Search results for "DENSITY FUNCTIONAL THEORY"
showing 10 items of 981 documents
Adsorption of the herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) by goethite.
2014
Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide was studied using density functional theory (DFT) calculations combined with molecular dynamics (MD). The important step made here lies in the use of a periodic DFT method enabling the study of a mineral surface of different protonation states, in strong contrast with previous molecular modeling studies limited to single protonation state corresponding to the point of zero charge. Different surface OH groups and MCPA proton states were used to mimic the strong effects of pH on the outer- and inner-sphere surface complexes that are theoretically possible, together with their binding energies, an…
A topological isomer of the Au25(SR)18−nanocluster
2020
Energetically low-lying structural isomers of the much-studied thiolate-protected gold cluster Au25(SR)18− are discovered from extensive (80 ns) molecular dynamics (MD) simulations using the reactive molecular force field ReaxFF and confirmed by density functional theory (DFT). A particularly interesting isomer is found, which is topologically connected to the known crystal structure by a low-barrier collective rotation of the icosahedral Au13 core. The isomerization takes place without breaking of any Au–S bonds. The predicted isomer is essentially iso-energetic with the known Au25(SR)18− structure, but has a distinctly different optical spectrum. It has a significantly larger collision cr…
Supramolecular functionalization and concomitant enhancement in properties of Au25 clusters
2014
We present a versatile approach for tuning the surface functionality of an atomically precise 25 atom gold cluster using specific host-guest interactions between ?-cyclodextrin (CD) and the ligand anchored on the cluster. The supramolecular interaction between the Au25 cluster protected by 4-(t-butyl)benzyl mercaptan, labeled Au25SBB18, and CD yielding Au25SBB18�?�CDn (n = 1, 2, 3, and 4) has been probed experimentally using various spectroscopic techniques and was further analyzed by density functional theory calculations and molecular modeling. The viability of our method in modifying the properties of differently functionalized Au25 clusters is demonstrated. Besides modifying their optoe…
First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases
2020
An extensive theoretical characterization of the singlet excited state manifold of the five canonical DNA/RNA nucleobases (thymine, cytosine, uracil, adenine and guanine) in gas-phase is carried out with time-dependent density functional theory (TD-DFT) and restricted active space second-order perturbation theory (RASPT2) approaches. Both ground state and excited state absorptions are analyzed and compared between these different theoretical approaches, assessing the performance of the hybrid B3LYP and CAM-B3LYP (long-range corrected) functionals with respect to the RASPT2 reference. By comparing the TD-DFT estimates with our reference for high-lying excited states, we are able to narrow do…
Gamow-Teller response in the configuration space of a density-functional-theory–rooted no-core configuration-interaction model
2018
Background: The atomic nucleus is a unique laboratory in which to study fundamental aspects of the electroweak interaction. This includes a question concerning in medium renormalization of the axial-vector current, which still lacks satisfactory explanation. Study of spin-isospin or Gamow-Teller (GT) response may provide valuable information on both the quenching of the axial-vector coupling constant as well as on nuclear structure and nuclear astrophysics.Purpose: We have performed a seminal calculation of the GT response by using the no-core configuration-interaction approach rooted in multireference density functional theory (DFT-NCCI). The model treats properly isospin and rotational sy…
"Recognition of a Novel Type X=N-Hal•••Hal' (X = , S, P; Hal = F, Cl, Br, I) Halogen Bonding"
2013
The chlorination of the eight-membered platinum(II) chelates (PtCl2{NHC(NR2)N(Ph)C(NH)- N(Ph)C(NR2)NH}) (R = Me (1); R2 = (CH2)5 (2)) with uncomplexed imino group with Cl2 gives complexes bearing the N−Cl moiety (PtCl4{NHC(NR2)N(Ph)C(NCl)N- (Ph)C(NR2)NH}) (R = Me (3); R2 = (CH2)5 (4)). X-ray study for 3 revealed a novel type intermolecular halogen bonding N−Cl···Cl − , formed between the Cl atom of the chlorinated imine and the chloride bound to the platinum(IV) center. The processing relevant structural data retrieved from the Cambridge Structural Database (CSDB) shows that this type of halogen bonding is realized in 18 more molecular species having XN−Hal moieties (X = C, P, S, V…
3 He NMR studies on helium-pyrrole, helium-indole, and helium-carbazole systems: a new tool for following chemistry of heterocyclic compounds
2014
The 3He nuclear magnetic shieldings were calculated for free helium atom and He–pyrrole, He–indole, and He–carbazole complexes. Several levels of theory, including Hartree–Fock (HF), Second-order Moller-Plesset Perturbation Theory (MP2), and Density Functional Theory (DFT) (VSXC, M062X, APFD, BHandHLYP, and mPW1PW91), combined with polarization-consistent pcS-2 and aug-pcS-2 basis sets were employed. Gauge-including atomic orbital (GIAO) calculated 3He nuclear magnetic shieldings reproduced accurately previously reported theoretical values for helium gas. 3He nuclear magnetic shieldings and energy changes as result of single helium atom approaching to the five-membered ring of pyrrole, indo…
Theoretical investigations of nitrogen doping on Co 3 O 4 for water dissociation catalytically activity
2018
We report the results of theoretical investigations of nitrogen doping on Co 3 O 4 (100) bulk by means of the plane-wave periodic density functional theory (DFT) calculations combined with the Hubbard-U approach and statistical thermodynamics.Using accurate DFT+U calculations, we have shown that bulk Co ions denote charges in value 0.017 - 0.57e. For further water adsorption process studies was selected structures with most changes in charges in Co ions: (3) structure for n = 25%, (2) structure forn = 12.5% and structure for (1) structure.
Interpretation of the U L3-edge EXAFS in uranium dioxide using molecular dynamics and density functional theory simulations
2016
X-ray absorption spectroscopy is employed to study the local structure of pure and Cr-doped UO2 at 300 K. The U L3-edge EXAFS spectrum is interpreted within the multiplescattering (MS) theory using the results of the classical and ab initio molecular dynamics simulations, allowing us to validate the accuracy of theoretical models. The Cr K-edge XANES is simulated within the full-multiple-scattering formalism considering a substitutional model (Cr at U site). It is shown that both unrelaxed and relaxed structures, produced by ab initio density functional theory (DFT) calculations, fail to describe the experiment.
Metal complex-DNA binding: Insights from molecular dynamics and DFT/MM calculations.
2012
Molecular dynamics (MD) simulations, followed by density functional theory/molecular mechanics (DFT/MM) calculations, provided a detailed structure of the binding site between the cationic metallointercalator (dipyrido [3,2-a:2',3'-c]phenazine)(glycinato)copper(II), [Cu(gly)(dppz)](+), and the two dodeca-deoxynucleotide duplexes [dodeca(dG-dC)]2 and [dodeca(dA-dT)]2. Three simultaneous DNA binding types were detected in the fully optimized DFT/MM structures: 1) metal coordination through exocyclic oxygen atoms of nitrogen bases; 2) intercalation of the dppz chromophore between stacked Watson-Crick AT-AT and GC-GC bases; and 3) hydrogen bonding between the glycinato ligand and amine groups o…