diamines appeared to be relatively stable. The presence of long aliphatic chains in molecules (adducts of nonane-1,9-diamines or rhodium(II) tetrakisoctanoate) increased adduct solubility. Hypothetical structures of the equatorial adduct of rhodium(II) tetraacetate with ethane-1,2-diamine and their NMR parameters were explored by means of DFT calculations. Copyright © 2013 John Wiley & Sons, Ltd.

Spectral analysis of the Earth's topographic potential via 2D-DFT: a new data-based degree variance model to degree 90,000

NASA Astrophysics Data System (ADS)

Rexer, Moritz; Hirt, Christian

2015-09-01

Classical degree variance models (such as Kaula's rule or the Tscherning-Rapp model) often rely on low-resolution gravity data and so are subject to extrapolation when used to describe the decay of the gravity field at short spatial scales. This paper presents a new degree variance model based on the recently published GGMplus near-global land areas 220 m resolution gravity maps (Geophys Res Lett 40(16):4279-4283, 2013). We investigate and use a 2D-DFT (discrete Fourier transform) approach to transform GGMplus gravity grids into degree variances. The method is described in detail and its approximation errors are studied using closed-loop experiments. Focus is placed on tiling, azimuth averaging, and windowing effects in the 2D-DFT method and on analytical fitting of degree variances. Approximation errors of the 2D-DFT procedure on the (spherical harmonic) degree variance are found to be at the 10-20 % level. The importance of the reference surface (sphere, ellipsoid or topography) of the gravity data for correct interpretation of degree variance spectra is highlighted. The effect of the underlying mass arrangement (spherical or ellipsoidal approximation) on the degree variances is found to be crucial at short spatial scales. A rule-of-thumb for transformation of spectra between spherical and ellipsoidal approximation is derived. Application of the 2D-DFT on GGMplus gravity maps yields a new degree variance model to degree 90,000. The model is supported by GRACE, GOCE, EGM2008 and forward-modelled gravity at 3 billion land points over all land areas within the SRTM data coverage and provides gravity signal variances at the surface of the topography. The model yields omission errors of 9 mGal for gravity (1.5 cm for geoid effects) at scales of 10 km, 4 mGal (1 mm) at 2-km scales, and 2 mGal (0.2 mm) at 1-km scales.

Pulse Propagation Effects in Optical 2D Fourier-Transform Spectroscopy: Theory.

PubMed

Spencer, Austin P; Li, Hebin; Cundiff, Steven T; Jonas, David M

2015-04-30

A solution to Maxwell's equations in the three-dimensional frequency domain is used to calculate rephasing two-dimensional Fourier transform (2DFT) spectra of the D2 line of atomic rubidium vapor in argon buffer gas. Experimental distortions from the spatial propagation of pulses through the sample are simulated in 2DFT spectra calculated for the homogeneous Bloch line shape model. Spectral features that appear at optical densities of up to 3 are investigated. As optical density increases, absorptive and dispersive distortions start with peak shape broadening, progress to peak splitting, and ultimately result in a previously unexplored coherent transient twisting of the split peaks. In contrast to the low optical density limit, where the 2D peak shape for the Bloch model depends only on the total dephasing time, these distortions of the 2D peak shape at finite optical density vary with the waiting time and the excited state lifetime through coherent transient effects. Experiment-specific conditions are explored, demonstrating the effects of varying beam overlap within the sample and of pseudo-time domain filtering. For beam overlap starting at the sample entrance, decreasing the length of beam overlap reduces the line width along the ωτ axis but also reduces signal intensity. A pseudo-time domain filter, where signal prior to the center of the last excitation pulse is excluded from the FID-referenced 2D signal, reduces propagation distortions along the ωt axis. It is demonstrated that 2DFT rephasing spectra cannot take advantage of an excitation-detection transformation that can eliminate propagation distortions in 2DFT relaxation spectra. Finally, the high optical density experimental 2DFT spectrum of rubidium vapor in argon buffer gas [J. Phys. Chem. A 2013, 117, 6279-6287] is quantitatively compared, in line width, in depth of peak splitting, and in coherent transient peak twisting, to a simulation with optical density higher than that reported.

Synthesis and XRD, FT-IR vibrational, UV-vis, and nonlinear optical exploration of novel tetra substituted imidazole derivatives: A synergistic experimental-computational analysis

NASA Astrophysics Data System (ADS)

Ahmad, Muhammad Saeed; Khalid, Muhammad; Shaheen, Muhammad Ashraf; Tahir, Muhammad Nawaz; Khan, Muhammad Usman; Braga, Ataualpa Albert Carmo; Shad, Hazoor Ahmad

2018-04-01

Heterocyclic compounds have potential applications in many fields of life. We synthesized novel tetra substituted imidazoles by four-component condensation of benzil, substituted aldehydes, substituted anilines and ammonium acetate as a source of ammonia and acetic acid as the solvent. Their chemical structures were resolved through X-ray crystallographic and spectroscopic (Fourier transform IR and UV-vis) techniques. In addition to experimental analysis, density functional theory (DFT) calculations at the B3LYP/6-311 + G(d,p) level were performed on 4-bromo-2-(1-(4-methoxyphenyl)-4,5-diphenyl-1H-imidazole-2-yl)phenol (1), 4-bromo-2-(1-(1-naphthalen-yl)-4,5-diphenyl-1H-imidazole-2-yl)phenol (2), and 2-(1-(2-chlorophenyl)-4,5-diphenyl-1-H-imidazole-2-yl)-6-methoxyphenol (3) to obtain the optimized geometry and spectroscopic (Fourier transform IR and UV-vis) and non-linear optical properties. Frontier molecular orbital analysis was performed at the Hartee-Fock/6-311+g(d,p) and DFT/B3LYP/6-311+G(d,p) levels of theory. Natural bond orbital (NBO) and UV-vis spectral analyses were performed at the M06-2X/6-31+G(d,p) and time-dependent DFT/B3LYP/6-311+G(d,p) levels, respectively. Overall, the DFT findings show good agreement with the experimental data. The hyper conjugative interaction network, which is responsible for the stability of compounds 1, 2 and 3 was explored by the NBO approach. The global reactivity parameters were explored with use of the energy of the frontier molecular orbitals. DFT calculations predict the first-order hyperpolarizabilities of compounds 1, 2 and 3 are 294.89 × 10-30, 219.45 × 10-30 and 146.77 × 10-30 esu, respectively. A two-state model was used to describe the non-linear optical properties of the compounds investigated.

Prospective memory and its correlates and predictors in schizophrenia: an extension of previous findings.

PubMed

Ungvari, Gabor S; Xiang, Yu-Tao; Tang, Wai-Kwong; Shum, David

2008-09-01

Prospective memory (PM) is the ability to remember to do something in the future without explicit prompts. Extending the number of subjects and the scope of our previously published study, this investigation examined the relationship between PM and socio-demographic and clinical factors, activities of daily living (ADL) and frontal lobe functions in patients with chronic schizophrenia. One hundred and ten Chinese schizophrenia patients, 60 from the previous study and 50 additional patients recruited for this study, and 110 matched healthy comparison subjects (HC) formed the study sample. Patients' clinical condition and activity of daily living were evaluated with the Brief Psychiatric Rating Scale (BPRS) and the Functional Needs Assessment (FNA). Time- and event-based PM tasks and three tests of prefrontal lobe functions (Design Fluency Test [DFT], Tower of London [TOL], Wisconsin Card Sorting Test [WCST]) were also administered. Patients' level of ADL and psychopathology were not associated with PM functions and only anticholinergic medications (ACM) showed a significant negative correlational relationship with PM tasks. Confirming the findings of the previous study, patients performed significantly more poorly on all two PM tasks than HC. Performance on time-based PM task significantly correlated with age, education level and DFT in HC and with age, DFT, TOL and WCST in patients. Patients' performance on the event-based PM correlated with DFT and one measure of WCST. In patients, TOL and age predicted the performance on time-based PM task; DFT and WCST predicted the event-based task. Involving a large sample of patients with matched controls, this study confirmed that PM is impaired in chronic schizophrenia. Deficient PM functions were related to prefrontal lobe dysfunction in both HC and patients but not to the patients' clinical condition, nor did they significantly affect ADL. ACMs determined certain aspects of PM.

Ab Initio High Pressure and Temperature Investigation on Cubic PbMoO3 Perovskite

NASA Astrophysics Data System (ADS)

Dar, Sajad Ahmad; Srivastava, Vipul; Sakalle, Umesh Kumar

2017-12-01

A combined high pressure and temperature investigation on recently reported cubic perovskite PbMoO3 have been performed within the most accurate density functional theory (DFT). The structure was found stable in cubic paramagnetic phase. The DFT calculated analytical and experimental lattice constant were found in good agreement. The analytical tolerance factor as well as the elastic properties further verifies the cubic stability for PbMoO3. The spin polarized electronic band structure and density of states presented metallic nature with symmetry in up and down states. The insignificant magnetic moment also confirms the paramagnetic nature for the compound. The high pressure elastic and mechanical study up to 35 GPa reveal the structural stability of the material in this pressure range. The compound was found to establish a ductile nature. The electrical conductivity obtained from the band structure results show a decreasing trend with increasing temperature. The temperature dependence of thermodynamic parameters such as specific heat ( C v), thermal expansion ( α) has also been evaluated.

Density functional theory studies on the structures and electronic communication of meso-ferrocenylporphyrins: long range orbital coupling via porphyrin core.

PubMed

Zhang, Lijuan; Qi, Dongdong; Zhang, Yuexing; Bian, Yongzhong; Jiang, Jianzhuang

2011-02-01

The molecular and electronic structures together with the electronic absorption spectra of a series of metal free meso-ferrocenylporphyrins, namely 5-ferrocenylporphyrin (1), 5,10-diferrocenylporphyrin (2), 5,15-diferrocenylporphyrin (3), 5,10,15-triferrocenylporphyrin (4), and 5,10,15,20-tetraferrocenylporphyrin (5) have been studied with the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. For the purpose of comparative studies, metal free porphyrin without any ferrocenyl group (0) and isolated ferrocene (6) were also calculated. The effects of the number and position of meso-attached ferrocenyl substituents on their molecular and electronic structures, atomic charges, molecular orbitals, and electronic absorption spectra of 1-5 were systematically investigated. The orbital coupling is investigated in detail, explaining well the long range coupling of ferrocenyl substituents connected via porphyrin core and the systematic change in the electronic absorption spectra of porphyrin compounds. Copyright © 2010 Elsevier Inc. All rights reserved.

Effect of vacancy defects on generalized stacking fault energy of fcc metals.

PubMed

Asadi, Ebrahim; Zaeem, Mohsen Asle; Moitra, Amitava; Tschopp, Mark A

2014-03-19

Molecular dynamics (MD) and density functional theory (DFT) studies were performed to investigate the influence of vacancy defects on generalized stacking fault (GSF) energy of fcc metals. MEAM and EAM potentials were used for MD simulations, and DFT calculations were performed to test the accuracy of different common parameter sets for MEAM and EAM potentials in predicting GSF with different fractions of vacancy defects. Vacancy defects were placed at the stacking fault plane or at nearby atomic layers. The effect of vacancy defects at the stacking fault plane and the plane directly underneath of it was dominant compared to the effect of vacancies at other adjacent planes. The effects of vacancy fraction, the distance between vacancies, and lateral relaxation of atoms on the GSF curves with vacancy defects were investigated. A very similar variation of normalized SFEs with respect to vacancy fractions were observed for Ni and Cu. MEAM potentials qualitatively captured the effect of vacancies on GSF.

Mechanistic Investigation of Molybdate-Catalysed Transfer Hydrodeoxygenation.

PubMed

Larsen, Daniel B; Petersen, Allan R; Dethlefsen, Johannes R; Teshome, Ayele; Fristrup, Peter

2016-11-07

The molybdate-catalysed transfer hydrodeoxygenation (HDO) of benzyl alcohol to toluene driven by oxidation of the solvent isopropyl alcohol to acetone has been investigated by using a combination of experimental and computational methods. A Hammett study that compared the relative rates for the transfer HDO of five para-substituted benzylic alcohols was carried out. Density-functional theory (DFT) calculations suggest a transition state with significant loss of aromaticity contributes to the lack of linearity observed in the Hammett study. The transfer HDO could also be carried out in neat PhCH 2 OH at 175 °C. Under these conditions, PhCH 2 OH underwent disproportionation to yield benzaldehyde, toluene, and significant amounts of bibenzyl. Isotopic-labelling experiments (using PhCH 2 OD and PhCD 2 OH) showed that incorporation of deuterium into the resultant toluene originated from the α position of benzyl alcohol, which is in line with the mechanism suggested by the DFT study. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental and theoretical investigation of relative optical band gaps in graphene generations

NASA Astrophysics Data System (ADS)

Bhatnagar, Deepika; Singh, Sukhbir; Yadav, Sriniwas; Kumar, Ashok; Kaur, Inderpreet

2017-01-01

Size and chemical functionalization dependant optical band gaps in graphene family nanomaterials were investigated by experimental and theoretical study using Tauc plot and density functional theory (DFT). We have synthesized graphene oxide through a modified Hummer’s method using graphene nanoplatelets and sequentially graphene quantum dots through hydrothermal reduction. The experimental results indicate that the optical band gap in graphene generations was altered by reducing the size of graphene sheets and attachment of chemical functionalities like epoxy, hydroxyl and carboxyl groups plays a crucial role in varying optical band gaps. It is further confirmed by DFT calculations that the π orbitals were more dominatingly participating in transitions shown by projected density of states and the molecular energy spectrum represented the effect of attached functional groups along with discreteness in energy levels. Theoretical results were found to be in good agreement with experimental results. All of the above different variants of graphene can be used in native or modified form for sensor design and optoelectronic applications.

Adsorption behavior of Fe atoms on a naphthalocyanine monolayer on Ag(111) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Ling -Hao; Wu, Rong -Ting; Bao, De -Liang

2015-05-29

Adsorption behavior of Fe atoms on a metal-free naphthalocyanine (H 2Nc) monolayer on Ag(111) surface at room temperature has been investigated using scanning tunneling microscopy combined with density functional theory (DFT) based calculations. We found that the Fe atoms adsorbed at the centers of H 2Nc molecules and formed Fe-H 2Nc complexes at low coverage. DFT calculations show that the configuration of Fe at the center of a molecule is the most stable site, in good agreement with the experimental observations. After an Fe-H 2Nc complex monolayer was formed, the extra Fe atoms self-assembled to Fe clusters of uniform sizemore » and adsorbed dispersively at the interstitial positions of Fe-H 2Nc complex monolayer. Furthermore, the H 2Nc monolayer grown on Ag(111) could be a good template to grow dispersed magnetic metal atoms and clusters at room temperature for further investigation of their magnetism-related properties.« less

Invited Paper - Density functional theory: coverage of dynamic and non-dynamic electron correlation effects

NASA Astrophysics Data System (ADS)

Cremer, Dieter

The electron correlation effects covered by density functional theory (DFT) can be assessed qualitatively by comparing DFT densities ρ(r) with suitable reference densities obtained with wavefunction theory (WFT) methods that cover typical electron correlation effects. The analysis of difference densities ρ(DFT)-ρ(WFT) reveals that LDA and GGA exchange (X) functionals mimic non-dynamic correlation effects in an unspecified way. It is shown that these long range correlation effects are caused by the self-interaction error (SIE) of standard X functionals. Self-interaction corrected (SIC) DFT exchange gives, similar to exact exchange, for the bonding region a delocalized exchange hole, and does not cover any correlation effects. Hence, the exchange SIE is responsible for the fact that DFT densities often resemble MP4 or MP2 densities. The correlation functional changes X-only DFT densities in a manner observed when higher order coupling effects between lower order N-electron correlation effects are included. Hybrid functionals lead to changes in the density similar to those caused by SICDFT, which simply reflects the fact that hybrid functionals have been developed to cover part of the SIE and its long range correlation effects in a balanced manner. In the case of spin-unrestricted DFT (UDFT), non-dynamic electron correlation effects enter the calculation both via the X functional and via the wavefunction, which may cause a double-counting of correlation effects. The use of UDFT in the form of permuted orbital and broken-symmetry DFT (PO-UDFT, BS-UDFT) can lead to reasonable descriptions of multireference systems provided certain conditions are fulfilled. More reliable, however, is a combination of DFT and WFT methods, which makes the routine description of multireference systems possible. The development of such methods implies a separation of dynamic and non-dynamic correlation effects. Strategies for accomplishing this goal are discussed in general and tested in practice for CAS (complete active space)-DFT.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

2016-03-01

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de

2016-03-21

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). Formore » the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.« less

Communication: Density functional theory embedding with the orthogonality constrained basis set expansion procedure

NASA Astrophysics Data System (ADS)

Culpitt, Tanner; Brorsen, Kurt R.; Hammes-Schiffer, Sharon

2017-06-01

Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT.

Energy level alignment and quantum conductance of functionalized metal-molecule junctions: Density functional theory versus GW calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Chengjun; Markussen, Troels; Thygesen, Kristian S., E-mail: thygesen@fysik.dtu.dk

We study the effect of functional groups (CH{sub 3}*4, OCH{sub 3}, CH{sub 3}, Cl, CN, F*4) on the electronic transport properties of 1,4-benzenediamine molecular junctions using the non-equilibrium Green function method. Exchange and correlation effects are included at various levels of theory, namely density functional theory (DFT), energy level-corrected DFT (DFT+Σ), Hartree-Fock and the many-body GW approximation. All methods reproduce the expected trends for the energy of the frontier orbitals according to the electron donating or withdrawing character of the substituent group. However, only the GW method predicts the correct ordering of the conductance amongst the molecules. The absolute GWmore » (DFT) conductance is within a factor of two (three) of the experimental values. Correcting the DFT orbital energies by a simple physically motivated scissors operator, Σ, can bring the DFT conductances close to experiments, but does not improve on the relative ordering. We ascribe this to a too strong pinning of the molecular energy levels to the metal Fermi level by DFT which suppresses the variation in orbital energy with functional group.« less

Small-Animal Imaging Using Diffuse Fluorescence Tomography.

PubMed

Davis, Scott C; Tichauer, Kenneth M

2016-01-01

Diffuse fluorescence tomography (DFT) has been developed to image the spatial distribution of fluorescence-tagged tracers in living tissue. This capability facilitates the recovery of any number of functional parameters, including enzymatic activity, receptor density, blood flow, and gene expression. However, deploying DFT effectively is complex and often requires years of know-how, especially for newer mutlimodal systems that combine DFT with conventional imaging systems. In this chapter, we step through the process of using MRI-DFT imaging of a receptor-targeted tracer in small animals.

Assessment of TD-DFT and LF-DFT for study of d − d transitions in first row transition metal hexaaqua complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlahović, Filip; Perić, Marko; Zlatar, Matija, E-mail: matijaz@chem.bg.ac.rs

2015-06-07

Herein, we present the systematic, comparative computational study of the d − d transitions in a series of first row transition metal hexaaqua complexes, [M(H{sub 2}O){sub 6}]{sup n+} (M{sup 2+/3+} = V {sup 2+/3+}, Cr{sup 2+/3+}, Mn{sup 2+/3+}, Fe{sup 2+/3+}, Co{sup 2+/3+}, Ni{sup 2+}) by the means of Time-dependent Density Functional Theory (TD-DFT) and Ligand Field Density Functional Theory (LF-DFT). Influence of various exchange-correlation (XC) approximations have been studied, and results have been compared to the experimental transition energies, as well as, to the previous high-level ab initio calculations. TD-DFT gives satisfactory results in the cases of d{sup 2}, d{supmore » 4}, and low-spin d{sup 6} complexes, but fails in the cases when transitions depend only on the ligand field splitting, and for states with strong character of double excitation. LF-DFT, as a non-empirical approach to the ligand field theory, takes into account in a balanced way both dynamic and non-dynamic correlation effects and hence accurately describes the multiplets of transition metal complexes, even in difficult cases such as sextet-quartet splitting in d{sup 5} complexes. Use of the XC functionals designed for the accurate description of the spin-state splitting, e.g., OPBE, OPBE0, or SSB-D, is found to be crucial for proper prediction of the spin-forbidden excitations by LF-DFT. It is shown that LF-DFT is a valuable alternative to both TD-DFT and ab initio methods.« less

Oxygen vacancy diffusion in bulk SrTiO3 from density functional theory calculations

DOE PAGES

Zhang, Lipeng; Liu, Bin; Zhuang, Houlong; ...

2016-04-01

Point defects and point defect diffusion contribute significantly to the properties of perovskite materials. However, even for the prototypical case of oxygen vacancies in SrTiO 3 (STO), predictions vary widely. Here we present a comprehensive and systematic study of the diffusion barriers for this material. We use density functional theory (DFT) and assess the role of different cell sizes, density functionals, and charge states. Our results show that vacancy-induced octahedral rotations, which are limited by the boundary conditions of the supercell, can significantly affect the computed oxygen vacancy diffusion energy barrier. The diffusion energy barrier of a charged oxygen vacancymore » is lower than that of a neutral one. Unexpectedly, we find that with increasing supercell size, the effects of the oxygen vacancy charge state, the type of DFT exchange and correlation functional on the energy barrier diminish, and the different DFT predictions asymptote to a value in the range of 0.39-0.49 eV. This work provides important insight and guidance that should be considered for investigations of point defect diffusion in other perovskite materials and in oxide superlattices.« less

Chromocene in porous polystyrene: an example of organometallic chemistry in confined spaces.

PubMed

Estephane, Jane; Groppo, Elena; Vitillo, Jenny G; Damin, Alessandro; Lamberti, Carlo; Bordiga, Silvia; Zecchina, Adriano

2009-04-07

In this work, we present an innovative approach to investigate the structure and the reactivity of a molecularly dispersed organometallic compound. The poly(4-ethylstyrene-co-divinylbenzene) microporous system (PS) is used as "solid solvent" able to molecularly disperse CrCp2, allowing: (i) its full characterization by means of spectroscopic techniques; (ii) the pressure and temperature dependent study of its interaction towards simple molecules like CO freely diffusing through the pores; (iii) the accurate determination of the reaction enthalpies by both direct microcalorimetric measurements and by an indirect spectroscopic approach. The experimental results are compared with quantum-mechanical calculations adopting the DFT approximation with two different functionals (namely BP86 and B3-LYP), showing the limitations and the potentialities of DFT methods in predicting the properties of open shell systems. It is concluded that modern DFT methods are able to give a coherent view of the vibrational properties of the CrCp2 molecule (and of the complex formed upon CO adsorption) that well match the experimental results, while the energetic predictions should be taken with care as they are significantly dependent on the functionals used.

Molecular conformational analysis, vibrational spectra and normal coordinate analysis of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene based on density functional theory calculations.

PubMed

Joseph, Lynnette; Sajan, D; Chaitanya, K; Isac, Jayakumary

2014-03-25

The conformational behavior and structural stability of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene (TDBE) were investigated by using density functional theory (DFT) method with the B3LYP/6-311++G(d,p) basis set combination. The vibrational wavenumbers of TDBE were computed at DFT level and complete vibrational assignments were made on the basis of normal coordinate analysis calculations (NCA). The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The infrared and Raman spectra were also predicted from the calculated intensities. The observed Fourier transform infrared (FTIR) and Fourier transform (FT) Raman vibrational wavenumbers were analyzed and compared with the theoretically predicted vibrational spectra. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Copyright © 2013 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okutsu, N.; Shimamura, K.; Shimizu, E.

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-Cmore » base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.« less

DFT+DMFT study of strain and interface effects in d1 and d2 t2 g-perovskites

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dymkowski, Krzysztof; Ederer, Claude

2015-03-01

Metal-insulator transitions in thin films of early-transition metal correlated oxides are linked to both epitaxial strain and electronic reconstruction at the film/substrate interface. We separately address these two key factors for LaTiO3 and LaVO3 through density functional theory plus dynamical mean-field theory (DFT+DMFT). We find that mere epitaxial strain suffices to induce an insulator-to-metal transition in LaTiO3, but not in LaVO3, in agreement with recent experiments. We show that this difference can be explained by the combined effect of strain-induced changes in the crystal field splitting of t2 g orbitals and different orbital filling in these two materials. The role of the interface is investigated through DFT+DMFT simulations of LaVO3/SrTiO3 heterostructures with varying superlattice periodicities and substrate terminations. Our aim is to assess whether the metallicity observed at the LaVO3/SrTiO3 interface could be driven by pure electronic reconstruction effects, rather than structural or stoichiometric reasons (such as, e.g., O-related defects).

Performance of some nucleation theories with a nonsharp droplet-vapor interface.

PubMed

Napari, Ismo; Julin, Jan; Vehkamäki, Hanna

2010-10-21

Nucleation theories involving the concept of nonsharp boundary between the droplet and vapor are compared to recent molecular dynamics (MD) simulation data of Lennard-Jones vapors at temperatures above the triple point. The theories are diffuse interface theory (DIT), extended modified liquid drop-dynamical nucleation theory (EMLD-DNT), square gradient theory (SGT), and density functional theory (DFT). Particular attention is paid to thermodynamic consistency in the comparison: the applied theories either use or, with a proper parameter adjustment, result in the same values of equilibrium vapor pressure, bulk liquid density, and surface tension as the MD simulations. Realistic pressure-density correlations are also used. The best agreement between the simulated nucleation rates and calculations is obtained from DFT, SGT, and EMLD-DNT, all of which, in the studied temperature range, show deviations of less than one order of magnitude in the nucleation rate. DIT underestimates the nucleation rate by up to two orders of magnitude. DFT and SGT give the best estimate of the molecular content of the critical nuclei. Overall, at the vapor conditions of this study, all the investigated theories perform better than classical nucleation theory in predicting nucleation rates.

Investigation of the Fe{sup 3+} centers in perovskite KMgF{sub 3} through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emül, Y.; Department of Software Engineering, Cumhuriyet University, 58140 Sivas; Erbahar, D.

2015-08-14

Analyses of the local crystal and electronic structure in the vicinity of Fe{sup 3+} centers in perovskite KMgF{sub 3} crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe{sup 3+} centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe{sup 3+} centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe{sup 3+} center case), FeF{sub 5}Omore » cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe{sup 3+} centers in KMgF{sub 3}.« less

Electronic and magnetic properties of small rhodium clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework.more » The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.« less

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-01

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

Experimental and theoretical studies of (FT-IR, FT-Raman, UV-Visible and DFT) 4-(6-methoxynaphthalen-2-yl) butan-2-one.

PubMed

Govindasamy, P; Gunasekaran, S

2015-01-01

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000-50 cm(-1) and 4000-450 cm(-1) respectively for 4-(6-methoxynaphthalen-2-yl) butan-2-one (abbreviated as 4MNBO) molecule. Theoretical calculations were performed by density functional theory (DFT/B3LYP) method using 6-311G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and calculated wavenumber value of most of the fundamentals were very small. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The UV-Vis spectrum was recorded in the methanol solution. The energy, wavelength and oscillator's strength were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Thermodynamic properties of 4MNBO at different temperature have been calculated. The molecular electrostatic potential surface (MESP) and Frontier molecular orbital's (FMO's) analysis were investigated using theoretical calculations. Copyright © 2015 Elsevier B.V. All rights reserved.

Vibrational frequency analysis, FT-IR, DFT and M06-2X studies on tert-Butyl N-(thiophen-2yl)carbamate.

PubMed

Sert, Yusuf; Singer, L M; Findlater, M; Doğan, Hatice; Çırak, Ç

2014-07-15

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized tert-Butyl N-(thiophen-2yl)carbamate have been investigated. The experimental FT-IR (4000-400 cm(-1)) spectrum of the molecule in the solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with the 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The vibrational frequencies have been assigned using potential energy distribution (PED) analysis by using VEDA 4 software. The computational optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with related literature results. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and are depicted. Copyright © 2014 Elsevier B.V. All rights reserved.

Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of 2,3,4,5,6-Pentafluoro-trans-cinnamic acid

NASA Astrophysics Data System (ADS)

Sert, Yusuf; Doğan, Hatice; Navarrete, Angélica; Somanathan, Ratnasamy; Aguirre, Gerardo; Çırak, Çağrı

2014-07-01

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized 2,3,4,5,6-Pentafluoro-trans-cinnamic acid have been investigated. The experimental FT-IR (4000-400 cm-1) and Laser-Raman spectra (4000-100 cm-1) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates.

PubMed

Masson, Olivier; Berghout, Abid; Béchade, Emilie; Jouin, Jenny; Thomas, Philippe; Asaka, Toru; Fukuda, Koichiro

2017-01-01

The local structure of apatite-type lanthanum silicates of general formula La 9.33+x (SiO 4 ) 6 O 2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO 4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions.

A comparison between artificial and natural water oxidation.

PubMed

Li, Xichen; Chen, Guangju; Schinzel, Sandra; Siegbahn, Per E M

2011-11-14

Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems. A recent high resolution X-ray structural investigation of PSII has confirmed the main features of the structure of the oxygen evolving complex (OEC) suggested by previous DFT cluster studies. The O-O bond formation mechanism suggested is of direct coupling (DC) type between an oxygen radical and a bridging oxo ligand. A similar DC mechanism is found for the Llobet catalyst, while an acid-base (AB) mechanism is preferred for the blue dimer. All of them require at least one oxygen radical. Full energy diagrams, including both redox and chemical steps, have been constructed illustrating similarities and differences to the natural system. Unlike previous DFT studies, the results of the present study suggest that the blue dimer is rate-limited by the initial redox steps, and the Llobet catalyst by O(2) release. The results could be useful for further improvement of the artificial systems.

Crystal growth, spectroscopic, DFT computational and third harmonic generation studies of nicotinic acid

NASA Astrophysics Data System (ADS)

Thaya Kumari, C. Rathika; Nageshwari, M.; Raman, R. Ganapathi; Caroline, M. Lydia

2018-07-01

An organic centrosymmetric nicotinic acid (NA) single crystal has been grown employing slow evaporation method in water. NA crystallizes in monoclinic system with centric space group P21/C. The experimental and theoretical investigation includes vibrational spectra based on Hartree - Fock (HF) and density functional theory (DFT) has been applied using different function at B3LYP level of theory using 6-311G++(d,p) basis set. The optical transparency of the title molecule was examined by TD- DFT analysis and for comparison basis experimental UV-Vis spectrum was recorded. The interaction of charge within the molecule was analyzed and the HOMO - LUMO energy gap was evaluated. The value of dipole moment, Mulliken charge and molecular electrostatic potential were estimated at the same level of theory. Also the first order hyper polarizability for NA was calculated. The dielectric behavior of the grown crystal was determined for few selected temperatures. The third order nonlinear response of NA has been examined using Z-scan technique and nonlinear susceptibility (χ3), nonlinear refraction (n2) and nonlinear absorption coefficient (β) has been calculated. The current results clearly indicate that the title compound is an excellent applicant in the domain of opto - electronic applications.

Multifunctional Composites of Chiral Valine Derivative Schiff Base Cu(II) Complexes and TiO2

PubMed Central

Takeshita, Yuki; Takakura, Kazuya; Akitsu, Takashiro

2015-01-01

We have prepared four new Cu(II) complexes containing valine moieties with imidazole ligands at the fourth coordination sites and examined their photo-induced reactions with TiO2 in order of understanding the reaction mechanisms. Under a nitrogen atmosphere, the intermolecular electron transfer reactions (essentially supramolecular interactions) of these systems, which resulted in the reduction of Cu(II) species to Cu(I) ones, occurred after UV light irradiation. In this study, we have investigated the conditions of the redox reactions in view of substituent effects of aldehyde moieties. The results of cyclic voltammetry (CV) on an rotating ring-disk electrode (RRDE) suggested that the substitution effects and redox potentials were correlated. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were also performed to simulate the UV–Vis and circular dichroism (CD) spectra; the results revealed a reasonably good correlation between the substituent effects and the highest occupied molecular orbitals and the lowest unoccupied molecular orbitals (HOMO-LUMO) gaps associated with the most intense transition bands. In addition, we summarized the substitution effects of Cu(II) complexes for their corresponding UV light-induced reactions. PMID:25686033

Band-edge engineering of Silicon by Surface Functionalization: a Combined Ab-initio and Photoemission Study

NASA Astrophysics Data System (ADS)

Li, Yan; O'Leary, Leslie; Lewis, Nathan; Galli, Giulia

2012-02-01

The electrode material choice is limited in solar to fuel formation devices because of the requirement of band-edge matching to the fixed fuel formation potential. This limitation can be relieved via band-edge engineering. The changes of band-edge positions of Si electrodes induced by the adsorption of H-, Cl-, Br- and short-chain alkyl groups were investigated by combining density functional (DFT), many-body perturbation theory (MBPT), and ultraviolet photoelectron spectroscopy. The band edge shifts are related to the formation of surface dipole moments, and determine the barrier height of electrons and holes in doped silicon surfaces. We find that the trends of the sign and magnitude of the computed surface dipoles as a function of the adsorbate may be explained by simple electronegative rules. We show that quasi-particle energies obtained within MBPT are in good agreement with experiment, while DFT values may exhibit substantial errors. However computed band edge differences are in good agreement with spectroscopic and electrical measurements even at the DFT level of theory. [1] Y. Li and G. Galli, Phys. Rev. B 82, 045321 (2010). [2] Y. Li, L. O'Leary, N. Lewis and G. Galli, to be submitted.

Structural investigation, spectroscopic and energy level studies of Schiff base: 2-[(3‧-N-salicylidenephenyl)benzimidazole] using experimental and DFT methods

NASA Astrophysics Data System (ADS)

Suman, G. R.; Bubbly, S. G.; Gudennavar, S. B.; Muthu, S.; Roopashree, B.; Gayatri, V.; Nanje Gowda, N. M.

2017-07-01

The Schiff base 2-[(3‧-N-salicylidenephenyl)benzimidazole] (Spbzl) was characterized by FT-Raman, 1H NMR, 13C NMR and single crystal X-ray diffraction technique. Crystallographic studies reveal the presence of two water molecules in the asymmetry unit which aid the intermolecular hydrogen bonding with imidazole ring, and the trans-conformation of the azomethine bond. Theoretical computations conducted using density functional theory (DFT) analysis support the experimental facts. Energy levels estimated by DFT studies are in good agreement with the values obtained from cyclic voltammetry technique. Frontier molecular orbital analysis shows that charge transfer has taken place from donor to acceptor moiety, which is also supported by the high hyperpolarizability values in both gaseous and solution phases, indicating high charge transfer capability of the molecule. A comparative theoretical study of Spbzl with derivative 4-((3-(1H-benzimidazol-2-yl)phenylimino)methyl)-3-hydroxybenzoic acid (Pbzlb) having an added anchor group COOH substituted at para position in the acceptor ring has been made. The result shows the feasibility of charge transfer to the semiconductor surface in dye sensitized solar cell (DSSC) applications for Pbzlb.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms.

PubMed

Mohamed, Gehad G; Hamed, Maher M; Zaki, Nadia G; Abdou, Mohamed M; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-05

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL -1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase. Copyright © 2017 Elsevier B.V. All rights reserved.

Triphenylamine based organic dyes for dye sensitized solar cells: A theoretical approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohankumar, V.; Pandian, Muthu Senthil; Ramasamy, P., E-mail: ramasamyp@ssn.edu.in

2016-05-23

The geometry, electronic structure and absorption spectra for newly designed triphenylamine based organic dyes were investigated by density functional theory (DFT) and time dependent density functional theory (TD-DFT) with the Becke 3-Parameter-Lee-Yang-parr(B3LYP) functional, where the 6-31G(d,p) basis set was employed. All calculations were performed using the Gaussian 09 software package. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Ultraviolet–visible (UV–vis) spectrum was simulated by TD-DFT in gas phase. The calculation shows that all of the dyes can potentially be good sensitizers for DSSC. The LUMOs are just above the conduction band of TiO{sub 2}more » and their HOMOs are under the reduction potential energy of the electrolytes (I{sup −}/I{sub 3}{sup −}) which can facilitate electron transfer from the excited dye to TiO{sub 2} and charge regeneration process after photo oxidation respectively. The simulated absorption spectrum of dyes match with solar spectrum. Frontier molecular orbital results show that among all the three dyes, the “dye 3” can be used as potential sensitizer for DSSC.« less

High performance of mixed halide perovskite solar cells: Role of halogen atom and plasmonic nanoparticles on the ideal current density of cell

NASA Astrophysics Data System (ADS)

Mohebpour, Mohammad Ali; Saffari, Mohaddeseh; Soleimani, Hamid Rahimpour; Tagani, Meysam Bagheri

2018-03-01

To be able to increase the efficiency of perovskite solar cells which is one of the most substantial challenges ahead in photovoltaic industry, the structural and optical properties of perovskite CH3NH3PbI3-xBrx for values x = 1-3 have been studied employing density functional theory (DFT). Using the optical constants extracted from DFT calculations, the amount of light reflectance and ideal current density of a simulated single-junction perovskite solar cell have been investigated. The results of DFT calculations indicate that adding halogen bromide to CH3NH3PbI3 compound causes the relocation of energy bands in band structure which its consequence is increasing the bandgap. In addition, the effect of increasing Br in this structure can be seen as a reduction in lattice constant, refractive index, extinction and absorption coefficient. As well, results of the simulation suggest a significant current density enhancement as much as 22% can be achieved by an optimized array of Platinum nanoparticles that is remarkable. This plan is able to be a prelude for accomplishment of solar cells with higher energy conversion efficiency.

Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates

PubMed Central

Masson, Olivier; Berghout, Abid; Béchade, Emilie; Jouin, Jenny; Thomas, Philippe; Asaka, Toru; Fukuda, Koichiro

2017-01-01

Abstract The local structure of apatite-type lanthanum silicates of general formula La9.33+x(SiO4)6O2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions. PMID:28970872

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates

NASA Astrophysics Data System (ADS)

Masson, Olivier; Berghout, Abid; Béchade, Emilie; Jouin, Jenny; Thomas, Philippe; Asaka, Toru; Fukuda, Koichiro

2017-12-01

The local structure of apatite-type lanthanum silicates of general formula La9.33+x(SiO4)6O2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions.

An EQT-cDFT approach to determine thermodynamic properties of confined fluids.

PubMed

Mashayak, S Y; Motevaselian, M H; Aluru, N R

2015-06-28

We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.

Hydrogen bond strengthening between o-nitroaniline and formaldehyde in electronic excited states: A theoretical study

NASA Astrophysics Data System (ADS)

Yang, Juan; Li, An Yong

2018-06-01

To study the hydrogen bonds upon photoexcited, the time dependent density function method (TD DFT) was performed to investigate the excited state hydrogen bond properties of between o-nitroaniline (ONA) and formaldehyde (CH2O). The optimized structures of the complex and the monomers both in the ground state and the electronically excited states are calculated using DFT and TD DFT method respectively. Quantum chemical calculations of the electronic and vibrational absorption spectra are also carried out by TD DFT method at the different level. The complex ONA⋯CH2O forms the intramolecular hydrogen bond and intermolecular hydrogen bonds. Since the strength of hydrogen bonds can be measured by studying the vibrational absorption spectra of the characteristic groups on the hydrogen bonding acceptor and donor, it evidently confirms that the hydrogen bonds is strengthened in the S1/S2/T1 excited states upon photoexcitation. As a result, the hydrogen bonds cause that the CH stretch frequency of the proton donor CH2O has a blue shift, and the electron excitations leads to a frequency red shift of Ndbnd O and Nsbnd H stretch modes in the o-nitroaniline(ONA) and a small frequency blue shift of CH stretch mode in the formaldehyde(CH2O) in the S1 and S2 excited states. The excited states S1, S2 and T1 are locally excited states where only the ONA moiety is excited, but the CH2O moiety remains in its ground state.

Melamine derivatives as effective corrosion inhibitors for mild steel in acidic solution: Chemical, electrochemical, surface and DFT studies

NASA Astrophysics Data System (ADS)

Verma, Chandrabhan; Haque, J.; Ebenso, Eno E.; Quraishi, M. A.

2018-06-01

In present study two condensation products of melamine (triazine) and glyoxal namely, 2,2-bis(4,6-diamino-1,3,5-triazin-2-ylamino)acetaldehyde (ME-1) and (N2,N2‧E,N2,N2‧E)-N2,N2‧-(ethane-1,2-diylidene)-bis-(1,3,5-triazine-2,4,6-triamine) (ME-2) are tested as mild steel corrosion inhibitors in acidic solution (1M HCl). The inhibition efficiency of ME-1 and ME-2 increases with increase in their concentrations and maximum values of 91.47% and 94.88% were derived, respectively at 100 mgL-1 (34.20 × 10-5 M) concentration. Adsorption of ME-1 and ME-2 on the surface of metal obeyed the Langmuir adsorption isotherm. Polarization investigation revealed that ME-1 and ME-2 act as mixed type inhibitors with minor cathodic prevalence. The chemical and electrochemical analyses also supported by surface characterization methods where significant smoothness in the surface morphologies was observed in the images of SEM and AFM spectra. Several DFT indices such as EHOMO and ELUMO, ΔE, η, σ, χ, μ and ΔN were derived for both ME-1 and ME-2 molecules and correlated with experimental results. The DFT studies have also been carried out for protonated or cationic form of the inhibitor molecules by considering that in acidic medium the heteroatoms of organic inhibitors easily undergo protonation. The experimental and density functional theory (DFT) studies (neutral and protonated) were in good agreement.

Ground state of Ho atoms on Pt(111) metal surfaces: Implications for magnetism

NASA Astrophysics Data System (ADS)

Karbowiak, M.; Rudowicz, C.

2016-05-01

We investigated the ground state of Ho atoms adsorbed on the Pt(111) surface, for which conflicting results exist. The density functional theory (DFT) calculations yielded the Ho ground state as | Jz=±8 > . Interpretation of x-ray absorption spectroscopy and x-ray magnetic circular dichroism spectra and the magnetization curves indicated the ground state as | Jz=±6 > . Superposition model is employed to predict the crystal-field (CF) parameters based on the structural data for the system Ho/Pt(111) obtained from the DFT modeling. Simultaneous diagonalization of the free-ion (HFI) and the trigonal CF Hamiltonian (HCF) within the whole configuration 4 f10 of H o3 + ion was performed. The role of the trigonal CF terms, neglected in the pure uniaxial CF model used previously for interpretation of experimental spectra, is found significant, whereas the sixth-rank CF terms may be neglected in agreement with the DFT predictions. The results provide substantial support for the experimental designation of the | Jz=±6 > ground state, albeit with subtle difference due to admixture of other | Jz> states, but run against the DFT-based designation of the | Jz=±8 > ground state. A subtle splitting of the ground energy level with the state (predominantly), | Jz=±6 > is predicted. This paper provides better insight into the single-ion magnetic behavior of the Ho/Pt(111) system by helping to resolve the controversy concerning the Ho ground state. Experimental techniques with greater resolution powers are suggested for direct confirmation of this splitting and C3 v symmetry experienced by the Ho atom.

Ab-initio and DFT methodologies for computing hyperpolarizabilities and susceptibilities of highly conjugated organic compounds for nonlinear optical applications

NASA Astrophysics Data System (ADS)

Karakas, A.; Karakaya, M.; Ceylan, Y.; El Kouari, Y.; Taboukhat, S.; Boughaleb, Y.; Sofiani, Z.

2016-06-01

In this talk, after a short introduction on the methodologies used for computing dipole polarizability (α), second and third-order hyperpolarizability and susceptibility; the results of theoretical studies performed on density functional theory (DFT) and ab-initio quantum mechanical calculations of nonlinear optical (NLO) properties for a few selected organic compounds and polymers will be explained. The electric dipole moments (μ) and dispersion-free first hyperpolarizabilities (β) for a family of azo-azulenes and a styrylquinolinium dye have been determined by DFT at B3LYP level. To reveal the frequency-dependent NLO behavior, the dynamic α, second hyperpolarizabilities (γ), second (χ(2)) and third-order (χ(3)) susceptibilites have been evaluated using time-dependent HartreeFock (TDHF) procedure. To provide an insight into the third-order NLO phenomena of a series of pyrrolo-tetrathiafulvalene-based molecules and pushpull azobenzene polymers, two-photon absorption (TPA) characterizations have been also investigated by means of TDHF. All computed results of the examined compounds are compared with their previous experimental findings and the measured data for similar structures in the literature. The one-photon absorption (OPA) characterizations of the title molecules have been theoretically obtained by configuration interaction (CI) method. The highest occupied molecular orbitals (HOMO), the lowest unoccupied molecular orbitals (LUMO) and the HOMO-LUMO band gaps have been revealed by DFT at B3LYP level for azo-azulenes, styrylquinolinium dye, push-pull azobenzene polymers and by parametrization method 6 (PM6) for pyrrolo-tetrathiafulvalene-based molecules.

Search for effective spin injection heterostructures based on half-metal Heusler alloys/gallium arsenide semiconductors: A theoretical investigation

NASA Astrophysics Data System (ADS)

Sivakumar, Chockalingam

Efficient electrical spin injection from half-metal (HM) electrodes into semiconducting (SC) channel material is a desirable aspect in spintronics, but a challenging one. Half-metals based on the Heusler alloy family are promising candidates as spin sources due to their compatibility with compound SCs, and very high Curie temperatures. Numerous efforts were made in the past two decades to grow atomically abrupt interfaces between HM_Heusler and SC heterostructures. However, diffusion of magnetic impurities into the semiconductor, defects and disorder near the interface, and formation of reacted phases were great challenges. A number of theoretical efforts were undertaken to understand the role of such material defects in destroying the half-metallicity and also to propose promising half-metal/SC heterostructures based on first principles. This dissertation summarizes the investigations undertaken to decode the complexity of, and to understand the various physical properties of, a number of real-world Heusler/SC heterostructure samples, based on the ab initio density functional theory (DFT) approach. In addition, it summarizes various results from the first principles-based search for promising half-metal/SC heterostructures. First, I present results from DFT-based predictive models of actual Co 2MnSi (CMS)/GaAs heterostructures grown in (001) texture. I investigate the physical, chemical, electronic, and magnetic properties to understand the complexity of these structures and to pinpoint the origin of interfacial effects, when present. Based on the investigations of such models, I discuss the utility of those actual samples in spintronic applications. Next, I summarise the results from an ab initio DFT-based survey of 6 half-Heusler half-metal/GaAs heterostructure models in (110) texture, since compound semiconductors such as GaAs have very long spin lifetime in (110) layering. I show 3 half-Heusler alloys (CoVAs, NiMnAs, and RhFeGe), that when interfaced with GaAs(110), fully preserve the half-metallicity at the interface. Finally, I show the advantages of inserting half-Heusler SCs, particularly CoTiAs and CoTiSb, as spacers in between CMS/GaAs systems in (110) layering. Based on DFT calculations, I show that CoTiAs is a promising spacer that could enhance the perpendicular magnetic anisotropy in CMS, while preserving the important half-metallic character at the heterojunctions between CMS/CoTiAs/GaAs(110). This spacer could also serve to prevent in-diffusion of magnetic impurities into the channel material.

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

NASA Astrophysics Data System (ADS)

Mishra, Soni; Tandon, Poonam; Eravuchira, Pinkie J.; El-Abassy, Rasha M.; Materny, Arnulf

2013-03-01

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4,5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule.

Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift.

PubMed

Kanematsu, Yusuke; Tachikawa, Masanori

2014-04-28

We have developed the multicomponent hybrid density functional theory [MC_(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC_(HF+DFT) method with PCM (MC_B3LYP/PCM). Our MC_B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents.

Accurate Induction Energies for Small Organic Molecules. 2. Development and Testing of Distributed Polarizability Models against SAPT(DFT) Energies.

PubMed

Misquitta, Alston J; Stone, Anthony J; Price, Sarah L

2008-01-01

In part 1 of this two-part investigation we set out the theoretical basis for constructing accurate models of the induction energy of clusters of moderately sized organic molecules. In this paper we use these techniques to develop a variety of accurate distributed polarizability models for a set of representative molecules that include formamide, N-methyl propanamide, benzene, and 3-azabicyclo[3.3.1]nonane-2,4-dione. We have also explored damping, penetration, and basis set effects. In particular, we have provided a way to treat the damping of the induction expansion. Different approximations to the induction energy are evaluated against accurate SAPT(DFT) energies, and we demonstrate the accuracy of our induction models on the formamide-water dimer.

Hydrogen bonding in malonaldehyde: a density functional and reparametrized semiempirical approach

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Hrenar, Tomica; Došlić, Nadja

2003-08-01

Intramolecular proton transfer in malonaldehyde (MA) has been investigated by density functional theory (DFT). The DFT results were used for the construction of a high quality semiempirical potential energy surface with a reparametrized PM3 Hamiltonian. A two-step reparameterization procedure is proposed in which (i) the PM3-MAIS core-core functions for the O-H and H-H interactions were used and a new functional form for the O-O correction function was proposed and (ii) a set of specific reaction parameters (SRP) has been obtained via genetic algorithm optimization. The quality of the reparametrized semiempirical potential energy surfaces was tested by calculating the tunneling splitting of vibrational levels and the anharmonic vibrational frequencies of the system. The applicability to multi-dimensional dynamics in large molecular systems is discussed.

The role of silicon, vacancies, and strain in carbon distribution for low temperature bainite

DOE PAGES

Sampath, S.; Rementeria, R.; Huang, X.; ...

2016-02-19

Here, we investigated the phenomenon of carbon supersaturation and carbon clustering in bainitic ferrite with atom probe tomography (APT) and ab-initio density functional theory (DFT) calculations. The experimental results show a homogeneous distribution of silicon in the microstructure, which contains both ferrite and retained austenite. This distribution is mimicked well by the computational approach. In addition, an accumulation of C in certain regions of the bainitic ferrite with C concentrations up to 13 at % is observed. Based on the DFT results, these clusters are explained as strained, tetragonal regions in the ferritic bainite, in which the solution enthalpy ofmore » C can reach large, negative values. It seems that Si itself only has a minor influence on this phenomenon.« less

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach

NASA Astrophysics Data System (ADS)

Suresh, D. M.; Amalanathan, M.; Sebastian, S.; Sajan, D.; Hubert Joe, I.; Bena Jothy, V.; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

A DFT study on surface-enhanced Raman spectroscopy of aromatic dithiol derivatives adsorbed on gold nanojunctions

NASA Astrophysics Data System (ADS)

You, Tingting; Lang, Xiufeng; Huang, Anping; Yin, Penggang

2018-01-01

A computational study on aromatic dithiol derivatives (HS-Ar-X-Ar-SH, X = O, S, Se, NH, CH2, Ndbnd N, CHdbnd CH, Ctbnd C) interacting with gold cluster(s) was presented to investigate the chemical enhancement mechanism related to surface-enhanced Raman spectroscopy (SERS) for molecular junctions. Density functional theory (DFT) were performed on derivatives molecules as well as their single-end-linked (SEL) or double-end-linked (DEL) complexes for geometric, spectra, electronic and excitation properties, leading to discussions on dominant factor during SERS process. The resulted enhancement factors of SEL and DEL complexes exhibited specific dependency on linking atom or functional group between two phenyls, which was in accordance with the variation of polarizabilities and molecule-cluster transition energy.

In and Si adatoms on Si(111)5×2-Au : Scanning tunneling microscopy and first-principles density functional calculations

NASA Astrophysics Data System (ADS)

Stępniak, A.; Nita, P.; Krawiec, M.; Jałochowski, M.

2009-09-01

Structural properties of monatomic indium chains on Si(111)5×2-Au surface are investigated by scanning tunneling microscopy (STM) and first-principles density functional calculations (DFT). The STM topography data show that submonolayer coverage of indium leads to a well-ordered chain structure with the same periodicity as the Si adatoms form on Si(111)5×2-Au surface. Bias-dependent STM topography and spectroscopy reveal two different mechanisms of In-atoms adsorption on the surface: bonding to Si adatoms and substitution for Si atoms in the adatom positions. Those mechanisms are further corroborated by DFT calculations. The obtained structural model of In-modified Si(111)5×2-Au surface remains in good agreement with the experimental data.

The plane-wave DFT investigations into the structure and the 11B solid-state NMR parameters of lithium fluorooxoborates

NASA Astrophysics Data System (ADS)

Czernek, Jiří; Brus, Jiří

2016-12-01

The strategy for an application of the first-principles calculations on crystalline systems to predict the 11B solid-state NMR powder-patterns is described, and its efficacy is demonstrated for two novel lithium-containing fluorooxborates, Li2B3O4F3 and Li2B6O9F2. This strategy involves the plane-wave DFT computations of the NMR parameters, whose values are then scaled and used in the spectral simulations, and are supposed to be directly applicable in the NMR crystallography studies of boron-containing systems. In particular, the GIPAW method and the PBE, PW91, and RPBE functionals are applied. Issues specific to the signal-assignment of the two compounds are also discussed.

Thermodynamics, kinetics, and catalytic effect of dehydrogenation from MgH2 stepped surfaces and nanocluster: a DFT study

NASA Astrophysics Data System (ADS)

Reich, Jason; Wang, Linlin; Johnson, Duane

2013-03-01

We detail the results of a Density Functional Theory (DFT) based study of hydrogen desorption, including thermodynamics and kinetics with(out) catalytic dopants, on stepped (110) rutile and nanocluster MgH2. We investigate competing configurations (optimal surface and nanoparticle configurations) using simulated annealing with additional converged results at 0 K, necessary for finding the low-energy, doped MgH2 nanostructures. Thermodynamics of hydrogen desorption from unique dopant sites will be shown, as well as activation energies using the Nudged Elastic Band algorithm. To compare to experiment, both stepped structures and nanoclusters are required to understanding and predict the effects of ball milling. We demonstrate how these model systems relate to the intermediary sized structures typically seen in ball milling experiments.

Band-gap corrected density functional theory calculations for InAs/GaSb type II superlattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jianwei; Zhang, Yong

2014-12-07

We performed pseudopotential based density functional theory (DFT) calculations for GaSb/InAs type II superlattices (T2SLs), with bandgap errors from the local density approximation mitigated by applying an empirical method to correct the bulk bandgaps. Specifically, this work (1) compared the calculated bandgaps with experimental data and non-self-consistent atomistic methods; (2) calculated the T2SL band structures with varying structural parameters; (3) investigated the interfacial effects associated with the no-common-atom heterostructure; and (4) studied the strain effect due to lattice mismatch between the two components. This work demonstrates the feasibility of applying the DFT method to more exotic heterostructures and defect problemsmore » related to this material system.« less

Structure, electronic and magnetic properties of Mn{sub n} (n=2-8) clusters: A DFT investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Vipin; Roy, Debesh R., E-mail: drr@ashd.svnit.ac.in

2016-05-06

A detail studyon the stability, electronic and magnetic properties of Mn{sub n} (n=2-8) cluster series is performed under the utilization ofdensity functional theory (DFT). The binding energy (B.E.), HOMO-LUMO energy gap (HLG), chemical hardness (η), ionization potential (I.P.), electron affinity (E.A)and electronegativity (χ) of these clusters are predicted. We have also studied the magnetic moments associated with the stable cluster isomers. The lowest energy structures for each cluster sizes aredetermined with a systematic search imposing all possible initial magnetic configuration on the cluster. All the calculations are carried out using a popular GGA functional PBE as proposed by Pardew, Burkemore » and Ernzerhof and implemented in the VASP program.« less

Photoionization of Benzene and Small Polycyclic Aromatic Hydrocarbons in Ultraviolet-Processed Astrophysical Ices: A Computational Study

NASA Technical Reports Server (NTRS)

Woon, D. E.; Park, J.-Y.

2004-01-01

We employed density functional theory (DFT) calculations to model the photoionization behavior of benzene and small polycyclic aromatic hydrocarbons when they are embedded in a matrix of water ice in order to investigate issues raised by recent experimental work by Gudipati and Allamandola. The ionization energies of benzene, naphthalene, anthracene, and pyrene were found to be lowered by 1.5-2.1 eV in water ice. Low-lying vertical electronic excitation energies were computed with time-dependent DFT for both neutral and ionized species and are found in both cases to be remarkably unaffected by the ice matrix. Chemical behavior in ultraviolet-photoprocessed ices is also discussed, with a focus on electron recombination and pathways leading to phenol and analogous products.

Comment on "Density functional theory analysis of structural and electronic properties of orthorhombic perovskite CH3NH3PbI3" by Y. Wang et al., Phys. Chem. Chem. Phys., 2014, 16, 1424-1429.

PubMed

Even, J; Pedesseau, L; Katan, C

2014-05-14

Yun Wang et al. used density functional theory (DFT) to investigate the orthorhombic phase of CH3NH3PbI3, which has recently shown outstanding properties for photovoltaic applications. Whereas their analysis of ground state properties may represent a valuable contribution to understanding this class of materials, effects of spin-orbit coupling (SOC) cannot be overlooked as was shown in earlier studies. Moreover, their discussion on optical properties may be misleading for non-DFT-experts, and the nice agreement between experimental and calculated band gap is fortuitous, stemming from error cancellations between SOC and many-body effects. Lastly, Bader charges suggest potential problems during crystal structure optimization.

Molecular structure and vibrational spectra of Irinotecan: a density functional theoretical study.

PubMed

Chinna Babu, P; Sundaraganesan, N; Sudha, S; Aroulmoji, V; Murano, E

2012-12-01

The solid phase FTIR and FT-Raman spectra of Irinotecan have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d) as basis set. The vibrational frequencies were calculated for Irinotecan by DFT method and were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. The infrared spectrum was also simulated from the calculated intensities. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations. Copyright © 2012 Elsevier B.V. All rights reserved.

Charge transfer properties of pentacene adsorbed on silver: DFT study

NASA Astrophysics Data System (ADS)

N, Rekha T.; Rajkumar, Beulah J. M.

2015-06-01

Charge transfer properties of pentacene adsorbed on silver is investigated using DFT methods. Optimized geometry of pentacene after adsorption on silver indicates distortion in hexagonal structure of the ring close to the silver cluster and deviations in co-planarity of carbon atoms due to the variations in bond angles and dihedral angles. Theoretically simulated absorption spectrum has a symmetric surface plasmon resonance peak around 486nm corresponding to the transfer of charge from HOMO-2 to LUMO. Theoretical SERS confirms the process of adsorption, tilted orientation of pentacene on silver surface and the charge transfers reported. Localization of electron density arising from redistribution of electrostatic potential together with a reduced bandgap of pentacene after adsorption on silver suggests its utility in the design of electro active organic semiconducting devices.

DFT and TD-DFT computation of charge transfer complex between o-phenylenediamine and 3,5-dinitrosalicylic acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afroz, Ziya; Zulkarnain,; Ahmad, Afaq, E-mail: afaqahmad3@gmail.com

2016-05-23

DFT and TD-DFT studies of o-phenylenediamine (PDA), 3,5-dinitrosalicylic acid (DNSA) and their charge transfer complex have been carried out at B3LYP/6-311G(d,p) level of theory. Molecular geometry and various other molecular properties like natural atomic charges, ionization potential, electron affinity, band gap, natural bond orbital (NBO) and frontier molecular analysis have been presented at same level of theory. Frontier molecular orbital and natural bond orbital analysis show the charge delocalization from PDA to DNSA.

Electronic properties of Fe3O4: LCAO calculations and Compton spectroscopy

NASA Astrophysics Data System (ADS)

Panwar, Kalpana; Tiwari, Shailja; Heda, N. L.

2018-04-01

We report the Compton profile (CP) measurements of Fe3O4 using 100 mCi241Am Compton spectrometer at momentum resolution of 0.55 a.u. The experimental CP has been compared with the linear combination of atomic orbitals (LCAO) data within density functional theory (DFT). The local density and generalized gradient approximation (LDA and GGA, respectively) have been used under the framework of DFT scheme. It is found that the DFT-GGA scheme gives the better agreement than to DFT-LDA. In addition, we have also computed the M ulliken's population (M P) and density of states (DOS) using the DFT scheme. M P data predicts the charge transfer from Fe to O atoms while DOS have confirmed the half metallic character of the compound.

Comparison of step-down and binary search algorithms for determination of defibrillation threshold in humans.

PubMed

Shorofsky, Stephen R; Peters, Robert W; Rashba, Eric J; Gold, Michael R

2004-02-01

Determination of DFT is an integral part of ICD implantation. Two commonly used methods of DFT determination, the step-down method and the binary search method, were compared in 44 patients undergoing ICD testing for standard clinical indications. The step-down protocol used an initial shock of 18 J. The binary search method began with a shock energy of 9 J and successive shock energies were increased or decreased depending on the success of the previous shock. The DFT was defined as the lowest energy that successfully terminated ventricular fibrillation. The binary search method has the advantage of requiring a predetermined number of shocks, but some have questioned its accuracy. The study found that (mean) DFT obtained by the step-down method was 8.2 +/- 5.0, whereas by the binary search method DFT was 8.1 +/- 0.7 J, P = NS. DFT differed by no more than one step between methods in 32 (71%) of patients. The number of shocks required to determine DFT by the step-down method was 4.6 +/- 1.4, whereas by definition, the binary search method always required three shocks. In conclusion, the binary search method is preferable because it is of comparable efficacy and requires fewer shocks.

DENSITY FUNCTIONAL THEORY (DFT) STUDIES OF C1 AND C2 HYDROCARBONS SPECIES ON PT CLUSTERS. (R825370C056)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Density functional theory: Foundations reviewed

NASA Astrophysics Data System (ADS)

Kryachko, Eugene S.; Ludeña, Eduardo V.

2014-11-01

Guided by the above motto (quotation), we review a broad range of issues lying at the foundations of Density Functional Theory, DFT, a theory which is currently omnipresent in our everyday computational study of atoms and molecules, solids and nano-materials, and which lies at the heart of modern many-body computational technologies. The key goal is to demonstrate that there are definitely the ways to improve DFT. We start by considering DFT in the larger context provided by reduced density matrix theory (RDMT) and natural orbital functional theory (NOFT), and examine the implications that N-representability conditions on the second-order reduced density matrix (2-RDM) have not only on RDMT and NOFT but, also, by extension, on the functionals of DFT. This examination is timely in view of the fact that necessary and sufficient N-representability conditions on the 2-RDM have recently been attained. In the second place, we review some problems appearing in the original formulation of the first Hohenberg-Kohn theorem which is still a subject of some controversy. In this vein we recall Lieb's comment on this proof and the extension to this proof given by Pino et al. (2009), and in this context examine the conditions that must be met in order that the one-to-one correspondence between ground-state densities and external potentials remains valid for finite subspaces (namely, the subspaces where all Kohn-Sham solutions are obtained in practical applications). We also consider the issue of whether the Kohn-Sham equations can be derived from basic principles or whether they are postulated. We examine this problem in relation to ab initio DFT. The possibility of postulating arbitrary Kohn-Sham-type equations, where the effective potential is by definition some arbitrary mixture of local and non-local terms, is discussed. We also deal with the issue of whether there exists a universal functional, or whether one should advocate instead the construction of problem-geared functionals. These problems are discussed by making reference to ab initio DFT as well as to the local-scaling-transformation version of DFT, LS-DFT. In addition, we examine the question of the accuracy of approximate exchange-correlation functionals in the light of their non-observance of the variational principle. Why do approximate functionals yield reasonable (and accurate) descriptions of many molecular and condensed matter properties? Are the conditions imposed on exchange and correlation functionals sufficiently adequate to produce accurate semi-empirical functionals? In this respect, we consider the question of whether the results reflect a true approach to chemical accuracy or are just the outcome of a virtuoso-like performance which cannot be systematically improved. We discuss the issue of the accuracy of the contemporary DFT results by contrasting them to those obtained by the alternative RDMT and NOFT. We discuss the possibility of improving DFT functionals by applying in a systematic way the N-representability conditions on the 2-RDM. In this respect, we emphasize the possibility of constructing 2-matrices in the context of the local scaling transformation version of DFT to which the N-representability condition of RDM theory may be applied. We end up our revision of HKS-DFT by considering some of the problems related to spin symmetry and discuss some current issues dealing with a proper treatment of open-shell systems. We are particularly concerned, as in the rest of this paper, mostly with foundational issues arising in the construction of functionals. We dedicate the whole Section 4 to the local-scaling transformation version of density functional theory, LS-DFT. The reason is that in this theory some of the fundamental problems that appear in HKS-DFT, have been solved. For example, in LS-DFT the functionals are, in principle, designed to fulfill v- and N-representability conditions from the outset. This is possible because LS-DFT is based on density transformation (local-scaling of coordinates proceeds through density transformation) and so, because these functionals are constructed from prototype N-particle wavefunctions, the ensuing density functionals already have built-in N-representability conditions. This theory is presented in great detail with the purpose of illustrating an alternative way to HKS-DFT which could be used to improve the construction of HKS-DFT functionals. Let us clearly indicate, however, that although appealing from a theoretical point of view, the actual application of LS-DFT to large systems has not taken place mostly because of technical difficulties. Thus, our aim in introducing this theory is to foster a better understanding of its foundations with the hope that it may promote a cross-hybridization with the already existing approaches. Also, to complete our previous discussion on symmetry, in particular, spin-symmetry, we discuss this issue from the perspective of LS-DFT. Finally, in Section 6, we discuss dispersion molecular forces emphasizing their relevance to DFT approaches.

An improved model for whole genome phylogenetic analysis by Fourier transform.

PubMed

Yin, Changchuan; Yau, Stephen S-T

2015-10-07

DNA sequence similarity comparison is one of the major steps in computational phylogenetic studies. The sequence comparison of closely related DNA sequences and genomes is usually performed by multiple sequence alignments (MSA). While the MSA method is accurate for some types of sequences, it may produce incorrect results when DNA sequences undergone rearrangements as in many bacterial and viral genomes. It is also limited by its computational complexity for comparing large volumes of data. Previously, we proposed an alignment-free method that exploits the full information contents of DNA sequences by Discrete Fourier Transform (DFT), but still with some limitations. Here, we present a significantly improved method for the similarity comparison of DNA sequences by DFT. In this method, we map DNA sequences into 2-dimensional (2D) numerical sequences and then apply DFT to transform the 2D numerical sequences into frequency domain. In the 2D mapping, the nucleotide composition of a DNA sequence is a determinant factor and the 2D mapping reduces the nucleotide composition bias in distance measure, and thus improving the similarity measure of DNA sequences. To compare the DFT power spectra of DNA sequences with different lengths, we propose an improved even scaling algorithm to extend shorter DFT power spectra to the longest length of the underlying sequences. After the DFT power spectra are evenly scaled, the spectra are in the same dimensionality of the Fourier frequency space, then the Euclidean distances of full Fourier power spectra of the DNA sequences are used as the dissimilarity metrics. The improved DFT method, with increased computational performance by 2D numerical representation, can be applicable to any DNA sequences of different length ranges. We assess the accuracy of the improved DFT similarity measure in hierarchical clustering of different DNA sequences including simulated and real datasets. The method yields accurate and reliable phylogenetic trees and demonstrates that the improved DFT dissimilarity measure is an efficient and effective similarity measure of DNA sequences. Due to its high efficiency and accuracy, the proposed DFT similarity measure is successfully applied on phylogenetic analysis for individual genes and large whole bacterial genomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

A complete computational and spectroscopic study of 2-bromo-1, 4-dichlorobenzene - A frequently used benzene derivative

NASA Astrophysics Data System (ADS)

Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.; Mary, Y. Sheena; Panicker, C. Yohannan; Kaya, S.; Armaković, Stevan; Armaković, Sanja J.

2018-01-01

The coupled experimental and theoretical vibrational investigation of 2-bromo-1, 4-dichlorobenzene (BDB) molecule has been carried out and they have been duly compared with standard values in order to produce the reliability of the results. Results of DFT analysis carried out using B3LYP functional with 6-31 + G/6-311++G (d,p) basis set revealed that BDB has higher electronic density. The molecular geometry, 13C &1H Nuclear Magnetic Resonance (NMR), Natural Bond Orbital (NBO) and Natural Atomic Charge analyses have been obtained by DFT calculations. Nonlinear optical (NLO) properties, quantum chemical descriptors and first order hyperpolarizability have been calculated. In addition, Local reactivity properties reflected through average local ionization energies (ALIE), Fukui functions and bond dissociation energies have also been investigated. Besides investigation of docking properties, molecular dynamics simulations were also taken in account with a view to identify atoms that have relatively important interactions with water molecules. The title compound forms a stable complex with isopentenylpyrophosphate transferase with a binding affinity value as -4.6 kCal./Mol. and shows inhibitory activity against isopentenylpyrophosphate transferase.

New-class of Semiconducting 2D materials: Tin Dichalcogenides (SnX2)

NASA Astrophysics Data System (ADS)

Ataca, Can; Wu, Kedi; Saritas, Kayahan; Tongay, Sefaattin; Grossman, Jeffrey C.

2015-03-01

Recent studies have focused on a new generation of atomically thin films of semiconducting materials. A broad family of two-dimensional (2D) semiconducting transition metal dichalcogenides (MX2) have been fabricated and investigated in monolayer, bilayer and few layer form. In this work, we investigated the electronic, optical and elastic properties of single and few layer and bulk SnX2 (X = S, Se) both theoretically and experimentally. Using density functional theory (DFT) we carried out stability analysis through phonon and electronic, optical and elastic structure calculations. Single-few layer SnX2s are mechanically exfoliated and Raman and photoluminescence (PL) measurements are taken. UV-Vis absorption spectrum together with PL measurements and DFT calculations yield an indirect gap of ~ 2.5 eV for SnS2 structures (bulk). Tunability of the energy band gap and indirect-direct gap transitions are investigated by controlling the number of layers and applied stress. Lowering the number of layers decreases the indirect gap (0.1-0.3 eV), but indirect-direct gap transition occurs when layer-layer distance is reduced. Due to flexibility in engineering the electronic and optical properties, SnX2 compounds are promising materials for future optoelectronic nanoscale applications.

Molecular structure, vibrational analysis (IR and Raman) and quantum chemical investigations of 1-aminoisoquinoline

NASA Astrophysics Data System (ADS)

Sivaprakash, S.; Prakash, S.; Mohan, S.; Jose, Sujin P.

2017-12-01

Quantum chemical calculations of energy and geometrical parameters of 1-aminoisoquinoline [1-AIQ] were carried out by using DFT/B3LYP method using 6-311G (d,p), 6-311G++(d,p) and cc-pVTZ basis sets. The vibrational wavenumbers were computed for the energetically most stable, optimized geometry. The vibrational assignments were performed on the basis of potential energy distribution (PED) using VEDA program. The NBO analysis was done to investigate the intra molecular charge transfer of the molecule. The frontier molecular orbital (FMO) analysis was carried out and the chemical reactivity descriptors of the molecule were studied. The Mulliken charge analysis, molecular electrostatic potential (MEP), HOMO-LUMO energy gap and the related properties were also investigated at B3LYP level. The absorption spectrum of the molecule was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). Fourier Transform Infrared spectrum (FT-IR) and Raman spectrum of 1-AIQ compound were analyzed and recorded in the range 4000-400 cm-1 and 3500-100 cm-1 respectively. The experimentally determined wavenumbers were compared with those calculated theoretically and they complement each other.

Acute effects of implantable cardioverter-defibrillator shocks on biomarkers of myocardial injury, apoptosis, heart failure, and systemic inflammation

PubMed Central

Brewster, Jordan; Sexton, Travis; Dhaliwal, Gary; Charnigo, Richard; Morales, Gustavo; Parrott, Kevin; Darrat, Yousef; Gurley, John; Smyth, Susan; Elayi, Claude S.

2017-01-01

Background ICD shocks are potentially associated with myocardial injury, altered hemodynamics, apoptosis and inflammatory signaling. Their precise cellular impact can be explored after defibrillation testing (DFT) via biomarkers. We evaluated changes in biomarkers after ICD shocks during DFT. Methods We prospectively enrolled outpatients presenting for first implantation of a cardiac device. Biomarkers indicative of myocardial injury, inflammation and apoptosis were measured before and after implantation, and compared between patients receiving DFT (DFT+) to those not (DFT−). Results Sixty-three patients were enrolled, 40 in the DFT+ group and 23 in the DFT− group. Average levels of troponin I, hsCRP, Calprotectin, NTproBNP, and sFas increased by >50% after cardiac device implantation compared to baseline. Increase in troponin never exceeded 50 fold upper limit of normal (2ng/mL). Troponin trended higher in the DFT+ group at 8 hours (median 0.18 ng/mL, IQR 0.11–0.48) versus the DFT− group (0.10 ng/mL, IQR 0.06–0.28, P=0.0501); NTproBNP had a similar trend (p=0.0581). sFas significantly increased in the DFT+ group from baseline (median 4663 pg/mL, IQR 2908–5679) to 24 hours (5039 pg/mL, IQR 3274–6261; p=0.0338) but not in the DFT− group (p=0.4705). Conclusion DFT testing is associated with acutely increased plasma levels of troponin and sFas, a biomarker of apoptosis, along with a trend towards higher NTproBNP. PMID:28156007

NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer's disease: an investigation by docking, molecular dynamics, and DFT studies.

PubMed

Azam, Faizul; Alabdullah, Nada Hussin; Ehmedat, Hadeel Mohammed; Abulifa, Abdullah Ramadan; Taban, Ismail; Upadhyayula, Sreedevi

2018-06-01

Aggregation of amyloid beta (Aβ) protein considered as one of contributors in development of Alzheimer's disease (AD). Several investigations have identified the importance of non-steroidal anti-inflammatory drugs (NSAIDs) as Aβ aggregation inhibitors. Here, we have examined the binding interactions of 24 NSAIDs belonging to eight different classes, with Aβ fibrils by exploiting docking and molecular dynamics studies. Minimum energy conformation of the docked NSAIDs were further optimized by density functional theory (DFT) employing Becke's three-parameter hybrid model, Lee-Yang-Parr (B3LYP) correlation functional method. DFT-based global reactivity descriptors, such as electron affinity, hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated to inspect the expediency of these descriptors for understanding the reactive nature and sites of the molecules. Few selected NSAID-Aβ fibrils complexes were subjected to molecular dynamics simulation to illustrate the stability of these complexes and the most prominent interactions during the simulated trajectory. All of the NSAIDs exhibited potential activity against Aβ fibrils in terms of predicted binding affinity. Sulindac was found to be the most active compound underscoring the contribution of indene methylene substitution, whereas acetaminophen was observed as least active NSAID. General structural requirements for interaction of NSAIDs with Aβ fibril include: aryl/heteroaryl aromatic moiety connected through a linker of 1-2 atoms to a distal aromatic group. Considering these structural requirements and electronic features, new potent agents can be designed and developed as potential Aβ fibril inhibitors for the treatment of AD.

Scavenging performance and antioxidant activity of γ-alumina nanoparticles towards DPPH free radical: Spectroscopic and DFT-D studies.

PubMed

Zamani, Mehdi; Moradi Delfani, Ali; Jabbari, Morteza

2018-05-03

The radical scavenging performance and antioxidant activity of γ-alumina nanoparticles towards 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical were investigated by spectroscopic and computational methods. The radical scavenging ability of γ-alumina nanoparticles in the media with different polarity (i.e. i-propanol and n-hexane) was evaluated by measuring the DPPH absorbance in UV-Vis absorption spectra. The structure and morphology of γ-alumina nanoparticles before and after adsorption of DPPH were studied using XRD, FT-IR and UV-Vis spectroscopic techniques. The adsorption of DPPH free radical on the clean and hydrated γ-alumina (1 1 0) surface was examined by dispersion corrected density functional theory (DFT-D) and natural bond orbital (NBO) calculations. Also, time-dependent density functional theory (TD-DFT) was used to predict the absorption spectra. The adsorption was occurred through the interaction of radical nitrogen N and NO 2 groups of DPPH with the acidic and basic sites of γ-alumina surface. The high potential for the adsorption of DPPH radical on γ-alumina nanoparticles was investigated. Interaction of DPPH with Brønsted and Lewis acidic sites of γ-alumina was more favored than Brønsted basic sites. The following order for the adsorption of DPPH over the different active sites of γ-alumina was predicted: Brønsted base < Lewis acid < Brønsted acid. These results are of great significance for the environmental application of γ-alumina nanoparticles in order to remove free radicals. Copyright © 2018. Published by Elsevier B.V.

Teaching Inorganic Photophysics and Photochemistry with Three Ruthenium(II) Polypyridyl Complexes: A Computer-Based Exercise

ERIC Educational Resources Information Center

Garino, Claudio; Terenzi, Alessio; Barone, Giampaolo; Salassa, Luca

2016-01-01

Among computational methods, DFT (density functional theory) and TD-DFT (time-dependent DFT) are widely used in research to describe, "inter alia," the optical properties of transition metal complexes. Inorganic/physical chemistry courses for undergraduate students treat such methods, but quite often only from the theoretical point of…

Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone.

PubMed

Genova, Alessandro; Pavanello, Michele

2015-12-16

In order to approximately satisfy the Bloch theorem, simulations of complex materials involving periodic systems are made n(k) times more complex by the need to sample the first Brillouin zone at n(k) points. By combining ideas from Kohn-Sham density-functional theory (DFT) and orbital-free DFT, for which no sampling is needed due to the absence of waves, subsystem DFT offers an interesting middle ground capable of sizable theoretical speedups against Kohn-Sham DFT. By splitting the supersystem into interacting subsystems, and mapping their quantum problem onto separate auxiliary Kohn-Sham systems, subsystem DFT allows an optimal topical sampling of the Brillouin zone. We elucidate this concept with two proof of principle simulations: a water bilayer on Pt[1 1 1]; and a complex system relevant to catalysis-a thiophene molecule physisorbed on a molybdenum sulfide monolayer deposited on top of an α-alumina support. For the latter system, a speedup of 300% is achieved against the subsystem DTF reference by using an optimized Brillouin zone sampling (600% against KS-DFT).

Using DFT Methods to Study Activators in Optical Materials

DOE PAGES

Du, Mao-Hua

2015-08-17

Density functional theory (DFT) calculations of various activators (ranging from transition metal ions, rare-earth ions, ns 2 ions, to self-trapped and dopant-bound excitons) in phosphors and scintillators are reviewed. As a single-particle ground-state theory, DFT calculations cannot reproduce the experimentally observed optical spectra, which involve transitions between multi-electronic states. However, DFT calculations can generally provide sufficiently accurate structural relaxation and distinguish different hybridization strengths between an activator and its ligands in different host compounds. This is important because the activator-ligand interaction often governs the trends in luminescence properties in phosphors and scintillators, and can be used to search for newmore » materials. DFT calculations of the electronic structure of the host compound and the positions of the activator levels relative to the host band edges in scintillators are also important for finding optimal host-activator combinations for high light yields and fast scintillation response. Mn 4+ activated red phosphors, scintillators activated by Ce 3+, Eu 2+, Tl +, and excitons are shown as examples of using DFT calculations in phosphor and scintillator research.« less

Excited State Studies of Polyacenes Using the All-Order Constricted Variational Density Functional Theory with Orbital Relaxation.

PubMed

Senn, Florian; Krykunov, Mykhaylo

2015-10-22

For the polyacenes series from naphthalene to hexacene, we present the vertical singlet excitation energies 1 (1)La and 1 (1)Lb, as well as the first triplet excitation energies obtained by the all-order constricted variational density functional theory with orbital relaxation (R-CV(∞)-DFT). R-CV(∞)-DFT is a further development of variational density functional theory (CV(∞)-DFT), which has already been successfully applied for the calculation of the vertical singlet excitation energies (1)La and (1)Lb for polyacenes,15 and we show that one obtains consistent excitation energies using the local density approximation as a functional for singlet as well as for triplet excitations when going beyond the linear response theory. Furthermore, we apply self-consistent field density functional theory (ΔSCF-DFT) and compare the obtained excitation energies for the first triplet excitations T1, where, due to the character of the transition, ΔSCF-DFT and R-CV(∞)-DFT become numerically equivalent, and for the singlet excitations 1 (1)La and 1 (1)Lb, where the two methods differ.

Embedding multiple watermarks in the DFT domain using low- and high-frequency bands

NASA Astrophysics Data System (ADS)

Ganic, Emir; Dexter, Scott D.; Eskicioglu, Ahmet M.

2005-03-01

Although semi-blind and blind watermarking schemes based on Discrete Cosine Transform (DCT) or Discrete Wavelet Transform (DWT) are robust to a number of attacks, they fail in the presence of geometric attacks such as rotation, scaling, and translation. The Discrete Fourier Transform (DFT) of a real image is conjugate symmetric, resulting in a symmetric DFT spectrum. Because of this property, the popularity of DFT-based watermarking has increased in the last few years. In a recent paper, we generalized a circular watermarking idea to embed multiple watermarks in lower and higher frequencies. Nevertheless, a circular watermark is visible in the DFT domain, providing a potential hacker with valuable information about the location of the watermark. In this paper, our focus is on embedding multiple watermarks that are not visible in the DFT domain. Using several frequency bands increases the overall robustness of the proposed watermarking scheme. Specifically, our experiments show that the watermark embedded in lower frequencies is robust to one set of attacks, and the watermark embedded in higher frequencies is robust to a different set of attacks.

Density functional theory for open-shell singlet biradicals

NASA Astrophysics Data System (ADS)

Gräfenstein, Jürgen; Kraka, Elfi; Cremer, Dieter

1998-05-01

The description of open-shell singlet (OSS) σ- π biradicals by density functional theory (DFT) requires at least a two-configurational (TC) or, in general, a MC-DFT approach, which bears many unsolved problems. These can be avoided by reformulating the TC description in the spirit of restricted open shell theory for singlets (ROSS) and developing an exchange-correlation functional for ROSS-DFT. ROSS-DFT turns out to lead to reliable descriptions of geometry and vibrational frequencies for OSS biradicals. The relative energies of the OSS states obtained at the ROSS-B3LYP/6-311G(d,p) level are often better than the corresponding ROSS-MP2 results. However, in those cases where spin polarization in a conjugated π systems plays a role, DFT predicts the triplet state related to the OSS state 2-4 kcal/mol too stable.

Antimycobacterial, antimicrobial activity, experimental (FT-IR, FT-Raman, NMR, UV-Vis, DSC) and DFT (transition state, chemical reactivity, NBO, NLO) studies on pyrrole-isonicotinyl hydrazine

NASA Astrophysics Data System (ADS)

Rawat, Poonam; Singh, R. N.; Ranjan, Alok; Ahmad, Sartaj; Saxena, Rajat

2017-05-01

As part of a study of pyrrole hydrazone, we have investigated quantum chemical calculations, molecular geometry, relative energy, vibrational properties and antimycobacterial/antimicrobial activity of pyrrole-2-carboxaldehyde isonicotinyl hydrazone (PCINH), by applying the density functional theory (DFT) and Hartree Fock (HF). Good reproduction of experimental values is obtained and with small percentage error in majority of the cases in comparison to theoretical result (DFT). The experimental FT-IR and Raman wavenumbers were compared with the respective theoretical values obtained from DFT calculations and found to agree well. In crystal structure studies the hydrated PCINH (syn-syn conformer) shows different conformation than from anhydrous form (syn-anti conformer). The rotational barrier between syn-syn and syn-anti conformers of PCINH is 12.7 kcal/mol in the gas phase. In this work, use of FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Vis spectroscopies has been made for full characterization of PCINH. A detailed interpretation of the vibrational spectrum was carried out with the aid of normal coordinate analysis using single scaling factor. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. The calculated nature of electronic transitions within molecule found to be π → π*. The electronic descriptors study indicates that PCINH can be used as robust synthon for synthesis of new heterocyclic compounds. The first static hyperpolarizability (β0) of PCINH is calculated as 33.89 × 10- 30 esu, (gas phase); 68.79 × 10- 30 (CHCl3), esu; 76.76 × 10- 30 esu (CH2Cl2), 85.16 × 10- 30 esu (DMSO). The solvent induced effects on the first static hyperpolarizability were studied and found to increase as dielectric constants of the solvents increases. Investigated molecule shows better NLO value than Para nitroaniline (PNA). The compound PCINH shows good antifungal and antibacterial activity against Aspergillus niger and gram-positive bacteria Bacillus subtilis, respectively. The compound also shows good antituberculosis activity against Mycobacterium tuberculosis H37Rv using the microplate alamar blue assay (MABA).

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA-based-radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.« less

First-principles analysis of structural and opto-electronic properties of indium tin oxide

NASA Astrophysics Data System (ADS)

Tripathi, Madhvendra Nath; Shida, Kazuhito; Sahara, Ryoji; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2012-05-01

Density functional theory (DFT) and DFT + U (DFT with on-site Coulomb repulsion corrections) calculations have been carried out to study the structural and opto-electronic properties of indium tin oxide (ITO) for both the oxidized and reduced environment conditions. Some of the results obtained by DFT calculations differ from the experimental observations, such as uncertain indication for the site preference of tin atom to replace indium atom at b-site or d-site, underestimation of local inward relaxation in the first oxygen polyhedra around tin atom, and also the improper estimation of electronic density of states and hence resulting in an inappropriate optical spectra of ITO. These discrepancies of theoretical outcomes with experimental observations in ITO arise mainly due to the underestimation of the cationic 4d levels within standard DFT calculations. Henceforth, the inclusion of on-site corrections within DFT + U framework significantly modifies the theoretical results in better agreement to the experimental observations. Within this framework, our calculations show that the indium b-site is preferential site over d-site for tin atom substitution in indium oxide under both the oxidized and reduced conditions. Moreover, the calculated average inward relaxation value of 0.16 Å around tin atom is in good agreement with the experimental value of 0.18 Å. Furthermore, DFT + U significantly modify the electronic structure and consequently induce modifications in the calculated optical spectra of ITO.

First-principles modeling of quantum nuclear effects and atomic interactions in solid 4He at high pressure

NASA Astrophysics Data System (ADS)

Cazorla, Claudio; Boronat, Jordi

2015-01-01

We present a first-principles computational study of solid 4He at T =0 K and pressures up to ˜160 GPa. Our computational strategy consists in using van der Waals density functional theory (DFT-vdW) to describe the electronic degrees of freedom in this material, and the diffusion Monte Carlo (DMC) method to solve the Schrödinger equation describing the behavior of the quantum nuclei. For this, we construct an analytical interaction function based on the pairwise Aziz potential that closely matches the volume variation of the cohesive energy calculated with DFT-vdW in dense helium. Interestingly, we find that the kinetic energy of solid 4He does not increase appreciably with compression for P ≥85 GPa. Also, we show that the Lindemann ratio in dense solid 4He amounts to 0.10 almost independently of pressure. The reliability of customary quasiharmonic DFT (QH DFT) approaches in describing quantum nuclear effects in solids is also studied. We find that QH DFT simulations, although provide a reasonable equation of state in agreement with experiments, are not able to reproduce correctly these critical effects in compressed 4He. In particular, we disclose huge discrepancies of at least ˜50 % in the calculated 4He kinetic energies using both the QH DFT and present DFT-DMC methods.

Diffusion quantum Monte Carlo and density functional calculations of the structural stability of bilayer arsenene

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Santana, Juan A.; Özaydin, H. Duygu; Ersan, Fatih; Aktürk, O. Üzengi; Aktürk, Ethem; Reboredo, Fernando A.

2018-06-01

We have studied the structural stability of monolayer and bilayer arsenene (As) in the buckled (b) and washboard (w) phases with diffusion quantum Monte Carlo (DMC) and density functional theory (DFT) calculations. DMC yields cohesive energies of 2.826(2) eV/atom for monolayer b-As and 2.792(3) eV/atom for w-As. In the case of bilayer As, DMC and DFT predict that AA-stacking is the more stable form of b-As, while AB is the most stable form of w-As. The DMC layer-layer binding energies for b-As-AA and w-As-AB are 30(1) and 53(1) meV/atom, respectively. The interlayer separations were estimated with DMC at 3.521(1) Å for b-As-AA and 3.145(1) Å for w-As-AB. A comparison of DMC and DFT results shows that the van der Waals density functional method yields energetic properties of arsenene close to DMC, while the DFT + D3 method closely reproduced the geometric properties from DMC. The electronic properties of monolayer and bilayer arsenene were explored with various DFT methods. The bandgap values vary significantly with the DFT method, but the results are generally qualitatively consistent. We expect the present work to be useful for future experiments attempting to prepare multilayer arsenene and for further development of DFT methods for weakly bonded systems.

Localized-overlap approach to calculations of intermolecular interactions

NASA Astrophysics Data System (ADS)

Rob, Fazle

Symmetry-adapted perturbation theory (SAPT) based on the density functional theory (DFT) description of the monomers [SAPT(DFT)] is one of the most robust tools for computing intermolecular interaction energies. Currently, one can use the SAPT(DFT) method to calculate interaction energies of dimers consisting of about a hundred atoms. To remove the methodological and technical limits and extend the size of the systems that can be calculated with the method, a novel approach has been proposed that redefines the electron densities and polarizabilities in a localized way. In the new method, accurate but computationally expensive quantum-chemical calculations are only applied for the regions where it is necessary and for other regions, where overlap effects of the wave functions are negligible, inexpensive asymptotic techniques are used. Unlike other hybrid methods, this new approach is mathematically rigorous. The main benefit of this method is that with the increasing size of the system the calculation scales linearly and, therefore, this approach will be denoted as local-overlap SAPT(DFT) or LSAPT(DFT). As a byproduct of developing LSAPT(DFT), some important problems concerning distributed molecular response, in particular, the unphysical charge-flow terms were eliminated. Additionally, to illustrate the capabilities of SAPT(DFT), a potential energy function has been developed for an energetic molecular crystal of 1,1-diamino-2,2-dinitroethylene (FOX-7), where an excellent agreement with the experimental data has been found.

On the calculation of charge transfer transitions with standard density functionals using constrained variational density functional theory.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo

2010-08-21

It is well known that time-dependent density functional theory (TD-DFT) based on standard gradient corrected functionals affords both a quantitative and qualitative incorrect picture of charge transfer transitions between two spatially separated regions. It is shown here that the well known failure can be traced back to the use of linear response theory. Further, it is demonstrated that the inclusion of higher order terms readily affords a qualitatively correct picture even for simple functionals based on the local density approximation. The inclusion of these terms is done within the framework of a newly developed variational approach to excitation energies called constrained variational density functional theory (CV-DFT). To second order [CV(2)-DFT] this theory is identical to adiabatic TD-DFT within the Tamm-Dancoff approximation. With inclusion of fourth order corrections [CV(4)-DFT] it affords a qualitative correct description of charge transfer transitions. It is finally demonstrated that the relaxation of the ground state Kohn-Sham orbitals to first order in response to the change in density on excitation together with CV(4)-DFT affords charge transfer excitations in good agreement with experiment. The new relaxed theory is termed R-CV(4)-DFT. The relaxed scheme represents an effective way in which to introduce double replacements into the description of single electron excitations, something that would otherwise require a frequency dependent kernel.

Role of 2',6'-dimethyl-l-tyrosine (Dmt) in some opioid lead compounds.

PubMed

Balboni, Gianfranco; Marzola, Erika; Sasaki, Yusuke; Ambo, Akihiro; Marczak, Ewa D; Lazarus, Lawrence H; Salvadori, Severo

2010-08-15

Here we evaluated how the interchange of the amino acids 2',6'-dimethyl-L-tyrosine (Dmt), 2',6'-difluoro-L-tyrosine (Dft), and tyrosine in position 1 can affect the pharmacological characterization of some reference opioid peptides and pseudopeptides. Generally, Dft and Tyr provide analogues with a similar pharmacological profile, despite different pK(a) values. Dmt/Tyr(Dft) replacement gives activity changes depending on the reference opioid in which the modification was made. Whereas, H-Dmt-Tic-Asp *-Bid is a potent and selective delta agonist (MVD, IC(50)=0.12nM); H-Dft-Tic-Asp *-Bid and H-Tyr-Tic-Asp *-Bid are potent and selective delta antagonists (pA(2)=8.95 and 8.85, respectively). When these amino acids are employed in the synthesis of deltorphin B and its Dmt(1) and Dft(1) analogues, the three compounds maintain a very similar delta agonism (MVD, IC(50) 0.32-0.53 nM) with a decrease in selectivity relative to the Dmt(1) analogue. In the less selective H-Dmt-Tic-Gly *-Bid the replacement of Dmt with Dft and Tyr retains the delta agonism but with a decrease in potency. Antagonists containing the Dmt-Tic pharmacophore do not support the exchange of Dmt with Dft or Tyr. Copyright 2010 Elsevier Ltd. All rights reserved.

Extended Subject Access to Hypertext Online Documentation. Parts I and II: The Search-Support and Maintenance Problems.

ERIC Educational Resources Information Center

Girill, T. R.; And Others

1991-01-01

Describes enhancements made to a hypertext information retrieval system at the National Energy Research Supercomputer Center (NERSC) called DFT (Document, Find, and Theseus). The enrichment of DFT's entry vocabulary is described, DFT and other hypertext systems are compared, and problems that occur due to the need for frequent updates are…

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Nanocarbon: Defect Architectures and Properties

NASA Astrophysics Data System (ADS)

Vuong, Amanda

The allotropes of carbon make its solid phases amongst the most diverse of any element. It can occur naturally as graphite and diamond, which have very different properties that make them suitable for a wide range of technological and commercial purposes. Recent developments in synthetic carbon include Highly Oriented Pyrolytic Graphite (HOPG) and nano-carbons, such as fullerenes, nanotubes and graphene. The main industrial application of bulk graphite is as an electrode material in steel production, but in purified nuclear graphite form, it is also used as a moderator in Advanced Gas-cooled Reactors across the United Kingdom. Both graphene and graphite are damaged over time when subjected to bombardment by electrons, neutrons or ions, and these have a wide range of effects on their physical and electrical properties, depending on the radiation flux and temperature. This research focuses on intrinsic defects in graphene and dimensional change in nuclear graphite. The method used here is computational chemistry, which complements physical experiments. Techniques used comprise of density functional theory (DFT) and molecular dynamics (MD), which are discussed in chapter 2 and chapter 3, respectively. The succeeding chapters describe the results of simulations performed to model defects in graphene and graphite. Chapter 4 presents the results of ab initio DFT calculations performed to investigate vacancy complexes that are formed in AA stacked bilayer graphene. In AB stacking, carbon atoms surrounding the lattice vacancies can form interlayer structures with sp2 bonding that are lower in energy compared to in-plane reconstructions. From the investigation of AA stacking, sp2 interlayer bonding of adjacent multivacancy defects in registry creates a type of stable sp2 bonded wormhole between the layers. Also, a new class of mezzanine structure characterised by sp3 interlayer bonding, resembling a prismatic vacancy loop has also been identified. The mezzanine, which is a V6 hexavacancy variant, where six sp3 carbon atoms sit midway between two carbon layers and bond to both, is substantially more stable than any other vacancy aggregate in AA stacked layers. Chapter 5 presents the results of ab initio DFT calculations performed to investigate the wormhole and mezzanine defect that were identified in chapter 4 and the ramp defect discovered by Trevethan et al.. DFT calculations were performed on these defects in twisted bilayer graphene. From the investigation of vacancy complexes in twisted bilayer graphene, it is found that vacancy complexes are unstable in the twisted region and are more favourable in formation energy when the stacking arrangement is close to AA or AB stacking. It has also been discovered that the ramp defect is more stable in the twisted bilayer graphene compared to the mezzanine defect. Chapter 6 presents the results of ab initio DFT calculations performed to investigate a form of extending defect, prismatic edge dislocation. Suarez-Martinez et al.'s research suggest the armchair core is disconnected from any other layer, whilst the zigzag core is connected. In the investigation here, the curvature of the mezzanine defect allows it to swing between the armchair, zigzag and Klein in the AA stacking. For the AB stacking configuration, the armchair and zigzag core are connected from any other layer. Chapter 7 present results of MD simulations using the adaptive intermolecular reactive empirical bond order (AIREBO) potential to investigate the dimensional change of graphite due to the formation of vacancies present in a single crystal. It has been identified that there is an expansion along the c-axis, whilst a contraction along the a- and b- axes due to the coalescence of vacancy forming in-plane and between the layers. The results here are in good agreement with experimental studies of low temperature irradiation. The final chapter gives conclusions to this work.

Spectroscopic (FT-IR and UV-Vis) and theoretical (HF and DFT) investigation of 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline

NASA Astrophysics Data System (ADS)

Ceylan, Ümit; Tarı, Gonca Özdemir; Gökce, Halil; Ağar, Erbil

2016-04-01

Crystal structure of the title compound, 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline, C13H12N2O2S, has been synthesized and characterized by FT-IR and UV-Vis spectrum. The compound crystallized in the monoclinic space group P 21/c with a = 11.3578 (4) Å, b = 7.4923 (2) Å, c = 14.9676 (6) Å and β = 99.589 (3)° and Z = 4 in the unit cell. The molecular geometry was also calculated using the Gaussian 03 software and structure was optimized using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set in ground state. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311++G(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. It was seen that the optimized structure was in excellent agreement with the X-ray crystal structure. The energetic behaviors of the title compound in solvent media were examined using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set applying the polarizable continuum model (PCM). In addition, the molecular orbitals (FMOs) analysis, molecular electrostatic potential (MEP), nonlinear optical and thermodynamic properties of the title compound were performed using the same methods with the 6-311++G(d,p) basis set.

FT-IR, UV-vis, 1H and 13C NMR spectra and the equilibrium structure of organic dye molecule disperse red 1 acrylate: a combined experimental and theoretical analysis.

PubMed

Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet

2011-12-01

This study reports the characterization of disperse red 1 acrylate compound by spectral techniques and quantum chemical calculations. The spectroscopic properties were analyzed by FT-IR, UV-vis, (1)H NMR and (13)C NMR techniques. FT-IR spectrum in solid state was recorded in the region 4000-400 cm(-1). The UV-vis absorption spectrum of the compound that dissolved in methanol was recorded in the range of 200-800 nm. The (1)H and (13)C NMR spectra were recorded in CDCl(3) solution. The structural and spectroscopic data of the molecule in the ground state were calculated using density functional theory (DFT) employing B3LYP exchange correlation and the 6-311++G(d,p) basis set. The vibrational wavenumbers were calculated and scaled values were compared with experimental FT-IR spectrum. A satisfactory consistency between the experimental and theoretical spectra was obtained and it shows that the hybrid DFT method is very useful in predicting accurate vibrational structure, especially for high-frequency region. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. A study on the electronic properties were performed by timedependent DFT (TD-DFT) and CIS(D) approach. To investigate non linear optical properties, the electric dipole moment μ, polarizability α, anisotropy of polarizability Δα and molecular first hyperpolarizability β were computed. The linear polarizabilities and first hyperpolarizabilities of the studied molecule indicate that the compound can be a good candidate of nonlinear optical materials. Copyright © 2011 Elsevier B.V. All rights reserved.

Electronic structure of dye-sensitized TiO2 clusters from many-body perturbation theory

NASA Astrophysics Data System (ADS)

Marom, Noa; Moussa, Jonathan E.; Ren, Xinguo; Tkatchenko, Alexandre; Chelikowsky, James R.

2011-12-01

The development of new types of solar cells is driven by the need for clean and sustainable energy. In this respect dye-sensitized solar cells (DSC) are considered as a promising route for departing from the traditional solid state cells. The physical insight provided by computational modeling may help develop improved DSCs. To this end, it is important to obtain an accurate description of the electronic structure, including the fundamental gaps and level alignment at the dye-TiO2 interface. This requires a treatment beyond ground-state density functional theory (DFT). We present a many-body perturbation theory study, within the G0W0 approximation, of two of the crystalline phases of dye-sensitized TiO2 clusters, reported by Benedict and Coppens, [J. Am. Chem. Soc.JACSAT0002-786310.1021/ja909600w 132, 2938 (2010)]. We obtain geometries in good agreement with the experiment by using DFT with the Tkatchenko-Scheffler van der Waals correction. We demonstrate that even when DFT gives a good description of the valence spectrum and a qualitatively correct picture of the electronic structure of the dye-TiO2 interface, G0W0 calculations yield more valuable quantitative information regarding the fundamental gaps and level alignment. In addition, we systematically investigate the issues pertaining to G0W0 calculations, namely: (i) convergence with respect to the number of basis functions, (ii) dependence on the mean-field starting point, and (iii) the validity of the assumption that the DFT wave function is a good approximation to the quasiparticle wave function. We show how these issues are manifested for dye molecules and for dye-sensitized TiO2 clusters.

Play the heavy: An effective mass study for α-Fe{sub 2}O{sub 3} and corundum oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neufeld, Ofer; Caspary Toroker, Maytal, E-mail: maytalc@tx.technion.ac.il

2016-04-28

Iron(III) oxide (α-Fe{sub 2}O{sub 3}) is a known water splitting catalyst commonly used in photoelectrochemical cells. These cells are severely impaired by poor conductivity in α-Fe{sub 2}O{sub 3}, and resolving the conductivity issue is therefore crucial. One of the most intrinsic properties of matter, which governs conductivity, is the carrier effective masses. In this work, we investigate the carrier effective masses in α-Fe{sub 2}O{sub 3} and other corundum oxides, including Al{sub 2}O{sub 3}, Cr{sub 2}O{sub 3}, Ga{sub 2}O{sub 3}, and In{sub 2}O{sub 3} with different theoretical constructs: density functional theory (DFT), DFT+U, hybrid DFT, and G{sub 0}W{sub 0}. We findmore » DFT sufficiently describes the carrier masses and a quasi-particle theory is only required for accuracies better than 30% for the conduction band effective mass. Additionally, we compare the density of states (DOS) and band effective mass approximations and conclude the DOS effective mass provides poor results whenever the band structure is anisotropic. We find that the charge carriers in Fe{sub 2}O{sub 3} “play the heavy” since they have large effective masses that reduce conductivity and device efficiency. Finally, we conclude that the less heavy electron effective masses of other corundum oxides studied relative to Fe{sub 2}O{sub 3} could contribute to efficiency improvements in Fe{sub 2}O{sub 3} upon Al{sub 2}O{sub 3}, Ga{sub 2}O{sub 3}, and In{sub 2}O{sub 3} coverage.« less

Toward Accurate Adsorption Energetics on Clay Surfaces

PubMed Central

2016-01-01

Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields a very broad range of adsorption energies, and it is unclear a priori which evaluation is better. QMC reveals that in the systems considered here it is essential to account for van der Waals (vdW) dispersion forces since this alters both the absolute and relative adsorption energies of water and methanol. We show, via FF simulations, that incorrect relative energies can lead to significant changes in the interfacial densities of water and methanol solutions at the kaolinite interface. Despite the clear improvements offered by the vdW-corrected and the vdW-inclusive functionals, absolute adsorption energies are often overestimated, suggesting that the treatment of vdW forces in DFT is not yet a solved problem. PMID:27917256

BH-DFTB/DFT calculations for iron clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aktürk, Abdurrahman; Sebetci, Ali, E-mail: asebetci@mevlana.edu.tr

2016-05-15

We present a study on the structural, electronic, and magnetic properties of Fe{sub n}(n  =  2  −  20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima havemore » been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe{sub 9−13}), centered hexagonal antiprism (Fe{sub 14−17}, Fe{sub 20}), and truncated decahedral (Fe{sub 17(2)}, Fe{sub 18−19}). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fe{sub n}(n = 2 − 20) clusters is between 2.4 and 3.6 μ{sub B} for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe{sub 13} icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.« less

Experimental and DFT simulation study of a novel felodipine cocrystal: Characterization, dissolving properties and thermal decomposition kinetics.

PubMed

Yang, Caiqin; Guo, Wei; Lin, Yulong; Lin, Qianqian; Wang, Jiaojiao; Wang, Jing; Zeng, Yanli

2018-05-30

In this study, a new cocrystal of felodipine (Fel) and glutaric acid (Glu) with a high dissolution rate was developed using the solvent ultrasonic method. The prepared cocrystal was characterized using X-ray powder diffraction, differential scanning calorimetry, thermogravimetric (TG) analysis, and infrared (IR) spectroscopy. To provide basic information about the optimization of pharmaceutical preparations of Fel-based cocrystals, this work investigated the thermal decomposition kinetics of the Fel-Glu cocrystal through non-isothermal thermogravimetry. Density functional theory (DFT) simulations were also performed on the Fel monomer and the trimolecular cocrystal compound for exploring the mechanisms underlying hydrogen bonding formation and thermal decomposition. Combined results of IR spectroscopy and DFT simulation verified that the Fel-Glu cocrystal formed via the NH⋯OC and CO⋯HO hydrogen bonds between Fel and Glu at the ratio of 1:2. The TG/derivative TG curves indicated that the thermal decomposition of the Fel-Glu cocrystal underwent a two-step process. The apparent activation energy (E a ) and pre-exponential factor (A) of the thermal decomposition for the first stage were 84.90 kJ mol -1 and 7.03 × 10 7  min -1 , respectively. The mechanism underlying thermal decomposition possibly involved nucleation and growth, with the integral mechanism function G(α) of α 3/2 . DFT calculation revealed that the hydrogen bonding between Fel and Glu weakened the terminal methoxyl, methyl, and ethyl groups in the Fel molecule. As a result, these groups were lost along with the Glu molecule in the first thermal decomposition. In conclusion, the formed cocrystal exhibited different thermal decomposition kinetics and showed different E a , A, and shelf life from the intact active pharmaceutical ingredient. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthesis, crystal structure, vibrational spectroscopy, optical properties and theoretical studies of a new organic-inorganic hybrid material: [((CH3)2NH2)(+)]6·[(BiBr6)(3-)]2.

PubMed

Ben Ahmed, A; Feki, H; Abid, Y

2014-12-10

A new organic-inorganic hybrid material, [((CH3)2NH2)(+)]6·[(BiBr6)(3-)]2, has been synthesized and characterized by X-ray diffraction, FT-IR, Raman spectroscopy and UV-Visible absorption. The studied compound crystallizes in the triclinic system, space group P1¯ with the following parameters: a=8.4749(6)(Å), b=17.1392(12)(Å), c=17.1392(12)(Å), α=117.339(0)°, β=99.487(0)°, γ=99.487(0)° and Z=2. The crystal lattice is composed of a two discrete (BiBr6)(3-) anions surrounded by six ((CH3)2NH2)(+) cations. Complex hydrogen bonding interactions between (BiBr6)(3-) and organic cations from a three-dimensional network. Theoretical calculations were performed using density functional theory (DFT) for studying the molecular structure, vibrational spectra and optical properties of the investigated molecule in the ground state. The full geometry optimization of designed system is performed using DFT method at B3LYP/LanL2DZ level of theory using the Gaussian03. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from FT-IR and Raman spectra are assigned based on the results of the theoretical calculations. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental UV-Visible spectrum. The results show good consistent with the experiment and confirm the contribution of metal orbital to the HOMO-LUMO boundary. Copyright © 2014 Elsevier B.V. All rights reserved.

TD-DFT Insight into Photodissociation of Co-C Bond in Coenzyme B12

NASA Astrophysics Data System (ADS)

Kozlowski, Pawel; Liu, Hui; Kornobis, Karina; Lodowski, Piotr; Jaworska, Maria

2013-12-01

Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo-C → σ*Co-C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a MLCT (metal-to-ligand charge transfer) and a σ bonding-ligand charge transfer (SBLCT) states.

Theoretical Investigation of OCN(-) Charge Transfer Complexes in Condensed Phase Media: Spectroscopic Properties in Amorphous Ice

NASA Technical Reports Server (NTRS)

Park, Jin-Young; Woon, David E.

2004-01-01

Density functional theory (DFT) calculations of cyanate (OCN(-)) charge-transfer complexes were performed to model the "XCN" feature observed in interstellar icy grain mantles. OCN(-) charge-transfer complexes were formed from precursor combinations of HNCO or HOCN with either NH3 or H2O. Three different solvation strategies for realistically modeling the ice matrix environment were explored, including (1) continuum solvation, (2) pure DFT cluster calculations, and (3) an ONIOM DFT/PM3 cluster calculation. The model complexes were evaluated by their ability to reproduce seven spectroscopic measurements associated with XCN: the band origin of the OCN(-) asymmetric stretching mode, shifts in that frequency due to isotopic substitutions of C, N, O, and H, plus two weak features. The continuum solvent field method produced results consistent with some of the experimental data but failed to account for other behavior due to its limited capacity to describe molecular interactions with solvent. DFT cluster calculations successfully reproduced the available spectroscopic measurements very well. In particular, the deuterium shift showed excellent agreement in complexes where OCN(-) was fully solvated. Detailed studies of representative complexes including from two to twelve water molecules allowed the exploration of various possible solvation structures and provided insights into solvation trends. Moreover, complexes arising from cyanic or isocyanic acid in pure water suggested an alternative mechanism for the formation of OCN(-) charge-transfer complexes without the need for a strong base such as NH3 to be present. An extended ONIOM (B3LYP/PM3) cluster calculation was also performed to assess the impact of a more realistic environment on HNCO dissociation in pure water.

Band structure and orbital character of monolayer MoS2 with eleven-band tight-binding model

NASA Astrophysics Data System (ADS)

Shahriari, Majid; Ghalambor Dezfuli, Abdolmohammad; Sabaeian, Mohammad

2018-02-01

In this paper, based on a tight-binding (TB) model, first we present the calculations of eigenvalues as band structure and then present the eigenvectors as probability amplitude for finding electron in atomic orbitals for monolayer MoS2 in the first Brillouin zone. In these calculations we are considering hopping processes between the nearest-neighbor Mo-S, the next nearest-neighbor in-plan Mo-Mo, and the next nearest-neighbor in-plan and out-of-plan S-S atoms in a three-atom based unit cell of two-dimensional rhombic MoS2. The hopping integrals have been solved in terms of Slater-Koster and crystal field parameters. These parameters are calculated by comparing TB model with the density function theory (DFT) in the high-symmetry k-points (i.e. the K- and Γ-points). In our TB model all the 4d Mo orbitals and the 3p S orbitals are considered and detailed analysis of the orbital character of each energy level at the main high-symmetry points of the Brillouin zone is described. In comparison with DFT calculations, our results of TB model show a very good agreement for bands near the Fermi level. However for other bands which are far from the Fermi level, some discrepancies between our TB model and DFT calculations are observed. Upon the accuracy of Slater-Koster and crystal field parameters, on the contrary of DFT, our model provide enough accuracy to calculate all allowed transitions between energy bands that are very crucial for investigating the linear and nonlinear optical properties of monolayer MoS2.

Spectroscopic investigations (FT-IR, UV, 1H and 13C NMR) and DFT/TD-DFT calculations of potential analgesic drug 2-[2-(dimethylamino)ethyl]-6-methoxy-4-(pyridin-2-yl)-1(2H)-phthalazinone

NASA Astrophysics Data System (ADS)

Sroczyński, Dariusz; Malinowski, Zbigniew

2017-12-01

The theoretical molecular geometry and the IR, UV, 1H and 13C NMR spectroscopic properties of 2-[2-(dimethylamino)ethyl]-6-methoxy-4-(pyridin-2-yl)-1(2H)-phthalazinone with the previously demonstrated in vivo analgesic activity were characterized. The conformational analysis, performed using the molecular mechanics method with the General AMBER Force Field (GAFF) and the Density Functional Theory (DFT) approach with the B3LYP hybrid functional and the 6-31 + g(d) basis sets, allowed to determine the most stable rotamer. The theoretical molecular geometry of this conformer was then calculated at the B3LYP/6-311++g(d,p) level of theory, and its phthalazinone core was compared with the experimental geometry of 1(2H)-phthalazinone. The calculated vibrational frequencies and the potential energy distribution enabled to assign the theoretical vibrational modes to the experimental FT-IR bands. The UV spectrum calculated with the Time-Dependent Density Functional Theory (TD-DFT) method in methanol identified the main electronic transitions and their character. 1H and 13C NMR chemical shifts simulated by the Gauge-Independent Atomic Orbital (GIAO) method in chloroform confirmed the previous assignment of the experimental resonance signals. The stability of the molecule was considered taking into account the hyperconjugation and electron density delocalization effects evaluated by the Natural Bond Orbital (NBO) method. The calculated spatial distribution of molecular electrostatic potential made possible to estimate the regions with nucleophilic and electrophilic properties. The results of the potentiodynamic polarization measurements were also indicated the corrosion inhibition activity of the title compound on 100Cr6 bearing steel in 1 mol dm-3 HCl solution.

Symmetry properties of the electron density and following from it limits on the KS-DFT applications

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.

2018-03-01

At present, the Density Functional Theory (DFT) approach elaborated by Kohn with co-authors more than 50 years ago became the most widely used method for study molecules and solids. Using modern computation facilities, it can be applied to systems with million atoms. In the atmosphere of such great popularity, it is particularly important to know the limits of the applicability of DFT methods. In this report, I will discuss two cases when the conventional DFT approaches, using only electron density ρ and its gradients, cannot be applied (I will not consider the Ψ-versions of DFT). The first case is quite evident. In the degenerated states, the electron density may not be defined, since electronic and nuclear motions cannot be separated, the vibronic interaction mixed them. The second case is related to the spin of the state. As it was rigorously proved by group theoretical methods at the theorem level, the electron density does not depend on the total spin S of the arbitrary N-electron state. It means that the Kohn-Sham equations have the same form for states with different S. The critical survey of elaborated DFT procedures, taking into account spin, shows that they modified only exchange functionals, the correlation functionals do not correspond to the spin of the state. The point is that the conception of spin cannot be defined in the framework of the electron density formalism, which corresponds to the one-particle reduced density matrix. This is the main reason of the problems arising in the study by DFT of magnetic properties of the transition metals. The possible way of resolving these problems can be found in the two-particle reduced density matrix formulation of DFT.

Understanding density functional theory (DFT) and completing it in practice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bagayoko, Diola

2014-12-15

We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma andmore » Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.« less

Normal mode and experimental analysis of TNT Raman spectrum

NASA Astrophysics Data System (ADS)

Liu, Yuemin; Perkins, Richard; Liu, Yucheng; Tzeng, Nianfeng

2017-04-01

In this study, a Raman spectrum of TNT was characterized through experiments and simulated using 22 hybrid density functional theory (DFT) methods. Among the different hybrid DFT methods, it was found that the most accurate simulation results of the Raman shift frequency were calculated by the O3LYP method. However, the deviations of the calculated Raman frequencies from the experimental value showed no dependency on the abilities of the DFT methods in recovering the correlation energy. The accuracies of the DFT methods in predicting the Raman bands are probably determined by the numerical grid and convergence criteria for optimizations of each DFT method. It was also decided that the prominent Raman shift 1362 cm-1 is mainly caused by symmetric stretching of the 4-nitro groups. Findings of this study can facilitate futuristic development of more effective surface enhanced Raman spectroscopy/scattering (SERS) substrates for explosive characterization and detection.

DFT Performance Prediction in FFTW

NASA Astrophysics Data System (ADS)

Gu, Liang; Li, Xiaoming

Fastest Fourier Transform in the West (FFTW) is an adaptive FFT library that generates highly efficient Discrete Fourier Transform (DFT) implementations. It is one of the fastest FFT libraries available and it outperforms many adaptive or hand-tuned DFT libraries. Its success largely relies on the huge search space spanned by several FFT algorithms and a set of compiler generated C code (called codelets) for small size DFTs. FFTW empirically finds the best algorithm by measuring the performance of different algorithm combinations. Although the empirical search works very well for FFTW, the search process does not explain why the best plan found performs best, and the search overhead grows polynomially as the DFT size increases. The opposite of empirical search is model-driven optimization. However, it is widely believed that model-driven optimization is inferior to empirical search and is particularly powerless to solve problems as complex as the optimization of DFT.

Nuclear shielding constants by density functional theory with gauge including atomic orbitals

NASA Astrophysics Data System (ADS)

Helgaker, Trygve; Wilson, Philip J.; Amos, Roger D.; Handy, Nicholas C.

2000-08-01

Recently, we introduced a new density-functional theory (DFT) approach for the calculation of NMR shielding constants. First, a hybrid DFT calculation (using 5% exact exchange) is performed on the molecule to determine Kohn-Sham orbitals and their energies; second, the constants are determined as in nonhybrid DFT theory, that is, the paramagnetic contribution to the constants is calculated from a noniterative, uncoupled sum-over-states expression. The initial results suggested that this semiempirical DFT approach gives shielding constants in good agreement with the best ab initio and experimental data; in this paper, we further validate this procedure, using London orbitals in the theory, having implemented DFT into the ab initio code DALTON. Calculations on a number of small and medium-sized molecules confirm that our approach produces shieldings in excellent agreement with experiment and the best ab initio results available, demonstrating its potential for the study of shielding constants of large systems.

Reprint of "Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)"

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2017-02-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.

Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2016-12-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.

Polymer density functional theory approach based on scaling second-order direct correlation function.

PubMed

Zhou, Shiqi

2006-06-01

A second-order direct correlation function (DCF) from solving the polymer-RISM integral equation is scaled up or down by an equation of state for bulk polymer, the resultant scaling second-order DCF is in better agreement with corresponding simulation results than the un-scaling second-order DCF. When the scaling second-order DCF is imported into a recently proposed LTDFA-based polymer DFT approach, an originally associated adjustable but mathematically meaningless parameter now becomes mathematically meaningful, i.e., the numerical value lies now between 0 and 1. When the adjustable parameter-free version of the LTDFA is used instead of the LTDFA, i.e., the adjustable parameter is fixed at 0.5, the resultant parameter-free version of the scaling LTDFA-based polymer DFT is also in good agreement with the corresponding simulation data for density profiles. The parameter-free version of the scaling LTDFA-based polymer DFT is employed to investigate the density profiles of a freely jointed tangent hard sphere chain near a variable sized central hard sphere, again the predictions reproduce accurately the simulational results. Importance of the present adjustable parameter-free version lies in its combination with a recently proposed universal theoretical way, in the resultant formalism, the contact theorem is still met by the adjustable parameter associated with the theoretical way.

Molecular structure, vibrational spectra, NBO analysis, first hyperpolarizability, and HOMO-LUMO studies of 2-amino-4-hydroxypyrimidine by density functional method

NASA Astrophysics Data System (ADS)

Jeyavijayan, S.

2015-04-01

This study is a comparative analysis of FTIR and FT-Raman spectra of 2-amino-4-hydroxypyrimidine. The total energies of different conformations have been obtained from DFT (B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The barrier of planarity between the most stable and planar form is also predicted. The molecular structure, vibrational wavenumbers, infrared intensities, Raman scattering activities were calculated for the molecule using the B3LYP density functional theory (DFT) method. The computed values of frequencies are scaled using multiple scaling factors to yield good coherence with the observed values. Reliable vibrational assignments were made on the basis of total energy distribution (TED) along with scaled quantum mechanical (SQM) method. The stability of the molecule arising from hyperconjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Non-linear properties such as electric dipole moment (μ), polarizability (α), and hyperpolarizability (β) values of the investigated molecule have been computed using B3LYP quantum chemical calculation. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides, molecular electrostatic potential (MEP), Mulliken's charges analysis, and several thermodynamic properties were performed by the DFT method.

Copper and Zinc Chelation as a Treatment of Alzheimer's Disease

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Bernholc, Jerry

2014-03-01

Alzheimer's disease (AD) is a neurodegenerative disorder affecting millions of people in the U.S. The cause of the disease remains unknown, but amyloid- β (A β), a short peptide, is considered causal its pathogenesis. At cellular level, AD is characterized by deposits mainly composed of A β that also contain elevated levels of transition metals ions. Targeting metals is a promising new strategy for AD treatment, which uses moderately strong metal chelators to sequester them from A β or the environment. PBT2 is a chelating compound that has been the most promising in clinical trials. In our work, we use computer simulations to investigate complexes of a close analog of PBT2 with Cu2+ and Zn2+ ions. The calculations employ KS/FD DFT method, which combines Kohn-Sham DFT with the frozen-density DFT to achieve efficient description of explicit solvent beyond the first solvation shell. Our work is based on recent experiments and examines both 1:1 and 2:1 chelator-metal stochiometries detected experimentally. The results show that copper attaches more strongly than zinc, find that 1:1 complexes involve water in the first coordination shell and determine which one of several possible 2:1 geometries is the most preferable.

Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of 2,3,4,5,6-Pentafluoro-trans-cinnamic acid.

PubMed

Sert, Yusuf; Doğan, Hatice; Navarrete, Angélica; Somanathan, Ratnasamy; Aguirre, Gerardo; Çırak, Çağrı

2014-07-15

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized 2,3,4,5,6-Pentafluoro-trans-cinnamic acid have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted. Copyright © 2014 Elsevier B.V. All rights reserved.

Symmetry and structure of carbon-nitrogen complexes in gallium arsenide from infrared spectroscopy and first-principles calculations

NASA Astrophysics Data System (ADS)

Künneth, Christopher; Kölbl, Simon; Wagner, Hans Edwin; Häublein, Volker; Kersch, Alfred; Alt, Hans Christian

2018-04-01

Molecular-like carbon-nitrogen complexes in GaAs are investigated both experimentally and theoretically. Two characteristic high-frequency stretching modes at 1973 and 2060 cm-1, detected by Fourier transform infrared absorption (FTIR) spectroscopy, appear in carbon- and nitrogen-implanted and annealed layers. From isotopic substitution, it is deduced that the chemical composition of the underlying complexes is CN2 and C2N, respectively. Piezospectroscopic FTIR measurements reveal that both centers have tetragonal symmetry. For density functional theory (DFT) calculations, linear entities are substituted for the As anion, with the axis oriented along the 〈1 0 0 〉 direction, in accordance with the experimentally ascertained symmetry. The DFT calculations support the stability of linear N-C-N and C-C-N complexes in the GaAs host crystal in the charge states ranging from + 3 to -3. The valence bonds of the complexes are analyzed using molecular-like orbitals from DFT. It turns out that internal bonds and bonds to the lattice are essentially independent of the charge state. The calculated vibrational mode frequencies are close to the experimental values and reproduce precisely the isotopic mass splitting from FTIR experiments. Finally, the formation energies show that under thermodynamic equilibrium CN2 is more stable than C2N.

Synthesis, spectroscopic, electrochemical and computational studies of rhenium(i) tricarbonyl complexes based on bidentate-coordinated 2,6-di(thiazol-2-yl)pyridine derivatives.

PubMed

Klemens, Tomasz; Czerwińska, Katarzyna; Szlapa-Kula, Agata; Kula, Slawomir; Switlicka, Anna; Kotowicz, Sonia; Siwy, Mariola; Bednarczyk, Katarzyna; Krompiec, Stanisław; Smolarek, Karolina; Maćkowski, Sebastian; Danikiewicz, Witold; Schab-Balcerzak, Ewa; Machura, Barbara

2017-07-25

Nine rhenium(i) complexes possessing three carbonyl groups together with a bidentate coordinated 2,6-di(thiazol-2-yl)pyridine derivative were synthesized to examine the impact of structure modification of the triimine ligand on the photophysical, thermal and electrochemical properties of [ReCl(CO) 3 (4-R n -dtpy-κ 2 N)]. The Re(i) complexes were fully characterized using IR, 1 H and 13 C, HRMS-ESI and single crystal X-ray analysis. Their thermal properties were evaluated using DSC and TGA measurements. Photoluminescence spectra of [ReCl(CO) 3 (4-R n -dtpy-κ 2 N)] were investigated in solution and in the solid state, at 298 and 77 K. Both emission wavelengths and quantum yields of [ReCl(CO) 3 (4-R n -dtpy-κ 2 N)] were found to be structure-related, demonstrating a crucial role of the substituent attached to the 2,6-di(thiazol-2-yl)pyridine skeleton. In order to fully understand the photophysical properties of [ReCl(CO) 3 (4-R n -dtpy-κ 2 N)], density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed. Furthermore, the complexes which showed appropriate solubility in chloroform were tested as an emissive active layer in OLED devices.

Vibrational spectroscopic study, charge transfer interaction and nonlinear optical properties of L-asparaginium picrate: a density functional theoretical approach.

PubMed

Elleuch, Nabil; Amamou, Walid; Ben Ahmed, Ali; Abid, Younes; Feki, Habib

2014-07-15

Single crystals of L-asparaginium picrate (LASP) were grown by slow evaporation technique at room temperature and were the subject of an X-ray powder diffraction study to confirm the crystalline nature of the synthesized compound. FT-IR and Raman spectra were recorded and analyzed with the aid of the density functional theory (DFT) calculations in order to make a suitable assignment of the observed bands. The optimum molecular geometry, normal mode wavenumbers, infrared and Raman intensities and the first hyperpolarizability were investigated with the help of B3LYP method using 6-31G(d) basis set. The theoretical FT-IR and Raman spectra of LASP were simulated and compared with the experimental data. A good agreement was shown and a reliable vibrational assignment was made. Natural bond orbital (NBO) analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of the title compound leading to high NLO activity. A study on the electronic properties was performed by time-dependent DFT (TD-DFT) approach. The lowering in the HOMO and LUMO energy gap explains the eventual charge transfer interactions that take place within the molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure Determination of Au on Pt(111) Surface: LEED, STM and DFT Study

PubMed Central

Krupski, Katarzyna; Moors, Marco; Jóźwik, Paweł; Kobiela, Tomasz; Krupski, Aleksander

2015-01-01

Low-energy electron diffraction (LEED), scanning tunneling microscopy (STM) and density functional theory (DFT) calculations have been used to investigate the atomic and electronic structure of gold deposited (between 0.8 and 1.0 monolayer) on the Pt(111) face in ultrahigh vacuum at room temperature. The analysis of LEED and STM measurements indicates two-dimensional growth of the first Au monolayer. Change of the measured surface lattice constant equal to 2.80 Å after Au adsorption was not observed. Based on DFT, the distance between the nearest atoms in the case of bare Pt(111) and Au/Pt(111) surface is equal to 2.83 Å, which gives 1% difference in comparison with STM values. The first and second interlayer spacing of the clean Pt(111) surface are expanded by +0.87% and contracted by −0.43%, respectively. The adsorption energy of the Au atom on the Pt(111) surface is dependent on the adsorption position, and there is a preference for a hollow fcc site. For the Au/Pt(111) surface, the top interlayer spacing is expanded by +2.16% with respect to the ideal bulk value. Changes in the electronic properties of the Au/Pt(111) system below the Fermi level connected to the interaction of Au atoms with Pt(111) surface are observed.

Photodissolution of ferrihydrite in the presence of oxalic acid: an in situ ATR-FTIR/DFT study.

PubMed

Bhandari, Narayan; Hausner, Douglas B; Kubicki, James D; Strongin, Daniel R

2010-11-02

The photodissolution of the iron oxyhydroxide, ferrihydrite, in the presence of oxalic acid was investigated with vibrational spectroscopy, density functional theory (DFT) calculations, and batch geochemical techniques that determined the composition of the solution phase during the dissolution process. Specifically, in situ attenuated total reflection Fourier transform infrared spectroscopy (ATR- FTIR) was used to determine the structure of the adsorbed layer during the dissolution process at a solution pH of 4.5. DFT based computations were used to interpret the vibrational data associated with the surface monolayer in order to help determine the structure of the adsorbed complexes. Results showed that at pH 4.5, oxalate adsorbed on ferrihydrite adopted a mononuclear bidentate (MNBD) binding geometry. Photodissolution at pH 4.5 exhibited an induction period where the rate of Fe(II) release was limited by a low concentration of adsorbed oxalate due to the site-blocking of carbonate that was intrinsic to the surface of the ferrihydrite starting material. Oxalate displaced this initial carbonate over time, and the dissolution rate showed a corresponding increase. Irradiation of oxalate/ferrihydrite at pH 4.5 also ultimately led to the appearance of carbonate reaction product (distinct from carbonate intrinsic to the starting material) on the surface.

Combine experimental and theoretical investigation on an alkaloid-Dimethylisoborreverine

NASA Astrophysics Data System (ADS)

Singh, Swapnil; Singh, Harshita; Karthick, T.; Agarwal, Parag; Erande, Rohan D.; Dethe, Dattatraya H.; Tandon, Poonam

2016-01-01

A combined experimental (FT-IR, 1H and 13C NMR) and theoretical approach is used to study the structure and properties of antimalarial drug dimethylisoborreverine (DMIB). Conformational analysis, has been performed by plotting one dimensional potential energy curve that was computed using density functional theory (DFT) with B3LYP/6-31G method and predicted conformer A1 as the most stable conformer. After full geometry optimization, harmonic wavenumbers were computed for conformer A1 at the DFT/B3LYP/6-311++G(d,P) level. A complete vibrational assignment of all the vibrational modes have been performed on the bases of the potential energy distribution (PED) and theoretical results were found to be in good agreement with the observed data. To predict the solvent effect, the UV-Vis spectra were calculated in different solvents by polarizable continuum model using TD-DFT method. Molecular docking studies were performed to test the biological activity of the sample using SWISSDOCK web server and Hex 8.0.0 software. The molecular electrostatic potential (MESP) was plotted to identify the reactive sites of the molecule. Natural bond orbital (NBO) analysis was performed to get a deep insight of intramolecular charge transfer. Thermodynamical parameters were calculated to predict the direction of chemical reaction.

Linoleic acid and its potassium and sodium salts: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Gocen, Tuğba; Haman Bayarı, Sevgi; Haluk Guven, Mehmet

2017-12-01

Linoleic acid (cis, cis-9,12-octodecadienoic acid) is the main polyunsaturated -omega 6- essential fatty acid. The conformational behaviour of linoleic acid (LA) in the gas phase was investigated by means of density functional theory (DFT). The structures of conformers of LA were fully optimized by using the B3LYP/6-311++G(d,p) method. The theory showed that the tttttts‧CssCs‧tt conformation of LA (conformer I) is the more stable than the other conformations. Fourier Transform Infrared (FTIR) and micro-Raman spectra of pure LA in liquid form were recorded in the region 4000-450 and 3500-100 cm-1, respectively. The DFT calculations on the molecular structure and vibrational spectra of the dimer form of most stable conformer of LA were also performed using the same method. The assignment of the vibrational modes was made based on calculated potential energy distributions (PEDs). The simulated spectra of dimer form of LA are in reasonably good agreement with the experimental spectra. The sodium and potassium salts of LA were synthesized and characterized by FTIR and Raman spectroscopy, X-ray diffraction and DFT calculations. Several molecular and electronic properties of LA and its salts such as HOMO-LUMO energies, chemical hardness and electronegativity were also calculated and interpreted.

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of ferulic acid by density functional study

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sundaraganesan, N.; Manoharan, S.

2009-10-01

Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of ferulic acid (FA) (4-hydroxy-3-methoxycinnamic acid) were carried out by using density functional (DFT/B3LYP/BLYP) method with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment ( μ) and the first hyperpolarizability ( β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the FA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of FA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title molecule have been constructed.

Rationalization of Hubbard U in CeOx from first principles: Unveiling the role of local structure in screening

NASA Astrophysics Data System (ADS)

Lu, Deyu; Liu, Ping

2014-03-01

DFT+U method has been widely employed in theoretical studies on various ceria systems to correct the delocalization bias in local and semi-local DFT functionals with moderate computational cost. To rationalize the Hubbard U of Ce 4f, we employed the first principles linear response method to compute Hubbard U for Ce in ceria clusters, bulks, and surfaces. We found that in contrast to the commonly used approach treating U as a constant, the Hubbard U varies in a wide range from 4.1 eV to 6.7 eV, and exhibits a strong correlation with the Ce coordination numbers and Ce-O bond lengths, rather than the Ce 4f valence state. The variation of the Hubbard U can be explained by the changes in the strength of local screening due to O --> Ce intersite transition. Our study represents a systematic, quantitative investigation of the relationship between the Hubbard U and the local atomic arrangement, enabling a DFT+environment-dependent U scheme that can have potential impact on catalysis research of strongly correlated systems. This work is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

Investigation of antimicrobial activities, DNA interaction, structural and spectroscopic properties of 2-chloro-6-(trifluoromethyl)pyridine

NASA Astrophysics Data System (ADS)

Evecen, Meryem; Kara, Mehmet; Idil, Onder; Tanak, Hasan

2017-06-01

2-Chloro-6-(trifluoromethyl)pyridine has been characterized by FT-IR, 1H and 13C NMR experiment. FT-IR spectra of the molecule has been recorded in the 4000-400 cm-1 region. The molecular structural parameters and vibrational frequencies were computed using the HF and DFT (B3LYP, B3PW91) methods with the 6-31+G(d,p) and 6-311++G(d,p) basis sets. 1H and 13C NMR Gauge Including Atomic Orbital (GIAO) chemical shifts of the compound were calculated using the density functional method (B3LYP) with the 6-311++G(d,p) basis set. The vibrational wavenumbers and chemical shifts were compared with the experimental data of the compound. Using the TD-DFT methodology, electronic absorption spectra of the compound have been computed. Besides, solvent effects on the excitation energies and chemical shifts were carried out using the integral equation formalism of the polarisable continuum model (IEF-PCM). DFT calculations of the compound, Mulliken's charges, molecular electrostatic potential (MEP), natural bond orbital (NBO) and thermodynamic properties were also obtained theoretically. In addition, the antimicrobial activities were tested by using minimal inhibitory concentration method (MIC) and also the effect of the molecule on pBR322 plasmid DNA was monitored byagarose gel electrophoresis experiments.

Exploring the kinetic and thermodynamic aspects of four-electron electrochemical reactions: electrocatalysis of oxygen evolution by metal oxides and biological systems.

PubMed

Wang, Vincent C-C

2016-08-10

Finding fundamental and general mechanisms for electrochemical reactions, such as the oxygen evolution reaction (OER) from water and reduction of CO2, plays vital roles in developing the desired electrocatalysts for facilitating solar fuel production. Recently, density functional theory (DFT) calculations have shown that there is a universal scaling relation of adsorption energy between key intermediate species, HO(ad) and HOO(ad), on the surface of metal oxides as OER electrocatalysts. In this paper, a kinetic and thermodynamic model for the four-electron electrochemical reaction based on previous OER mechanisms proposed by DFT calculations is developed to further investigate the electrocatalytic properties over a wide range of metal oxides and photosystem II. The OER activity of metal oxides (i.e. electrocatalytic current) calculated from the DFT-calculated equilibrium potentials with kinetic properties, such as the rate constants for interfacial electron transfer and catalytic turnover, can lead to a volcano-shaped trend that agrees with the results observed in experiments. In addition, the kinetic aspects of the impact on the electrocatalysts are evaluated. Finally, comparing the results of metal oxides and photosystem II, and fitting experimental voltammograms give further insights into kinetic and thermodynamic roles. Here, the general guidelines for designing OER electrocatalysts with unified kinetic and thermodynamic properties are presented.

Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.

PubMed

Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

2013-01-15

Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (ωB97X, ωB97, LC-ωPBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ωB97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ωB97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ωB97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

Stereoselective green synthesis and molecular structures of highly functionalized spirooxindole-pyrrolidine hybrids - A combined experimental and theoretical investigation

NASA Astrophysics Data System (ADS)

Kumar, Raju Suresh; Almansour, Abdulrahman I.; Arumugam, Natarajan; Soliman, Saied M.; Kumar, Raju Ranjith; Altaf, Mohammad; Ghabbour, Hazem A.; Krishnamoorthy, Bellie Sundaram

2018-01-01

Highly functionalized spirooxindole-pyrrolidine hybrids have been synthesized stereoselectively through a [3 + 2] cycloaddition strategy in an ionic liquid, 1-butyl-3-methylimidazolium bromide ([bmim]Br). The structure of these spiro heterocyclic hybrids was elucidated using one and two dimensional NMR spectroscopy, single crystal X-ray crystallographic studies and Density Functional Theory (DFT) calculations. The calculated geometric parameters are in good agreement with the experimental data obtained from the X-ray structures. The Natural Bond Orbital (NBO) calculations on these molecules confirm the electron rich carbonyl oxygen and electron deficient NH groups. The 1H and 13C NMR chemical shifts calculated using GIAO method are in good agreement with the experimental data. The DFT computed polarizability values also suggest the possible NLO activity of these molecules.

Role of Kekulé and Non-Kekulé Structures in the Radical Character of Alternant Polycyclic Aromatic Hydrocarbons: A TAO-DFT Study

PubMed Central

Yeh, Chia-Nan; Chai, Jeng-Da

2016-01-01

We investigate the role of Kekulé and non-Kekulé structures in the radical character of alternant polycyclic aromatic hydrocarbons (PAHs) using thermally-assisted-occupation density functional theory (TAO-DFT), an efficient electronic structure method for the study of large ground-state systems with strong static correlation effects. Our results reveal that the studies of Kekulé and non-Kekulé structures qualitatively describe the radical character of alternant PAHs, which could be useful when electronic structure calculations are infeasible due to the expensive computational cost. In addition, our results support previous findings on the increase in radical character with increasing system size. For alternant PAHs with the same number of aromatic rings, the geometrical arrangements of aromatic rings are responsible for their radical character. PMID:27457289

Electronic structure, mechanical and thermodynamic properties of BaPaO3 under pressure.

PubMed

Khandy, Shakeel Ahmad; Islam, Ishtihadah; Gupta, Dinesh C; Laref, Amel

2018-05-07

Density functional theory (DFT)-based investigations have been put forward on the elastic, mechanical, and thermo-dynamical properties of BaPaO 3 . The pressure dependence of electronic band structure and other physical properties has been carefully analyzed. The increase in Bulk modulus and decrease in lattice constant is seen on going from 0 to 30 GPa. The predicted lattice constants describe this material as anisotropic and ductile in nature at ambient conditions. Post-DFT calculations using quasi-harmonic Debye model are employed to envisage the pressure-dependent thermodynamic properties like Debye temperature, specific heat capacity, Grüneisen parameter, thermal expansion, etc. Also, the computed Debye temperature and melting temperature of BaPaO 3 at 0 K are 523 K and 1764.75 K, respectively.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuo, Hiroki; Kitanaka, Yuuki; Inoue, Ryotaro

We investigate the mechanism of a switchable diode behavior observed in ferroelectric SrRuO{sub 3}/BiFeO{sub 3} (BFO)/SrRuO{sub 3} capacitors. We experimentally demonstrate that the switchable diode effect observed in the capacitors is induced by the polarization reversal in the BFO film. The conductivity in an Ohmic region in different oxidation states provides direct evidence that electron hole acts as the majority carrier, delivering p-type conduction. Density functional theory (DFT) calculations show that the p-type conduction arises from an unoccupied gap state of Fe{sup 4+} in an FeO{sub 5} pyramid which is derived from Bi vacancy. Our experimental and DFT study leadsmore » to the conclusion that the switchable diode effect originates from an asymmetric band bending in the top and bottom depletion layers modulated by ferroelectric polarization and oxygen vacancies.« less

Protonated o-semiquinone radical as a mimetic of the humic acids native radicals: A DFT approach to the molecular structure and EPR properties

NASA Astrophysics Data System (ADS)

Witwicki, Maciej; Jezierska, Julia

2012-06-01

Organic radicals are known to be an indispensable component of the humic acids (HA) structure. In HA two forms of radicals, stable (native) and short-lived (transient), are identified. Importantly, these radical forms can be easily differentiated by electron paramagnetic resonance (EPR) spectroscopy. This article provides a DFT-based insight into the electronic and molecular structure of the native radicals. The molecular models including an increase of the radical aromaticity and the hydrogen bonding between the radical and other functional groups of HA are taken under investigation. In consequence the interesting pieces of information on the structure of the native radical centers in HA are revealed and discussed, especially in terms of differences between the electronic structure of the native and transient forms.

Atomic Defects and Doping of Monolayer NbSe2.

PubMed

Nguyen, Lan; Komsa, Hannu-Pekka; Khestanova, Ekaterina; Kashtiban, Reza J; Peters, Jonathan J P; Lawlor, Sean; Sanchez, Ana M; Sloan, Jeremy; Gorbachev, Roman V; Grigorieva, Irina V; Krasheninnikov, Arkady V; Haigh, Sarah J

2017-03-28

We have investigated the structure of atomic defects within monolayer NbSe 2 encapsulated in graphene by combining atomic resolution transmission electron microscope imaging, density functional theory (DFT) calculations, and strain mapping using geometric phase analysis. We demonstrate the presence of stable Nb and Se monovacancies in monolayer material and reveal that Se monovacancies are the most frequently observed defects, consistent with DFT calculations of their formation energy. We reveal that adventitious impurities of C, N, and O can substitute into the NbSe 2 lattice stabilizing Se divacancies. We further observe evidence of Pt substitution into both Se and Nb vacancy sites. This knowledge of the character and relative frequency of different atomic defects provides the potential to better understand and control the unusual electronic and magnetic properties of this exciting two-dimensional material.

The Role of Sodium in Tuning Product Distribution in Syngas Conversion by Rh Catalysts

DOE PAGES

Yang, Nuoya; Liu, Xinyan; Asundi, Arun S.; ...

2017-10-23

Alkali metal oxides commonly exist as impurities or promoters in syngas conversion catalysts and can significantly influence the activity and selectivity towards higher oxygenate products. In this study, we investigate the effects of sodium oxide on silica-supported Rh catalysts by experimentally introducing different amounts of sodium and monitoring the change in reactivity and CO adsorption behavior. The experimental results combined with density functional theory (DFT) calculations show that sodium selectively blocks step/defect sites on Rh surfaces, leading to reduced activity but higher C 2 oxygenate selectivity. DFT calculations also suggest that sodium present on Rh terrace sites can facilitate COmore » dissociation, potentially increasing C 2 oxygenate production. The overall activity and selectivity toward various products can be changed significantly based on the degree of site blocking by the added sodium.« less

Dye-sensitized solar cells and complexes between pyridines and iodines. A NMR, IR and DFT study.

PubMed

Hansen, Poul Erik; Nguyen, Phuong Tuyet; Krake, Jacob; Spanget-Larsen, Jens; Lund, Torben

2012-12-01

Interactions between triiodide (I(3)(-)) and 4-tert-butylpyridine (4TBP) as postulated in dye-sensitized solar cells (DSC) are investigated by means of (13)C NMR and IR spectroscopy supported by DFT calculations. The charge transfer (CT) complex 4TBP·I(2) and potential salts such as (4TBP)(2)I(+), I(3)(-) were synthesized and characterized by IR and (13)C NMR spectroscopy. However, mixing (butyl)(4)N(+), I(3)(-) and 4TBP at concentrations comparable to those of the DSC solar cell did not lead to any reaction. Neither CT complexes nor cationic species like (4TBP)(2)I(+) were observed, judging from the (13)C NMR spectroscopic evidence. This questions the previously proposed formation of (4TBP)(2)I(+) in DSC cells. Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis, characterization of (3E)-1-(6-chloro-2-methyl-4-phenyl quinolin-3-Yl)-3-aryl prop-2-en-1-ones through IR, NMR, single crystal X-ray diffraction and insights into their electronic structure using DFT calculations

NASA Astrophysics Data System (ADS)

Sarveswari, S.; Srikanth, A.; Arul Murugan, N.; Vijayakumar, V.; Jasinski, Jerry P.; Beauchesne, Hanna C.; Jarvis, Ethan E.

2015-02-01

3E-1-(6-Chloro-2-methyl-4-phenylquinolin-3-yl)-3-arylprop-2-en-1-ones were synthesized and characterized by FTIR, 1H NMR, 13C NMR, HSQC, DEPT-135. In addition the compound 3E-1-(6-chloro-2-methyl-4-phenylquinolin-3-yl)-3-(2,5-dimethoxyphenyl)prop-2-en-1-one was subjected to the single crystal X-ray diffraction studies. Density functional theory calculations were carried out for this chalcone and its derivatives to investigate into their electronic structure, chemical reactivity, linear and non-linear optical properties. The structure predicted from DFT for chalcone is in good agreement with the structure from XRD measurement.

Synthesis, characterization and calculated non-linear optical properties of two new chalcones

NASA Astrophysics Data System (ADS)

Singh, Ashok Kumar; Saxena, Gunjan; Prasad, Rajendra; Kumar, Abhinav

2012-06-01

Two new chalcones viz 3-(4-(benzyloxy)phenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (1) and 3-(4-chlorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (2) have been prepared and characterized by micro analyses, 1H NMR, IR, UV-Vis spectroscopy and single crystal X-ray. The first static hyperpolarizability (β) for both the compounds has been investigated by density functional theory (DFT). Also, the solvent-induced effects on the non-linear optical properties (NLO) were studied by using self-consistent reaction field (SCRF) method. As the solvent polarity increases, the β value increases monotonically. The electronic absorption bands of both 1 and 2 have been assigned by time dependent density functional theory (TD-DFT). Both the compounds displayed better non-linear optical (NLO) responses than the standard p-nitroaniline (pNA).

Synthesis of a zinc(II) complex with hexadentate N4S2 donor thioether ligand: X-ray structure, DNA binding study and DFT computation

NASA Astrophysics Data System (ADS)

Mondal, Apurba Sau; Jana, Mahendra Sekhar; Manna, Chandan Kumar; Naskar, Rahul; Mondal, Tapan Kumar

2018-07-01

A new zinc(II) complex, [Zn(L)](ClO4) with hexadentate N4S2 donor azo-thioether ligand (HL) was synthesized and characterized by several spectroscopic techniques. The structure was confirmed by single crystal X-ray analysis. The interaction of the complex with CT DNA was investigated by UV-vis method and binding constant is found to be 6.6 × 104 M-1. Competitive binding titration with ethidium bromide (EB) by fluorescence titration method reveals that the complex efficiently displaces EB from EB-DNA system and the Stern-Volmer dynamic quenching constant, Ksv is found to be 2.6 × 104 M-1. DFT and TDDFT calculations were carried out to interpret the electronic structure and electronic spectra of the complex.

How Does Lithiation Affect Electro-Optical Features of Corannulene (C20H10) and Quadrannulene (C16H8) Buckybowls?

NASA Astrophysics Data System (ADS)

Shakerzadeh, Ehsan; Kazemimoghadam, Fatemeh; Anota, Ernesto Chigo

2018-04-01

The influence of lithiation process on the HOMO-LUMO gap and the first hyperpolarizability values of corannulene (C20H10) and quadrannulene (C16H8) buckybowls are investigated using density functional theory (DFT) calculations. Lithiation is performed at the bridging position of the C-C bond of benzene rings of quadrannulene and corannulene. The HOMO-LUMO gap of lithiated buckybowls is reduced with respect to pristine ones. The results indicate that the lithiation process causes the remarkable enhancement of the first hyperpolarizability. The time-dependent density functional theory (TD-DFT) calculations are also performed to understand how lithiation affects the first hyperpolarizability values. The present results might be valuable for further theoretical and experimental studies on the electronic and nonlinear optical properties of buckybowl compounds.

Imaging of the outer valence orbitals of CO by electron momentum spectroscopy — Comparison with high level MRSD-CI and DFT calculations

NASA Astrophysics Data System (ADS)

Fan, X. W.; Chen, X. J.; Zhou, S. J.; Zheng, Y.; Brion, C. E.; Frey, R.; Davidson, E. R.

1997-09-01

A newly constructed energy dispersive multichannel electron momentum spectrometer has been used to image the electron density of the outer valence orbitals of CO with high precision. Binding energy spectra are obtained at a coincidence energy resolution of 1.2 eV fwhm. The measured electron density profiles in momentum space for the outer valence orbitals of CO are compared with cross sections calculated using SCF wavefunctions with basis sets of varying complexity up to near-Hartree-Fock limit in quality. The effects of correlation and electronic relaxation on the calculated momentum profiles are investigated using large MRSD-CI calculations of the full ion-neutral overlap distributions, as well as large basis set DFT calculations with local and non-local (gradient corrected) functionals.

The Role of Sodium in Tuning Product Distribution in Syngas Conversion by Rh Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Nuoya; Liu, Xinyan; Asundi, Arun S.

Alkali metal oxides commonly exist as impurities or promoters in syngas conversion catalysts and can significantly influence the activity and selectivity towards higher oxygenate products. In this study, we investigate the effects of sodium oxide on silica-supported Rh catalysts by experimentally introducing different amounts of sodium and monitoring the change in reactivity and CO adsorption behavior. The experimental results combined with density functional theory (DFT) calculations show that sodium selectively blocks step/defect sites on Rh surfaces, leading to reduced activity but higher C 2 oxygenate selectivity. DFT calculations also suggest that sodium present on Rh terrace sites can facilitate COmore » dissociation, potentially increasing C 2 oxygenate production. The overall activity and selectivity toward various products can be changed significantly based on the degree of site blocking by the added sodium.« less

Multicomponent DFT study of geometrical H/D isotope effect on hydrogen-bonded organic conductor, κ-H3(Cat EDT-ST)2

NASA Astrophysics Data System (ADS)

Yamamoto, Kaichi; Kanematsu, Yusuke; Nagashima, Umpei; Ueda, Akira; Mori, Hatsumi; Tachikawa, Masanori

2017-04-01

We theoretically investigated a significant contraction of the hydrogen-bonding O⋯O distance upon H/D substitution in our recently developed purely organic crystals, κ-H3(Cat-EDT-ST)2 (H-ST) and its isotopologue κ-D3(Cat-EDT-ST)2 (D-ST), having π-electron systems coupled with hydrogen-bonding fluctuation. The origin of this geometrical H/D isotope effect was elucidated by using the multicomponent DFT method, which takes the H/D nuclear quantum effect into account. The optimized O⋯O distance in H-ST was found to be longer than that in D-ST due to the anharmonicity of the potential energy curve along the Osbnd H bond direction, which was in reasonable agreement with the experimental trend.

Phase transition and intramolecular hydrogen bonding in nitro derivatives of ortho-hydroxy acetophenones

NASA Astrophysics Data System (ADS)

Filarowski, A.; Kochel, A.; Koll, A.; Bator, G.; Mukherjee, S.

2006-03-01

The crystal structures of two ortho-hydroxy aryl ketones (5-chloro-3-nitro-2-hydroxyacetophenone, 5-methyl-3-nitro-2-hydroxyacetophenone and the complex 5-chloro-3-nitro-2-hydroxyacetophenone with 2-aminobenzoic acid (anthranilic acid)) were determined by X-ray diffraction. The existence of an intramolecular hydrogen bond of enol character between the hydroxyl and acetyl groups was found by the X-ray method. The enol character was also confirmed by DFT (B3LYP/6-31+G(d,p)) calculations. A phase transition was found at 138 K in 5-chloro-3-nitro-2-hydroxyacetophenone. This phase transition was investigated by differential scanning calorimetry (DSC), dilatometry, and the dielectric method. A study of the nitro-group dynamics in the ortho-hydroxy acetophenones was carried out with DFT (B3LYP/6-31+G(d,p)) calculations.

DFT STUDY OF THE HYDROLYSIS OF SOME S-TRIAZINES

EPA Science Inventory

The acid-catalyzed hydrolysis of atrazine and related 2-chloro-s-triazines to the corresponding 2-hydroxy-s-triazines was investigated using the B3LYP hybrid density functional theory method. Gas-phase calculations were performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of ...

Anisotropy and temperature dependence of structural, thermodynamic, and elastic properties of crystalline cellulose Iβ: a first-principles investigation

Treesearch

ShunLi Shang; Louis G. Hector Jr.; Paul Saxe; Zi-Kui Liu; Robert J. Moon; Pablo D. Zavattieri

2014-01-01

Anisotropy and temperature dependence of structural, thermodynamic and elastic properties of crystalline cellulose Iβ were computed with first-principles density functional theory (DFT) and a semi-empirical correction for van der Waals interactions. Specifically, we report the computed temperature variation (up to 500...