B3LYP Geometry Optimizations Research Articles

Exploration of the Mechanism of the Dimerization of Hydroxymethylsilanetriol Using Electronic Structure Methods.

Hydroxymethylsilanetriol undergoes condensation reactions to form new structures with an organic part in the formed bridges. As a first step to explore the formation of these bridges, we studied the corresponding mechanisms using simple models and theoretical methods. Three mechanisms were studied for the formation of dimers of hydroxymethylsilanetriol with bridges: Si–O–C–Si, Si–O–Si, and Si–C–O–C–Si. Energies are calculated using M06/6–311+G(d,p) single-point calculations on B3LYP-optimized geometries in solution and including B3LYP thermodynamic corrections. The first mechanism for the formation of the Si–O–C–Si bridge consists of one step. The second mechanism for the formation of the Si–O–Si bridge consists of two steps. The barrier for the last mechanism for the formation of the Si–C–O–C–Si bridge is too high and cannot occur at room temperature. The energy barriers are 31.8, 27.6, and 65.9 kcal mol–1 for the first, second, and third mechanisms, respectively. When adding one explicit water molecule, these energies are 25.9, 22.9, and 80.3 kcal mol–1, respectively. The first and second mechanisms can occur at room temperature, which is in agreement with the experimental results.

Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation.

Abnormalities in zinc metabolism have been linked to many diseases, including different kinds of cancers and neurological diseases. The present study investigates the fragmentation pathways of a zinc chaperon using a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analog methanobactin peptide-5, amb5). DFT/M05-2X and B3LYP geometry optimizations of [amb5-3H+Zn(II)]- predicted three lowest energy conformers with different chelating motifs. Direct dynamics simulations, using the PM7 semiempirical electronic structure method, were performed for these conformers, labeled a, b, and c, to obtain their fragmentation pathways at different temperatures in the range 1600-2250 K. The simulation results were compared with negative ion mode mass spectrometry experiments. For conformer a, the number of primary dissociation pathways are 11, 14, 24, 70, and 71 at 1600, 1750, 1875, 2000, and 2250 K, respectively. However, there are only 6, 10, 13, 14, and 19 pathways corresponding to these temperatures that have a probability of 2% or more. For conformer b, there are 67 pathways at 2000 K and 71 pathways at 2250 K. For conformer c, 17 pathways were observed at 2000 K. For conformer a, for two of the most common pathways involving C-C bond dissociation, Arrhenius parameters were calculated. The frequency factors and activation energies are smaller than those for C-C homolytic dissociation in alkanes due to increased stability of the product ions as a result of hydrogen bonding. The activation energies agree with the PM7 barriers for the C-C dissociations. Comparison of the simulation and experimental fragmentation ion yields shows the simulations predict double or triple cleavages of the backbone with Zn(II) retaining its binding sites, whereas the experiment exhibits single cleavages of the backbone accompanied by cleavage of two of the Zn(II) binding sites, resulting in b- and y-type ions.

Hydrogen gas formation from the photolysis of rhenium hydrides – mechanistic and computational studies

The photolysis of 4,4'-disubstituted, 2,2'-bipyridine fac-Re(bpy)(CO)3H derivatives produces stoichiometric H2 gas. The rate of production varies greatly depending on the electronic nature of the disubstituted bipyridine (bpy) with halogenated substituents increasing the rate. Isotope labeling studies along with B3LYP geometry optimization DFT modeling studies indicate a mechanism involving a Re-H-Re bridging complex that leads to a dimeric Re-Re(η2-H2) state prior to dissociating H2 gas.

Multiscale Computational Simulation of Amorphous Silicates’ Structural, Dielectric, and Vibrational Spectroscopic Properties

Silicates are among the most abundant and important inorganic materials, not only in the Earth’s crust, but also in the interstellar medium in the form of micro/nanoparticles or embedded in the matrices of comets, meteorites, and other asteroidal bodies. Although the crystalline phases of silicates are indeed present in nature, amorphous forms are also highly abundant. Here, we report a theoretical investigation of the structural, dielectric, and vibrational properties of the amorphous bulk for forsterite (Mg2SiO4) as a silicate test case by a combined approach of classical molecular dynamics (MD) simulations for structure evolution and periodic quantum mechanical Density Functional Theory (DFT) calculations for electronic structure analysis. Using classical MD based on an empirical partial charge rigid ionic model within a melt-quenching scheme at different temperatures performed with the GULP 4.0 code, amorphous bulk structures for Mg2SiO4 were generated using the crystalline phase as the initial guess. This has been done for bulk structures with three different unit cell sizes, adopting a super-cell approach; that is, 1 × 1 × 2, 2 × 1 × 2, and 2 × 2 × 2. The radial distribution functions indicated a good degree of amorphization of the structures. Periodic B3LYP-geometry optimizations performed with the CRYSTAL14 code on the generated amorphous systems were used to analyze their structure; to calculate their high-frequency dielectric constants (ε∞); and to simulate their IR, Raman, and reflectance spectra, which were compared with the experimental and theoretical crystalline Mg2SiO4. The most significant changes of the physicochemical properties of the amorphous systems compared to the crystalline ones are presented and discussed (e.g., larger deviations in the bond distances and angles, broadening of the IR bands, etc.), which are consistent with their disordered nature. It is also shown that by increasing the unit cell size, the bulk structures present a larger degree of amorphization.

Spectroscopic investigations and theoretical calculations of DABCO induced xanthene bridged self-assembled zinc(II) porphyrin dimer

An in-depth study of the electronic structure of a 1,4-diazabicyclo[2.2.2]octane (DABCO) induced molecular self-assembled xanthene-bridged and amide-bonded porphyrin dimer is reported. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations are used to identify trends in the optical spectroscopic properties. B3LYP geometry optimization predicts the formation of an almost perfectly eclipsed structure with respect to the two porphyrin rings with the analogous pyrrole nitrogens separated by 7.7–8.1 Å. The observed distinctive derivative-shaped band morphology of the pseudo-Faraday-A[Formula: see text] terms in the MCD spectra has been used to identify the main electronic Q and B-bands and to validate the TD-DFT calculations. The absence of a discernible splitting of the redox steps or a quenching of the fluorescence demonstrates that there is no significant exciton coupling between the two porphyrin rings.

In Silico Prediction of Cytochrome P450-Mediated Biotransformations of Xenobiotics: A Case Study of Epoxidation.

Predicting the biotransformation of xenobiotics is important in toxicology; however, as more compounds are synthesized than can be investigated experimentally, powerful computational methods are urgently needed to prescreen potentially useful candidates. Cytochrome P450 enzymes (P450s) are the major enzymes involved in xenobiotic metabolism, and many substances are bioactivated by P450s to form active compounds. An example is the conversion of olefinic substrates to epoxides, which are intermediates in the metabolic activation of many known or suspected carcinogens. We have calculated the activation energies for epoxidation by the active species of P450 enzymes (an iron-oxo porphyrin cation radical oxidant, compound I) for a diverse set of 36 olefinic substrates with state-of-the-art density functional theory (DFT) methods. Activation energies can be estimated by the computationally less demanding method of calculating the ionization potentials of the substrates, which provides a useful and simple predictive model based on the reaction mechanism; however, the preclassification of these diverse substrates into weakly polar and strongly polar groups is a prerequisite for the construction of specific predictive models with good predictability for P450 epoxidation. This approach has been supported by both internal and external validations. Furthermore, the relation between the activation energies for the regioselective epoxidation and hydroxylation reactions of P450s and experimental data has been investigated. The results show that the computational method used in this work, single-point energy calculations with the B3LYP functional including zero-point energy and solvation and dispersion corrections based on B3LYP-optimized geometries, performs well in reproducing the experimental trends of the epoxidation and hydroxylation reactions.

Efficiency enhancement in solution processed small-molecule based organic solar cells utilizing various phthalocyanine–tetrabenzoporphyrin hybrid macrocycles

A study on efficiency enhancement in solution processed small-molecule based organic solar cells (OSCs) utilizing various phthalocyanine–tetrabenzoporphyrin hybrid macrocycles is reported. By replacement of aza links at meso position by methine groups, the optical absorption at B band of porphyrinoid complexes is improved, the energy bandgap is enlarged, and stacking of the discotic molecules is probably changed from pseudohexagonal structures to 2-D rectangular lattices. Results from molecular orbital (MO) calculation by using B3LYP-optimized geometries calculated with 6-31G(d) indicate that the intensification of optical absorption and the modification of electronic band structure is mainly due to the difference of MO coefficients at meso positions, resulting in a marked lifting of the degeneracy of the MOs derived from highest occupied molecular orbitals and/or lowest unoccupied molecular orbitals. By controlling the numbers of aza links at meso position, active layer thickness and nanoscale phase separation, the external quantum efficiency at B band and power conversion efficiency of OSCs utilizing phthalocyanine–tetrabenzoporphyrin hybrid macrocycles is improved to 53% and 5.3%, respectively.

Variations of bistricyclic aromatic enes: mono-bridged tetraarylethene naphthologs

The syntheses, molecular and crystal structures, NMR spectroscopic study, and DFT computational study of naphthologs of mono-bridged (X = –, O, S, Se, and Te) tetraarylethene (BAE-1s) 11–25 with α,α-, β,β-, and α,β-dinaphthalenyl substituents have been reported. The BAE-1s have been prepared by Barton–Kellog twofold extrusion from the respective chalcogenothiones and diazomethylenebisnaphthylenes. Complete assignments of 1H- and 13C-NMR spectra of 11–25 have been made through 2-dimensional correlation spectroscopy (DQF-COSY, HSQC, HMBC, and NOESY). The corresponding intermediates, thiiranes 33–47, have been also isolated (except 38), and their molecular and crystal structures have been determined. The molecular structures of BAE-1s 12–15, 20, and 22–25 adopted folded-twisted conformations with considerably folded (φ = 30°–57°) tricyclic moieties. The α,α- and α,β-dinaphthalenyl derivatives are more overcrowded than β,β-dinaphthalenyl derivatives. The relief of the steric strain due to the overcrowding around C9 = C9′ caused by the presence of naphthalenyl substituents was achieved by their twisting around the single bonds that connect the α-naphthalenyl and β-naphthalenyl moieties to C9′. The 1H-NMR spectra have shown shielding of H2, H7 of 11–25 and the pronounced deshielding of H8′, H8″ of α,α-dinaphthalenyl-substituted BAE-1s 13–15 in contrast to β,β-dinaphthalenyl-substituted BAE-1s 16–20. The upfield shifts of H2, H7 suggested conformations in which these hydrogens are located above the planes of the opposing naphthalene rings. DFT calculations of 11–20 have been performed at B3LYP/6-31G(d) and B3LYP/SDD. The results have shown that the global minima of BAE-1s without a chalcogen bridge 11 and 16 are twisted (–sc,–sc)-C 2-t conformations. The global minima of BAE-1s with a chalcogen bridge are folded-twisted (–sc,–ac)-C 1-ft conformations for α,α-dinaphthalenyl-substituted BAE-1s 12–15 and either anti- or syn-(–sc,ac)-C 1-ft conformations for β,β-dinaphthalenyl-substituted BAE-1s 17–20. The pronounced differences between the α,α-dinaphthalenyl and the β,β-dinaphthalenyl derivatives are noted. Dispersion-corrected B3LYP calculations stabilize significantly the α,α-dinaphthalenyl derivatives versus the β,β-dinaphthalenyl derivatives. The geometrical parameters of BAEs-1 11–15 and 20, derived from their molecular X-ray structures and from their B3LYP-optimized geometries are in a good agreement.

Computationally assisted assignment of kahalalide Y configuration using an NMR-constrained conformational search.

Assignment of the absolute configuration of cyclic peptides frequently yields challenges, leaving one or more stereogenic centers unassigned due to small quantities of sample and the limited utility of Marfey's or other methods for assigning amino or hydroxy acids. Here, we report isolation of kahalalide Y (1) from Bryopsis pennata for the first time; in addition, the application of a combination of molecular modeling and NOE distance constraint calculations was utilized to determine the conformation of 1 and the absolute configuration of the final stereogenic center of 1. Using the Schrödinger suite, the structure of 1 was sketched in Maestro and minimized using the OPLS2005 force field in Macromodel. A conformational search was performed separately for structures having an R or S configuration at C-3 of the beta-hydroxy fatty acid subunit that completes the cyclic scaffold of 1, after which multiple minimizations for all generated conformers were carried out. The lowest energy conformers of R and S stereoisomers were then subjected to B3LYP geometry optimizations including solvent effects. The S stereoisomer was shown to be in excellent agreement with the NOE-derived distance constraints and hydrogen-bonding stability studies.

Synthesis, 15N NMR spectra and GIAO calculated data of the seven positional isomers of 15N-labeled N,N-dimethylsulfamoylquinoline

Abstract The one-step synthesis of positional isomers of N , N -dimethylsulfamoylquinoline are presented. Seven newly synthesized compounds have been characterized by elemental analyses, MS, 1 H and 15 N NMR spectral data. The long-range correlations between the ring protons and the endocyclic nitrogen atoms were observed in the gHMBC experiments. The spectral positions of the nitrogen atoms from the sulfonamide groups were drawn from the 1D spectra of the 15 N-labeled sulfonamide isotopomers. Correlations between the experimentally determined chemical shifts and GIAO calculated isotropic shielding constants were found. The GIAO calculations were based on HF-, MP2-, and B3LYP-optimized geometries and were performed at the HF, BLYP, and B3LYP levels of theory.

Theoretical study on the reaction of magnesium with water in the gas-phase

The reaction of magnesium with water is of interest for propulsion and hydrogen generation. Reaction mechanism of Mg with water was investigated by ab initio quantum chemical methods. The geometries and frequencies of all reactants, products, intermediates and transition states were calculated at the B3LYP/6-311G++(3df, 2p) level. Energies at a higher level of accuracy were obtained at G2M (CC2) level using the B3LYP-optimized geometries. The Mg and water firstly formed an atom-molecule adduct Mg ⋅ OH 2 , and then either formed MgOH + H by a H-dissociation process or formed HMgOH by the process of H-migration from one to the other side of the adduct molecule. The barrier heights of two processes are 48.28 kcal/mol and 32.51 kcal/mol. The rate constants were calculated by using the variational transition state theory with the zero-curvature tunneling correction in a temperature range of 1000–5000 K. The results showed that H-migration process was dominant in the studied temperature range and the branch ratio of H-dissociation process appeared bigger at higher temperature.

Vibronic Spectra of Jet-Cooled 2-Aminopurine·H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations

For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine·H(2)O monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift δν of the S(1) ← S(0) transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (δν = -889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H(2)O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D(e) = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)ππ* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S(0) state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)ππ* state to the lower-lying (1)nπ* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)ππ* state of B is planar and decoupled from the (1)nπ* state. These observations agree with the calculations, which predict the (1)nπ* above the (1)ππ* state for isomer B but below the (1)ππ* for both 9H-2AP and isomer A.

Kinetics and Thermodynamics of the Monomer−Dimer Equilibria of Dialkoxydibutylstannanes

Enthalpies and entropies of dimerization have been determined as functions of concentration for dibutyltin dipropoxide, dibutyltin dibutoxide, and dibutyltin diisopropoxide in toluene-d8 and cyclohexane-d12 solutions from the variation in 119Sn NMR chemical shifts with temperature. The values of ΔH and ΔS obtained in toluene-d8 for dibutyltin dibutoxide were −69.5 ± 3.0 kJ mol−1 and −197 ± 10 J mol−1 K−1, respectively, and for dibutyltin diisopropoxide −67.1 ± 1.4 kJ mol−1 and −244 ± 9 J mol−1 K−1, respectively. Enthalpies and entropies of activation for this process for dibutyltin diisopropoxide have been derived by simulation of the temperature-dependent broadening of the 119Sn NMR spectra. The free energy of activation for dimerization was 33 kJ mol−1. The same thermodynamic parameters for a greater range of dibutyltin dialkoxides were derived theoretically by using MP2 single-point calculations on B3LYP-optimized geometries using the LANL2DZdp basis set with diffuse and polarization functions and its effective core potential for tin and 6-311G(2d,p)//6-31G(d,p) for other atoms. Quite good agreement with the experimental results was achieved with this level of theory. The present study confirms that steric effects dictate the degree of dimerization for dibutyltin dialkoxides, with monomers becoming favored at room temperature when the alkoxide groups are changed from primary to secondary.

Origin of the Enhanced Interaction of Molecular Hydrogen with Extraframework Cu+ and FeO+ Cations in Zeolite Hosts. A Periodic DFT Study

The interactions of hydrogen molecules with Cu+ and FeO+ extraframework cations in chabazite were studied using periodic DFT (B3LYP) calculations. Dispersion forces were accounted for by adding Grimme’s correction to the DFT energy at the B3LYP-optimized geometries. Two potential binding sites are found for FeO+ cations inside chabazite as for Cu+. The preferred site I is located in the middle of the six-membered ring, where FeO+ coordinates to three oxygen atoms of the zeolite framework, while in the less stable site IV FeO+ coordinates to two oxygen atoms of the eight-membered ring (ΔE = 17.3 kJ mol−1). The interaction of H2 with FeO+ (Eads = −17.5 kJ mol−1) is weaker than that with Cu+ (Eads = −85 kJ mol−1), so that binding is only favorable at the more open site IV, where no framework reorganization is needed. For both CuCHA and FeOCHA, the geometry of the adsorbed H2−M+ complex is governed by M d → H2 σ* back-donation, which also contributes to a large extent to the final adsorption energy and controls the barrier to H2 rotation. The M−H distance, the polarization of the metal d orbital involved in the back-donation toward the H2 molecule, as well as the H2 charge density show that the M d → H2 σ* back-donation is larger in H2−Cu+ than in H2−FeO+. Both the binding energy and the barrier to rotation are therefore much greater for H2−CuCHA than for H2−FeOCHA (15.1 vs 7.4 kJ mol−1), in agreement with the available experimental data. A comparison between site I and site IV along with results on the possible adsorption of a second H2 molecule per cation site suggests that the different adsorption sites observed by experiment are more likely due to the presence of different metal cation environments rather than binding of more than one H2 per cation site.

Synthesis, Structures, and Optical and Electrochemical Properties of Benzoporphycenes

The first facile syntheses of free-base di- and tetrabenzoporphycenes and their metal complexes are reported, based on retro-Diels-Alder reactions of the corresponding bicyclo[2.2.2]octadiene-fused porphycenes, prepared by McMurray coupling of alpha,alpha'-diformyldipyrrole. The photophysical and electrochemical properties are analyzed based on UV/Vis absorption, magnetic circular dichroism (MCD), and fluorescence emission, lifetime and quantum yield measurements, cyclic and differential pulse voltammetry (CV and DPV) and time-dependent DFT calculations based on B3LYP geometry optimizations. Benzoporphycenes are found to be prime candidates for future use in photodynamic therapy.

Geometric Dependence of the B3LYP-Predicted Magnetic Shieldings and Chemical Shifts

We perform a systematic investigation of how the B3LYP/6-311+G(2d,p) calculated 13C nuclear magnetic shielding constants depend on the 6-31G(d)-optimized geometries for a set of 18 molecules with various chemical environments. For absolute shieldings, the Hartree-Fock (HF)-optimized geometries lead to a mean absolute deviation (MAD) of 5.65 ppm, while the BLYP- and B3LYP-optimized geometries give MADs of 13.07 and 10.14 ppm, respectively. For chemical shifts, the HF, BLYP and B3LYP geometries lead to MADs of 2.36, 5.80, and 4.43 ppm, respectively. We find that the deshielding tendency of B3LYP can be effectively compensated by using the HF-optimized geometries. When we apply the B3LYP//HF protocol to versicolorin A and 5alpha-androstan-3,17-dione, MADs of 1.86 and 1.41 ppm, respectively, are obtained for chemical shifts, in satisfactory agreement with the experiment.

Electronic Structure of the [MNH2]+ (M = Sc−Cu) Complexes

B3LYP geometry optimizations for the [MNH2]+ complexes of the first-row transition metal cations (Sc+-Cu+) were performed. Without any exception the ground states of these unsaturated amide complexes were calculated to possess planar geometries. CASPT2 binding energies that were corrected for zero-point energies and including relativistic effects show a qualitative trend across the series that closely resembles the experimental observations. The electronic structures for the complexes of the early and middle transition metal cations (Sc+-Co+) differ from the electronic structures derived for the complexes of the late transition metal cations (Ni+ and Cu+). For the former complexes the relative higher position of the 3d orbitals above the singly occupied 2p(pi) HOMO of the uncoordinated NH2 induces an electron transfer from the 3d shell to 2p(pi). The stabilization of the 3d orbitals from the left to the right along the first-row transition metal series causes these orbitals to become situated below the HOMO of the NH2 ligand for Ni+ and Cu+, preventing a transfer from occurring in the [MNH2]+ complexes of these metal cations. Analysis of the low-lying states of the amide complexes revealed a rather unique characteristic of their electronic structures that was found across the entire series. Rather exceptionally for the whole of chemistry, pi-type interactions were calculated to be stronger than the corresponding sigma-type interactions. The origin of this extraordinary behavior can be ascribed to the low-lying sp2 lone pair orbital of the NH2 ligand with respect to the 3d level.

Magnetic circular dichroism spectroscopy and TD-DFT calculations of metal phthalocyanine anion and cation radical species

The results of INDO/s and TD-DFT calculations for neutral ZnPc (−2), unligated [ ZnPc (−1)]+ and chloride anion ligated [( Cl ) ZnPc (−1)] cation radicals, the [ ZnPc (−3)]− radical anion and [ ZnPc (−4)]2− dianion species, performed on a set of B3LYP geometry optimizations are compared with magnetic circular dichroism spectral data. The two calculation methods predict spectra that are broadly similar. The TD-DFT calculations provide a significantly closer agreement with the experimental band centers in the UV region than was previously the case with INDO/s based calculations. The assignment of several key spectral features remains problematic, however, when band polarization information derived from magnetic circular dichroism spectroscopy is taken into consideration.

Theoretical investigation of the electronic coupling element in bis-ruthenium porphyrin dimers

The electronic coupling element for electron transfer is studied in three ruthenium-porphyrin dimers. The dimers are models for compounds that have been previously studied experimentally and allow investigation of orientation effects and linkage effects and comparison of axial ligand effects on the electronic coupling. The geometries used in this study were obtained from B3LYP geometry optimizations in a DZ basis, and the coupling element was calculated as half the energy splitting between pairs of symmetry-related orbitals using Hartree–Fock, B3LYP Kohn–Sham, or INDO orbitals. The results suggest that all three methods give qualitatively similar values of the coupling at a given geometry and that the coupling involving the highest occupied molecular orbital can be changed markedly by changes in orientation or by changes in ligation external to the main pathways for coupling. Following discussion of the results we suggest directions in which future methodological developments will be critical in furthering our ability to understand and predict electron transport.

Electronic structure and spectra of rhodium(II) tetracarboxylate complexes

The DFT B3LYP geometry optimization was carried out and the IR spectra were calculated for rhodium(II) tetracarboxylate complexes Rh2(O2CR)4 (R = H, CH3, CF3, C6H5) and for the compound Rh2(O2CH)4(H2O)2 with two axially coordinated water molecules. A minor influence of the substituent R on the electronic structure and geometric and spectral characteristics of the cage was noted. From the calculation results, it was concluded that the Rh(II)-Rh(II) stretching vibrations should be attributed to about 300 cm−1. The results obtained for rhodium(II) dimers were compared with analogous data for Mo2(O2CH)4. Analysis of the electronic structure including consideration of the natural bond orbitals indicates the presence of a strong Rh(II)-Rh(II) single bond and a quadruple Mo(IV)-Mo(IV) bond. The electronic spectra of Rh2(O2CR)4 (R = H, C6H5) and Rh2(O2CH)4(H2O)2 were simulated by the TDDFT technique.