Density Functional Theory Frequency Calculations Research Articles

Accurate Computation of the Absorption Spectrum of Chlorophyll a with Pair Natural Orbital Coupled Cluster Methods.

The ability to accurately compute low-energy excited states of chlorophylls is critically important for understanding the vital roles they play in light harvesting, energy transfer, and photosynthetic charge separation. The challenge for quantum chemical methods arises both from the intrinsic complexity of the electronic structure problem and, in the case of biological models, from the need to account for protein–pigment interactions. In this work, we report electronic structure calculations of unprecedented accuracy for the low-energy excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD) in combination with sufficiently large and flexible basis sets. The results of our DLPNO–STEOM-CCSD calculations are compared with more approximate approaches. The results demonstrate that, in contrast to time-dependent density functional theory, the DLPNO–STEOM-CCSD method provides a balanced performance for both absorption bands. In addition to vertical excitation energies, we have calculated the vibronic spectrum for the Q and B bands through a combination of DLPNO–STEOM-CCSD and ground-state density functional theory frequency calculations. These results serve as a basis for comparison with gas-phase experiments.

Structural, spectroscopic and theoretical studies of sodium (2-carbamoylphenoxy) acetate salt

Sodium (2-carbamoylphenoxy) acetate salt crystal belongs to the P-1 space group of triclinic system, Z = 2. The asymmetric part of the unit cell consists of four (2-carbamoylphenoxy) acetate (CBA) molecules. Three Na+ ions are surrounded by six O atoms and one Na+ ion is surrounded by five O atoms. The mean Na1+ … O and Na2+ … O distance is 2.47 Å while Na3+ … O is 2.43 Å and Na4+ … O is 2.49 Å. The supramolecular self-assembly of the four (2-carbamoylphenoxy) acetate molecules is realized by hydrogen bonds, and a variety of intermolecular interactions. The interactions within the bulk of the crystal structure were highlighted with Hirshfeld surfaces. FT-IR and Raman spectra of the studied compound are reported for the first time. Assignments of the normal modes was done with the aid of density functional theory frequency calculations on the monomer and two dimers, at B3LYP/6-311 + G(2d,p) level of theory.

Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide.

Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.

Hydrocarbon/Water Interactions: Encouraging Energetics and Structures from DFT but Disconcerting Discrepancies for Hessian Indices.

In this work, ab initio electronic structure computations have been used to systematically examine the structures and energetics of nine small hydrocarbon molecules interacting with water. Full geometry optimizations and harmonic vibrational frequency calculations were performed on 30 unique dimer configurations with the MP2 method and a triple-ζ correlation consistent basis set (cc-pVTZ for H and aug-cc-pVTZ for C and O, denoted haTZ). Three different estimates of the CCSD(T) complete basis set (CBS) limit interaction energies were determined for all 30 MP2 optimized hydrocarbon/water structures, and they never deviate from their mean by more than 0.07 kcal mol(-1). MP2 and CCSD(T) interaction energies are virtually identical (within 0.05 kcal mol(-1)) for dimer configurations primarily exhibiting CH···O and OH···C type interactions, but MP2 overbinds appreciably in some dimers that exhibited OH···π type interactions, by as much as 0.3 to 0.4 kcal mol(-1) (or ≈10%) for the unsaturated cyclic hydrocarbons examined (1,3-cyclobutadiene, 1,3-cyclopentadiene, and benzene). Four density functional theory (DFT) methods (B3LYP, B97-D, ωB97X-D, and M06-2X) were also applied to all 30 systems with the haTZ basis set to compare optimized structures, energetics, and numbers of imaginary vibrational frequencies (ni). The B97-D, ωB97X-D, and M06-2X functionals provide quite reasonable structures and energetics, which is consistent with other studies. This work, however, finds that all 4 DFT methods examined struggle to reliably characterize these potential energy surfaces (PESs). For example, the values of ni from the DFT frequency calculations differed from the corresponding MP2 results for approximately one-third of the stationary points located.

Infrared Spectra and Quantum Chemical Calculations of the Bridge-Bonded HC(F)LnF2 (Ln = La–Lu) Complexes

Lanthanide metal atoms, produced by laser ablation, were condensed with CHF3 (CDF3) in excess argon or neon at 4 K, and new infrared absorptions are assigned to the oxidative addition product fluoromethylene lanthanide difluoride complex on the basis of deuterium substitution and density functional theory frequency calculations. Two dominant bands in the 500 cm–1 region are identified as metal–fluorine stretching modes. A band in the mid-600 cm–1 region is diagnostic for the unusual fluorine bridge bond C–(F)–Ln. Our calculations show that most of the bridged HC(F)LnF2 structures are 3–6 kcal/mol lower in energy than the open CHF-LnF2 structures, which is in contrast to the open structures observed for the corresponding CH2-LnF2 methylene lanthanide difluorides. Argon-to-neon matrix shifts are 15–16 cm–1 to the blue for stretching of the almost purely ionic Ln–F bonds, as expected, but 10 cm–1 to the red for the bridge C–(F)–Ln stretching mode, which arises because Ar binds more strongly to the electropositive Ln center, decreasing the bridge bonding, and thus allowing a higher C–F stretching frequency.

Matrix Infrared Spectroscopic and Computational Investigation of Late Lanthanide Metal Hydride Species MHx(H2)y (M = Tb−Lu, x = 1−4, y = 0−3)

Laser-ablated late lanthanide metal atoms were condensed with pure hydrogen at 4 K, and new infrared absorptions are assigned to binary metal hydrides on the basis of deuterium substitution and density functional theory frequency calculations. The dominant absorptions in the 1330-1400 cm(-1) region are identified as LnH(3) complexes with very weak ligand bands near 3900 cm(-1). With ytterbium, YbH and YbH(2) were the major initial products, but YbH(3) increased at their expense upon sample irradiation. Evidence is also presented for the LuH and ErH molecules and the tetrahydride anions in solid hydrogen.

Bonding Analyses, Formation Energies, and Vibrational Properties of M−R2dtc Complexes (M = Ag(I), Ni(II), Cu(II), or Zn(II))

Detailed theoretical studies based on density functional theory (DFT)/B3LYP calculations of dimethyl- and diethyldithiocarbamate complexes of Ni(II), Cu(II), Zn(II), and Ag(I) are performed to characterize the metal-ligand bonding type as well as the metal-ligand bonding strength depending on the metal and the dialkyl substituent. The metal-ligand interactions in the studied complexes are investigated by means of charge decomposition analysis, energy partitioning analysis (EPA), and natural bond orbital analysis. According to the EPA calculations, the electrostatic attraction is the dominant contribution to the M-S2(R2dtc) (dtc=dithiocarbamate) bonding. The electrostatic and the orbital energies follow the order of the total binding energy, and hence both contributions are responsible for the binding energy order of M(R2dtc)2 complexes. The stability of the M(R2dtc)2 complexes is estimated by means of calculated formation reaction energies in the gas phase and solution, and it decreases in the order Ni(R2dtc)2>Cu(R2dtc)2>Zn(R2dtc)2. Larger formation reaction energies are found for M(Et2dtc)2 than for M(Me2dtc)2 complexes. The calculations predict stabilization of M(II)(R2dtc)2 complexes going from the gas phase to a polar solvent and destabilization of the bidentate AgR2dtc complex in a polar solvent. Gas-phase frequency calculations of all possible bonding types, symmetrical, asymmetrical, and uni- and bidentate, predict one band due to the nu(CS) IR absorption, and therefore the number of the bands in the 1060-920 cm(-1) region could not be used to discern the metal-ligand bonding type. Periodic DFT frequency calculations for Cu(Et2dtc)2 reveal that the splitting observed in the solid-state spectra of the complexes arises from the nonplanar MS4 fragment and intermolecular contacts but not from asymmetrical bonding. The calculations suggest that the important vibrational characteristic that can be used to discern uni- and bidentate bonding is the Raman activity of the nu(CS) band: It is very high for the unidentate dtc bonding (nu(C=S)) and low for the bidentate bonding (nuas(CS)).

Group 4 Transition-Metal Atom Reactions with CS2 and OCS: Infrared Spectra and Density Functional Calculations of SMCS, SM-(η2-CS), SMCO, and OMCS in Solid Argon

Laser-ablated titanium, zirconium, and hafnium atoms were reacted with CS2 and OCS molecules during condensation in excess argon. With CS2, the SMCS and S-M(eta2-CS) products were formed on sample deposition. Photolysis increased both complexes, while annealing favored the lower energy S-M(eta2-CS) side-bound isomer. The OCS reactions produced SMCO, OMCS, and the simple M(eta2-CO)S adduct. Product absorptions are identified by comparison with density functional theory frequency calculations and isotopic substitutions. Investigations with OCS emphasized differences in the CS and CO bond insertion products.

Infrared Spectra of CH3−MoH, CH2MoH2, and CH⋮MoH3 Formed by Activation of CH4 by Molybdenum Atoms

Reaction of laser-ablated Mo atoms with CH(4) in excess argon forms the CH(3)-MoH, CH(2)=MoH(2), and CH(triple bond)MoH(3) molecules, which are identified from infrared spectra by isotopic substitution and density functional theory frequency calculations. These simple methyl, methylidene, and methylidyne molybdenum hydride molecules are reversibly interconverted by alpha-H transfers upon visible and ultraviolet irradiations. The methylidene dihydride CH(2)=MoH(2) exhibits CH(2) and MoH(2) distortion and agostic interaction to a lesser degree than CH(2)=ZrH(2). Molybdenum methylidyne trihydride CH(triple bond)MoH(3) is a stable C(3v) symmetry molecule.

Infrared Spectra of the Novel Si2H2 and Si2H4 Species and the SiH1,2,3 Intermediates in Solid Neon, Argon, and Deuterium

Laser-ablated silicon atoms react extensively with hydrogen to form the silicon hydrides SiH1,2,3,4 and the disilicon hydrides Si2H2,4,6. Infrared spectra and density functional theory frequency calculations with HD and D2 substitution are used to identify these species in solid neon, argon, and deuterium. The novel dibridged Si2H2 species is characterized by an antisymmetric Si−H−Si stretching mode at 1100.3 cm-1 and the trans-folded Si2H4 intermediate by antisymmetric SiH2 stretching and bending modes at 2151.6 and 858.5 cm-1 in solid neon. The SiH3- anion is identified by photosensitive absorptions at 1856 and 1837 cm-1 in solid neon. Silicon atoms in pure deuterium gave primarily SiD4 with some SiD3, Si2D6, and Si2D4 and no evidence for SiD and SiD2, but SiD3- and SiD2- were observed.

The reaction of permanganyl chloride with olefins: intermediates and mechanism as derived from matrix-isolation studies and density functional theory calculations.

Density functional theory (DFT) calculations predict that the [2+3] addition of tetramethylethylene (TME) to the MnO2 moiety of MnO3Cl is thermodynamically favoured over [2+1] addition (epoxidation), while the kinetic barriers for both reactions are of comparable height. However, in an experimental investigation of the TME/MnO3Cl system by means of matrix-isolation techniques, selective formation of the epoxidation product [ClO2Mn[O[C(CH3)2]2]] (1) was observed. Compound 1 was characterised by IR spectroscopy with the aid of isotopic-enrich-ment experiments in combination with DFT frequency calculations. This result, at first sight surprising, is supported by studies in solution, and, even with the numerically equal energy barriers suggested by the calculations, it can be rationalised in terms of the much broader reaction channel leading to epoxidation as opposed to the much more narrow approach path for formation of the glycolate.

Matrix Isolation FTIR Spectroscopic and Density Functional Theoretical Studies of the Nickel, Copper, and Silver Carbonyl Chlorides

The nickel, copper, and silver metal carbonyl chloride molecules have been prepared and isolated in solid argon by cocondensation of the species generated from 1064 nm laser ablation of metal chlorides with carbon monoxide in excess argon at 11 K. On the basis of isotopic substitution experiments and density functional theory frequency calculations, infrared absorptions at 2118.7, 2156.8, and 2184.0 cm-1 are assigned to the C−O stretching vibrations of the Ni(CO)Cl, Cu(CO)Cl, and Ag(CO)Cl molecules. Density functional calculations predicted that the M(CO)Cl (M = Ni, Cu, Ag) molecules are linear; the binding energies with respect to MCl + CO were estimated to be 37.7, 34.2, and 17.8 kcal/mol, respectively. In addition, evidence is also presented for the M(CO)Cl2, M(CO)2Cl, and M(CO)2Cl2 (M = Ni, Cu) molecules.

Reactions of Laser-Ablated Boron Atoms with Methyl Halides in Excess Argon. Infrared Spectra and Density Functional Theory Calculations on CH3BX, CH2BX, and CHBX (X = F,Cl,Br)

Laser-ablated boron atoms react with methyl fluoride in an argon stream to form two major products: CH2BF and CHBF. In similar reactions of boron with methyl chloride and methyl bromide, both CH2BX and CHBX are also observed, as well as the primary insertion products, CH3BCl and CH3BBr, respectively. Infrared spectra of isotopic combinations of B and CH3X and density functional theory frequency calculations provide evidence for the product identification. Both products form via insertion into the C−X bond followed by loss of one or two H atoms for all reactions. Comparisons are made with the products of the reactions of B with C2H6, CH3NH2, and CH3OH, all of which are isoelectronic with CH3F. The calculations not only predict the vibrational frequencies exceptionally well, but also predict that there is no dative bonding in either CH2BX or CHBX, despite the empty p-orbital on B and the filled p-orbitals on the halogen atom.

Infrared spectra of BeNO and MgNO in solid argon

Laser-ablated Be atoms were reacted with NO in excess Ar during condensation at 10 K. Absorptions due to BeNO (913.8 cm −1) and BeOBeNO (1483.0 cm −1) are identified based on isotopic substitution and density functional theory frequency calculations. Similar experiments with Mg gave MgNO at 1461.3 cm −1.

An infrared spectroscopic and density functional investigation of dinitrogen activation by group IV metal atoms

Reactions of laser-ablated Ti, Zr, and Hf atoms with N2 in excess argon and excess dinitrogen have produced the MN and (N2)xMN molecules in addition to M(μ–N)2M with no dinitrogen bond. Evidence is presented for simple η1–N2 and higher complexes for each metal. The observation of cyclic Ti(N2) and Zr(N2) molecules with N–N stretching frequencies at 1125.9 and 1022.8 cm−1, respectively, indicate significant activation of the dinitrogen bond. The identification of product molecules is based on isotopic substitution and the results of density functional theory frequency calculations.

Reactions of laser-ablated iron atoms with carbon monoxide: Infrared spectra and density functional calculations of FexCO, Fe(CO)x, and Fe(CO)x− (x=1,2,3) in solid argon

Laser-ablated iron atoms have been reacted with CO molecules during condensation in excess argon. The FeCO molecule is observed at 1922.0 cm−1 in solid argon based on concentration studies, isotopic shifts, and density functional theory frequency calculations; the argon matrix redshifts this band 27.0 cm−1 (1.4%) from the high-resolution gas phase measurement. Absorptions at 1879.2 and 1984.8 cm−1 are assigned from isotopic substitution and density functional theory frequency calculations to the antisymmetric and symmetric vibrations of a bent Fe(CO)2 molecule in the matrix. The Fe(CO)x (x=3,4,5) molecules are also observed on annealing in agreement with earlier matrix work. Iron carbonyl ions were also produced and trapped: photosensitive absorptions at 1770.3, 1721.9, 1815.0, 1786.5, and 1853.5 cm−1 are assigned to FeCO−, Fe(CO)2−, Fe(CO)3−, and Fe(CO)4−, respectively, and a weak photosensitive 2081.5 cm−1 band is assigned to FeCO+. Polynuclear metal carbonyls were also formed on annealing; based on different CO concentration and laser power experiments and isotopic substitution, an 1897.7 cm−1 absorption is assigned to Fe2CO and a 1948.5 cm−1 band to Fe3CO.

Density Functional Theory Study of Transition-Metal Compounds Containing Metal−Metal Bonds. 2. Molecular Structures and Vibrational Spectra of Dinuclear Tetracarboxylate Compounds of Molybdenum and Rhodium

Vibrational spectra have been calculated for the first time for dinuclear transition-metal compounds containing metal−metal bonds. The calculations were carried out by employing different forms of density functional theory (DFT) and basis functions of different sizes at fully optimized molecular geometry. The calculated frequencies essentially reproduced fundamentals observed in experimental infrared and Raman spectra. It is shown that DFT frequency calculations can be a very important and valuable tool to assist in analyzing and assigning measured infrared and Raman spectra and to predict vibrational frequencies for large transition-metal compounds with metal−metal bonds. The molecules included in this study were M2(O2CH)4 (M = Mo, Rh), Rh2(O2CH)4(H2O)2, and M2(O2CCH3)4 (M = Mo, Rh). Significant differences are found between the formate and acetate molecules.

The nature of C 10H 2+ in mass spectra of polynuclear aromatic hydrocarbons

Ab initio and density functional theory (DFT) calculations have been performed to determine the heats of reaction for the process C 16H 10 + → C 10H 2 + that takes place in an ion trap mass spectrometer. Comparisons have been made with the experimental and derived data available for this process. The theoretical values at the DFT level verify the experimental heats of reaction within 0.4-0.8 eV. Furthermore, the structure of the product ion, C 10H 2 +, has been investigated. Several structures have been proposed, and the ab initio and DFT geometry optimizations and frequency calculations have been performed to determine the most stable species. At the level of theory and the approximations that were used in this work, the linear form of C 10H 2 + is the most stable species of three different geometries considered.