Theoretical DFT Study Research Articles

Interaction of Ga3 cluster with molecular hydrogen: combined DFT and CCSD(T) theoretical study

We have explored the lowest doublet and quartet potential energy surfaces (PES) for the reaction of gallium trimer with H2. This reaction was studied experimentally by Margrave and co-workers in a noble gas matrix. The detailed reaction paths ending up with the low-energy Ga3H2 hydride isomers have been predicted based on the high level ab initio coupled-cluster calculations (CCSD(T)) with large basis set. We have found that the reaction occuring on the lowest doublet PES is described by the activation barrier for H2 cleavage of about 15 kcal/mol, consistent with experiment. In the most stable Ga3H2 hydride structure, whose formation is exothermic by 15 kcal/mol, both H atoms assume three-fold bridged positions. The diterminal planar structure of Ga3H2, proposed experimentally from the observed IR spectra, is found to be only 1 kcal/mol less stable than the dibridged form.

DNA bindings of a novel anticancer drug, trans-[PtCl2(isopropylamine)(3-picoline)], and kinetic competition of purine bases with protein residues in the bifunctional substitutions: a theoretical DFT study

The coordination of an activated novel anticancer drug, trans-[PtCl2(ipa)(3-pico)] (ipa = isopropylamine, 3-pico = 3-methylpyridine), to DNA in a two-step process has been studied using a combination of DFT theory and IEF–PCM approach. The computed free energy barrier for the first substitution is 16.9/16.9 kcal/mol for trans-Pt-chloroaqua → trans-/cis-Pt–guanine monoadduct, 18.7/18.7 kcal/mol for trans-Pt-chloroaqua → trans-/cis-Pt–adenine monoadduct. Barriers of 20.2/20.2 kcal/mol are evaluated for trans-Pt-diaqua → trans-/cis-Pt–guanine monoadduct, 26.0/26.0 kcal/mol for trans-Pt-diaqua → trans-/cis-Pt–adenine monoadduct. In the second substitution starting from trans-Pt–guanine monoadduct to trans-diadducts, the reaction barrier for (G–Pt–G) head-to-head formation is 22.2 kcal/mol, while 22.0 kcal/mol is evaluated for the head-to-tail configuration. Barriers for (A–Pt–G) head-to-head and head-to-tail formation are 25.7/28.9 kcal/mol, respectively. The observed preference for guanine is explained in terms of remarkable larger complexation energy for the initial reactant complex as well as the lower barrier height for the substitutions. In the competition reactions, cysteine residue stabilizes the transition state (ΔG aq/ZPE = 13.1 kcal/mol) for platination more efficiently than purine bases and other protein residues.

Tautomeric forms of N-(5-nitrosalicylidene)-2-butylamine: Experimental and theoretical DFT study

Tautomeric forms of N-(5-nitrosalicylidene)-2-butylamine in various solvents were studied with the IR and NMR ( 1H, 13C) spectroscopy. Also computational studies of keto-amine (O···HN) and enol-imine (OH···N) tautomers of N-(5-nitrosalicylidene)-2-butylamine molecule in the ground state were carried out with the DFT and SCRF theory at B3LYP/6-31G(d,p) level. Experimental data show that the solvent can invert the keto-amino: enol-imine equilibrium. The enol-imine tautomer prevails in non polar CCl 4 and weakly polar CDCl 3 or CD 2Cl 2 solvents, while in polar CD 3CN solvent the keto-amine form dominates. Theoretical results agree qualitatively with the experimental findings and suggest also that predominance of particular tautomers can be influenced by the aliphatic chain geometry. Theoretical enol-imine model structure corresponding to the vacuum or non polar environment e.g.CCl 4 is more stable than the keto-amino counterpart. On the contrary, the keto-amino form is predicted to be more stable than the enol-imine form in aqueous or in CH 3CN polar environments. A satisfactory correlation between theoretical 1H and 13C shielding constants and experimental 1H and 13C chemical shifts becomes an additional argument that the three-dimension structures predicted theoretically should appear in the experimental conditions.

Spectroscopic and theoretical study of amlodipine besylate

In this work, a joint experimental (FT-IR, FT-Raman, NMR) and theoretical DFT study on 3-ethyl-5-methyl-2-(2-aminoethoxymethyl)-4-(2-chlorophenyl)-1,4-dihydro-6-methyl-3,5-pyridinedicarboxylate benzenesulphonate (amlodipine besylate) compound is reported. The experimental vibrational spectra have been assigned based on DFT calculations performed at B3LYP level of theory using the standard 6-31G(d) basis set and a uniform scaling of the calculated wave numbers. The mean deviation in reproducing the whole Raman and FT-IR spectra by B3LYP/6-31G(d) calculations is 7.7 and 6.0 cm −1, respectively. The experimental 1H NMR spectrum of amlodipine besylate was successfully reproduced by theoretical DFT calculations of the nuclear magnetic shielding tensors, using the GIAO method. The molecular electrostatic potential of the molecule has been calculated and used for predicting site candidates for electrophilic attack.

Organocatalytic activity of 4-hydroxy-prolinamide alcohol with different noncovalent coordination sites in asymmetric Michael and direct aldol reactions

4-Hydroxy-prolinamide alcohol with different noncoordination sites as a molecule showed excellent asymmetric catalytic activity in both the Michael reaction (up to 98% ee) and the direct aldol reaction (up to >99% ee), and the catalyzing reactions with high enantioselectivity are supported by a DFT theoretical study of their transition state.

What Silicon Nanocluster is Most Likely Formed in Etching Experiments? Theoretical DFT Study

Density functional calculations at the B3LYP/6-31G* level were performed for Si nanoclusters of ca. 1 nm in size. The structural, energetic, electronic as well as the estimated absorption spectra by the time-dependent DFT (TDDFT) calculations using varied functionals and basis sets for the representative cluster models are all in favor of the formation of most probable Si35H36 nanocluster in recent electrochemical etching experiments. The nanostructure has a complete H-termination at the borderline regions and lacks from the presence of any defects like surface Si-Si dimer units formed via self-healing of dangling Si-Si bonds or from any relatively short H...H contacts.

Theoretical Study of the Asymmetric Conjugate Alkenylation of Enones Catalyzed by Binaphthols

To rationalize the experimental results observed in the asymmetric conjugate addition of alkenylboronates to enones catalyzed by binaphthols and shed light into the factors controlling the rate, the selectivity, and the substituent effects of this process, a theoretical DFT study has been performed. The calculations suggest the catalytic cycle is finely balanced. Reversible exchange of methoxy ligands gives rise to the binaphthol-derived alkenylboronate, which is highly Lewis acidic and strongly coordinates to the enone carbonyl in a reversible fashion, lowering the energy barrier for the subsequent conjugate addition step. The key asymmetric step goes through a sofalike transition structure in which the boron atom is strongly bound to the carbonyl oxygen and lies in the plane of the enone moiety. A steric clash between one of the iodine atoms of the ligand and one face of the enone seems to be responsible for the facial discrimination. The alternative reaction channel in which only one methoxy ligand of the alkenylboronate is exchanged was investigated too and was computed to be disfavored. The [4 + 2] and the [4 + 3] pathways for the competitive hetero-Diels-Alder reaction were also found to be disfavored relative to the conjugate alkenylboration. In addition, the effects of substitution on the enone and the alkenylboronate have been evaluated. Calculations correctly reproduced the experimental reactivity trends and enantiomeric ratios.

Controlled Direct Synthesis of C-Mono- and C-Disubstituted Derivatives of [3,3′-Co(1,2-C2B9H11)2]− with Organosilane Groups: Theoretical Calculations Compared with Experimental Results

Mono- and dilithium salts of [3,3'-Co(1,2-C(2)B(9)H(11))(2)](-), (1(-)), react with different chlorosilanes (Me(2)SiHCl, Me(2)SiCl(2), Me(3)SiCl and MeSiHCl(2)) with an accurate control of the temperature to give a set of novel C(c)-mono- (C(c) = C(cluster)) and C(c)-disubstituted cobaltabis(dicarbollide) derivatives with silyl functions: [1-SiMe(2)H-3,3'-Co(1,2-C(2)B(9)H(10))(1',2'-C(2)B(9)H(11))](-) (3(-)); [1,1'-mu-SiMe(2)-3,3'-Co(1,2-C(2)B(9)H(10))(2)](-) (4(-)); [1,1'-mu-SiMeH-3,3'-Co(1,2-C(2)B(9)H(10))(2)](-) (5(-)); [1-SiMe(3)-3,3'-Co(1,2-C(2)B(9)H(10))(1',2'-C(2)B(9)H(11))](-) (6(-)) and [1,1'-(SiMe(3))(2)-3,3'-Co(1,2-C(2)B(9)H(10))(2)](-) (7(-)). In a similar way, the [8,8'-mu-(1'',2''-C(6)H(4))-1,1'-mu-SiMe(2)-3,3'-Co(1,2-C(2)B(9)H(9))(2)](-) (8(-)); [8,8'-mu-(1'',2''-C(6)H(4))-1,1'-mu-SiMeH-3,3'-Co(1,2-C(2)B(9)H(9))(2)](-) (9(-)) and [8,8'-mu-(1'',2''-C(6)H(4))-1-SiMe(3)-3,3'-Co(1,2-C(2)B(9)H(9))(1',2'-C(2)B(9)H(10))](-) (10(-)) ions have been prepared from [8,8'-mu-(1'',2''-C(6)H(4))-3,3'-Co(1,2-C(2)B(9)H(10))(2)](-) (2(-)). Thus, depending on the chlorosilane, the temperature and the stoichiometry of nBuLi used, it has been possible to control the number of substituents on the C(c) atoms and the nature of the attached silyl function. All compounds were characterised by NMR and UV/Vis spectroscopy and MALDI-TOF mass spectrometry; [NMe(4)]-3, [NMe(4)]-4 and [NMe(4)]-7 were successfully isolated in crystalline forms suitable for X-ray diffraction analyses. The 4(-) and 8(-) ions, which contain one bridging -mu-SiMe(2) group between each of the dicarbollide clusters, were unexpectedly obtained from the reaction of the monolithium salts of 1(-) and 2(-), respectively, with Me(2)SiHCl at -78 degrees C in 1,2-dimethoxyethane. This suggests that an intramolecular reaction has taken place, in which the acidic C(c)-H proton reacts with the hydridic Si-H, with subsequent loss of H(2). Some aspects of this reaction have been studied by using DFT calculations and have been compared with experimental results. In addition, DFT theoretical studies at the B3 LYP/6-311G(d,p) level of theory were applied to optimise the geometries of ions 1(-)-10(-) and calculate their relative energies. Results indicate that the racemic mixtures, rac form, are more stable than the meso isomers. A good concordance between theoretical studies and experimental results has been achieved.

A DFT study of the hydration of monophosphate complexes of iron (III), [formula omitted

A systematic theoretical DFT study of the bonding between the cation Fe 3+ and the anion H 2 PO 4 - was carried out. The role of water ligands is presented. Several isomers with tetrahedral, bipyramidal and octahedral environments around the iron ion were investigated. 5-fold coordination of the Fe 3+ cation is found when 5 and 6 water molecules are included. Calculated infrared spectra are also presented.

Origin of Enantioselective Hydrogenation of Ketones by RuH2(diphosphine)(diamine) Catalysts: A Theoretical Study

The origin of the enantioselective hydrogenation of acetophenone by the (S-BINAP)RuH2(S,S-cydn) (cydn = 1,2-cyclohexanediamine) catalyst has been investigated by a theoretical DFT study. Computations for hydrogenation of acetone and acetophenone by the model system RuH2(PH3)2(en) (en = 1,2 ethylenediamine) confirm the previously proposed mechanism. These calculations show that reaction involving two of the four NH protons, which adopt a pseudoaxial orientation in the catalyst, is favored by ca. 2 kcal/mol over reaction involving the other two pseudoequatorial protons. The results for the model system reacting with acetophenone show that approach of the ketone with the phenyl group oriented away from the phosphine ligands (“out” approach) is favored by weak hydrogen bonding between the ketone phenyl group and one of the ruthenium-coordinated NH2 groups. In the full (S-BINAP)RuH2(S,S-cydn) catalyst, steric interactions also contribute to establishing the R selectivity in hydrogenation, and the magnitude of this selectivity is reproduced semiquantitatively. Study of the mismatched (S-BINAP)RuH2(R,R-cydn) also semiquantitatively reproduces the much reduced R selectivity of this catalyst and contributes to rationalizing it. Transfer of the less favored pseudoequatorial NH2 proton plays a key role in this case. It is shown that the results can also be used to discuss selectivity in other related systems.

Theoretical DFT study of ethylene hydroformylation on platinum complexes with hydrophosphoryl ligands

The DFT quantum-chemical modeling of the catalytic cycle of alkene hydroformylation on organoplatinum hydride [(R2PO)2H]-Pt(PR3)(H) shows that reversible shifts of proton in the –PR2OH···O=PR2– chain inside quasi-chelate ligand [(R2PO)2H] proceed in several reaction steps thus providing fine tuning of electron density in the catalytic centre and acting as a molecular switch.

Experimental and DFT theoretical studies of SERS effect on gold nanowires array

Gold nanowires array with diameter from 90 to 110 nm was prepared on AAO template by laser molecular beam epitaxy (LMBE), and surface-enhanced Raman scattering (SERS) spectrum of probe molecules nicotinic acid (NA) were recorded on the gold nanowires array. The Raman and SERS spectrum of NA using DFT-B3PW91 with lanl2dz based on two models were calculated, and compared with the experimental results. It was found the calculated frequencies were in good agreement with experimental values, which indicates that there are two enhanced mechanism which electromagnetic enhancement and charge transfer enhancement, on the gold nanowires array regarding SERS effect.

Unpaired and σ Bond Electrons as H, Cl, and Li Bond Acceptors: An Anomalous One-Electron Blue-Shifting Chlorine Bond

Ab initio, DFT, and AIM theoretical studies on H-, Cl-, and Li-bonded complexes have been carried out with typical lone pair (H2O), pi (C2H4) and sigma (H2) bonded pairs, and unpaired (CH3) electrons as acceptors and HF, ClF, and LiF as donors. Optimization and frequency calculations have been carried out at reasonably high levels (MP2, DFT(B3LYP), and QCISD) with large basis sets up to aug-cc-pVTZ. Not surprisingly, all HF complexes show red shift in stretching frequency and the shift is correlated to the binding energy. However, the FCl...CH3 complex shows a large blue shift (about 200 cm-1), which appears to be the largest blue shift predicted for any weakly bound complex yet. Analysis of the normal modes of the complex indicates that the shift is due to the mixing of modes between donor and acceptor and it is qualitatively different from the blue shifts reported thus far in hydrogen-bonded complexes. For Cl- and Li-bonded complexes, a correlation between frequency shift and binding energy is not found. However, AIM theoretical analysis shows the similarity in all these interactions. The electron density at the bond critical point shows a strong correlation with the binding energy for H-, Cl-, and Li-bonded complexes. This appears to be the first report on a one-electron chlorine bond.

Theoretical DFT Study of Fragmentation and Association of Heme and Hemin

The electronic and geometric structures, energy stability, and normal vibrational frequencies of heme, hemine, and their stepwise fragmentation products (with successive loss of two carboxymethyl, four methyl, and two vinyl peripheral groups) in the states with different multiplicity were calculated using the density functional theory (the B3LYP method) with several basis sets. At the same level, the structure and stability of neutral and positively charged dimers of the ferri- and ferroporphyrines were also computed. The computational results are compared with available experimental data. The trends in the behavior of these properties of heme and hemin are analyzed upon the stepwise fragmentation and association and with a change in the multiplicity and external charge. The structure and energetic stability of complexes of the species with molecular oxygen are discussed.

Electron affinity of perhalogenated benzenes: A theoretical DFT study

The potential energy surfaces (PES) of unsubstituted and perhalogenated benzene anions ( C 6 X 6 - , X = F, Cl, Br, and I) were explored by means of DFT-B3LYP calculations. In the F and Cl cases seven extrema were located and characterized. In the Br and I cases only one minimum and two extrema were found. In each case the minimum was recomputed at the CCSD(T) level. The electron affinities of C 6X 6 were calculated (ZPE included). The results obtained agree well with the experimental determinations when available. The values obtained in the X = Br and the X = I cases are expected to be valuable predictions.

The platinum-olefin binding energy in series of (PH3)2Pt(olefin) complexes - a theoretical study

Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics bearing coordinated olefins with general formula (R1R2C = CR3R4)Pt(PH3)2 [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin substituents.

Unusual ferromagnetic coupling interaction in carboxylato-bridged Mn(II) complexes: Ab initio MRCI(SD) and DFT theoretical studies

For the title complexes the ab initio calculations of the ground and low-lying exited states have been carried out at level of MRCI(SD)+Q method. Through mapping to the spin model space the magnetic coupling constant (2.33 cm −1) between the Mn(II) ions was obtained, comparing with experimental value of 0.49 cm −1, and it is found that the Lande rule of the magnetic behavior is valid for the magnetic system. The DFT–BS calculations were used to examine the magneto-structural correlation. It is shown that as increase of the bridge-bonding angle the transition from ferromagnetic to antiferromagnetic coupling may occur, consistent with experimentally observations.

1,4-Phenylene-di( N- l-alanylaminomethylphosphonate) a new diaminophosphonate peptide receptor for lysine and arginine

New diaminophosphonate peptide receptor composed of two aminomethylphosphonic acid fragments attached to phenyl ring in para position was described. Intermolecular interactions between such host molecule and unprotected cationic forms of lysine and arginine (guest molecules) were studied by means of NMR spectroscopy and ESI-MS spectrometry in both methanol and water solutions. Unfortunately, no complexation induced shifts in NMR spectra were observed for these host–guest systems in water solution. However, the performed studies have shown that in methanol complexes in host to guest ratio of 1:1 and 1:2 are formed and they precipitate from the solution, while in water 1:1 complexes are only seen and supramolecular interactions between host and guest discovered using 1H- and 31P NMR T 1 relaxation method suggest that they are present as ionic pairs in aqueous solution. The supramolecular studies were supported by DFT theoretical studies performed for free receptor and its molecular complexes with Lys and Arg.

A theoretical study of solvent effects on Kolbe–Schmitt reaction kinetics

A theoretical DFT study was employed to confirm the Kolbe–Schmitt reaction mechanism and investigate solvent effects on this reaction. The use of a solvent in the Kolbe–Schmitt reaction is desirable to facilitate a homogeneous reaction mixture and potentially improve the reaction rate. The candidate solvents were designed using computer aided molecular design (CAMD) and tested using DFT solvation calculations. The results from the quantum mechanical calculations were then used to determine the rate constants for each elementary step, the overall reaction yields and the corresponding residence time. The methodology was tested on the reaction without solvent, with solvents reported in the literature, and with the designed solvents. The study revealed that in the presence of solvents with high dielectric constant the reaction becomes reversible, leading to low product yields.

Ionization potential and electron affinity of VC n ( n=1–8) open-chain clusters: A theoretical study

A DFT theoretical study of the VC n + , and VC n − ( n=1–8) open-chain clusters has been carried out using the B3LYP method. Results for several molecular properties which could help in their possible experimental characterization, such as equilibrium geometries, electronic energies, dipole moments, and vibrational frequencies are provided. For the VC n + open-chain clusters the lowest-lying states correspond to triplet states for n-odd members, whereas for n-even species the ground state is found to be a quintet one. In the case of VC n − species the electronic ground state is found to be a quintet for odd n and a triplet for even n. From the incremental binding energies we can deduce an even–odd parity effect, with n-odd clusters being more stable than n-even ones in the cationic clusters, whereas in the anionic system this effect is reversed. The ionization potentials and electron affinities of VC n linear clusters also exhibit a clear parity alternation trend, with n-even clusters having higher values than n-odd ones.