Calculated Equilibrium Geometries Research Articles

Bonding Analysis of the Ge‐Ge Bonds in the Octagermacubane Ge8(Sit‐butyl2methyl)6

AbstractQuantum chemical calculations have been carried out at the BP86/def2‐SVP level on Ge8(Sit‐butyl2methyl)6(1) and the bonding situation has been analyzed with a variety of methods. The calculated equilibrium geometry of1is in good agreement with the reported x‐ray structure analysis. The D3 correction for dispersion interactions as a sum of pairwise attractions leads to an overestimate of the effect of dispersion forces. Calculations at BP86‐D3(BJ)/def2‐SVP give shorter bonds for Ge(I)−Ge(I) than for Ge(0)−Ge(I), which is in contrast to the experimental values and the BP86/def2‐SVP results. The NBO analysis suggests that the best Lewis structure of1has lone‐pair orbitals at the Ge(0) atoms with occupation numbers of 1.70 e. A lone‐pair character at Ge(0) albeit with less weight is also suggested by the shape of the HOMO, which is an antibonding orbital between the Ge(0) atoms with small contributions from the Ge(I) atoms. The LUMO of1is the corresponding bonding combination of the Ge(0) AOs, which can be explained with the reluctance of the heavier main‐group atoms to s/p hybridization of the valence orbitals. The calculated bond order values suggest significant direct Ge(0)−Ge(0) interactions. This is supported by the shape of the HOMO and by the results of EDA‐NOCV calculations. The deformation densities and the orbitals associated with the pairwise orbital interaction show that there is a direct charge flow between the Ge(0) atoms of the two fragments, but it is not completely separated from the Ge(0)−Ge(I) and Ge(I)−Ge(I) bond formation. The QTAIM calculations suggest that1has a cubic structure with a cage critical point but not a bond critical point for the Ge(0)−Ge(0) interactions. The dispersion interactions of the large substituents in1have a significant influence on the stability of the compound.

Interaction potentials, electric moments, polarizabilities, and chemical reactions of YbCu, YbAg, and YbAu molecules

Ultracold YbAg molecules have been recently proposed as promising candidates for electron electric dipole moment searches Verma et al (2020 Phys. Rev. Lett. 125 153201). Here, we calculate potential energy curves, permanent electric dipole and quadrupole moments, and static electric dipole polarizabilities for the YbCu, YbAg, and YbAu molecules in their ground electronic states. We use the coupled cluster method restricted to single, double, and noniterative triple excitations with large Gaussian basis sets, while the scalar relativistic effects are included within the small-core energy-consistent pseudopotentials. We find that the studied molecules are relatively strongly bound with the well depths of 5708 cm−1, 5253 cm−1, and 13349 cm−1 and equilibrium distances of 5.50 bohr, 5.79 bohr, and 5.55 bohr for YbCu, YbAg, and YbAu, respectively. They have large permanent electric dipole moments of 3.2D, 3.3D, and 5.3D at equilibrium distances, respectively. We also calculate equilibrium geometries and energies of corresponding trimers. The studied molecules are chemically reactive unless they are segregated in an optical lattice or shielded with external fields. The investigated molecules may find application in ultracold controlled chemistry, dipolar many-body physics, or precision measurement experiments.

Rovibrational spectroscopic constants and anharmonic force fields of CH3AsH2 and CH2AsH3: An ab inito study

The spectroscopic constants and anharmonic force fields of Methylarsine and its isomer are systematically studied by B3LYP, CAM-B3LYP, M06-2X methods utilizing the cc-PVTZ and cc-PVQZ basis sets. The calculated equilibrium geometries, fundamental frequencies, and nuclear quadrupole coupling constants, et al of CH3AsH2 are supported by experimental or theoretical data. The harmonic frequencies, anharmonic constants, et al of CH3AsH2 are predicted for the first time. The anharmonic force fields and spectroscopic constants of CH2AsH3 are also investigated with the same theoretical level. The IR spectra of CH3AsH2 and CH2AsH3 are predicted theoretically, and the red-shifts are found in their peaks.

Ab initio study of spectroscopic properties and anharmonic force fields of MNH2 (M = Li, Na, K)

The spectroscopic properties and anharmonic force fields of NaNH2 are studied in present work by DFT (B3P86 and B3PW91) and MP2 methods in combination with 6-311++G(2d, 2p) and 6-311++G(3df, 2pd) basis sets. The calculated equilibrium geometry, ground state rotational constants and centrifugal distortion constants of NaNH2 at B3P86/6-311++G(3df, 2pd) theoretical level agree very well with the corresponding experimental values. Noteworthy, some spectroscopic constants and anharmonic force fields of NaNH2, which have not been experimentally measured, are firstly predicted. In addition, the spectroscopic properties of KNH2 are also predicted at the B3P86/6-311++G(3df, 2pd) level of theory. The influences of metal atoms on the equilibrium geometry, anharmonic constants, rotational constants, centrifugal distortion constants of MNH2 (M = Li, Na, K) are analyzed intuitively. One can find that the metal atoms affect the rotational constants, part of centrifugal distortion constants (DK, DJK, HK, and HKJ), M-N bond length and some anharmonic constants of MNH2.

Analytic energy gradients for the self-consistent direct random phase approximation.

Analytic energy gradients with respect to nuclear coordinates are derived and implemented for the self-consistent direct random phase approximation (sc-dRPA) method. In contrast to the more common non-self-consistent dRPA methods, the sc-dRPA method does not require a choice for the approach to generate the Kohn-Sham orbitals and eigenvalues serving as input for the dRPA correlation functional. The fact that the sc-dRPA total energy is variational facilitates the calculation of analytic gradients. The analytic gradients are tested against numerical ones and then used to calculate equilibrium geometries and vibrational frequencies for various molecules including weakly bonded dimers and transition metal compounds. The sc-dRPA method can compete in accuracy with Møller-Plesset perturbation theory of second order and with conventional density-functional methods within the generalized gradient approximation or of hybrid type. Indeed, sc-dRPA geometries and vibrational frequencies are most accurate in many cases. Moreover, the sc-dRPA method is robust in the sense that it is applicable to all considered molecules, whereas conventional density-functional methods are not applicable to dispersion bonded dimers, and Møller-Plesset perturbation theory of second order erroneously predicts a number of molecules to be unbound and yields completely wrong vibrational frequencies in some cases. The coupled cluster singles doubles methods yield geometries and vibrational frequencies of a quality that is inferior to that of the other considered methods.

Spectroscopic constants and anharmonic force fields of F2SO: An ab inito study

The equilibrium geometry, spectroscopic constants and anharmonic force field of F2SO (X∼1A′) have been reported employing B3LYP, B3P86, B3PW91 and MP2 methods combining with Dunning’s correlation-consistent cc-pVQZ, cc-pV5Z, aug-cc-pVQZ and aug-cc-pV5Z basis sets. The calculated equilibrium geometry, equilibrium rotational constants and fundamental vibrational frequencies of F2SO well reproduce the previous theoretical or experimental values. The calculated equilibrium geometry verifies that F2SO has pyramidal structure and Cs symmetry instead of C1 symmetry. The ground-state rotational constants, harmonic vibrational frequencies, anharmonic constants, quartic and sextic centrifugal distortion constants, cubic and quartic force constants, vibration-rotation interaction constants, and Coriolis coupling constants of F2SO are also predicted. The calculated results show that B3P86 and MP2 methods are superior to B3LYP and B3PW91 methods for the spectroscopic constants of F2SO, we hope that our predictions can provide the useful data for the experiment study of the corresponding spectroscopic constants of F2SO.

Experimental and theoretical study of valence electronic structure of tetrabromomethane by (e,2e) electron momentum spectroscopy

We report a measurement of the valence orbital momentum profiles of tetrabromomethane (${\mathrm{CBr}}_{4}$) using symmetric noncoplanar $(e,2e)$ experiments at the impact energies of about 600 and 1200 eV. The experimental momentum profiles for the individual orbitals $5{t}_{1}, 13{t}_{2}, 5e, 12{t}_{2}$, and $9{a}_{1}$ and the branching ratio of $5{t}_{1}$ to $13{t}_{2}$ and $5e$ to $13{t}_{2}$ are obtained and compared with two kinds of calculations under the plane-wave impulse approximation. One is theoretical momentum profiles that have been calculated at the equilibrium geometry, the other is those that involve vibrational effects using a thermal sampling molecular dynamics method. The calculations considering molecular vibrations are in better agreement with experiment than the equilibrium geometry calculations, indicating the important role of nuclear motions on the valence orbital electronic structures of ${\mathrm{CBr}}_{4}$. The distorted-wave effects are observed in the experimental momentum profiles of $5{t}_{1}, 5e$, and $12{t}_{2}$ which display dynamic dependencies on the impact energies. A multicenter interference or bond oscillation effect has been observed from the momentum profile ratios of $5{t}_{1}$ to $13{t}_{2}$ and $5e$ to $13{t}_{2}$ which has direct information about the bond length of a molecule.

Optimization of structures, biochemical properties of ketorolac and its degradation products based on computational studies.

Ketorolac (KTR) is used as an analgesic drug with an efficacy close to that of the opioid family. It is mainly used for the short term treatment of post-operative pain. It can inhibit the prostaglandin synthesis by blocking cyclooxygenase (COX). In this investigation, the inherent stability and biochemical interaction of Ketorolac (KTR) and its degradation products have been studiedon the basis of quantum mechanical approaches. Density functional theory (DFT) with B3LYP/ 6-31G (d) has been employed to optimize the structures. Thermodynamic properties, frontier molecular orbital features, dipole moment, electrostatic potential, equilibrium geometry, vibrational frequencies and atomic partial charges of these optimized structureswere investigated. Molecular docking has been performed against prostaglandin H2 (PGH2) synthase protein 5F19 to search the binding affinity and mode(s). ADMET prediction has performed to evaluate the absorption, metabolism and carcinogenic properties. The equilibrium geometry calculations support the optimized structures. Thermodynamic results disclosed the thermal stability of all structures. From molecular orbital data, all the degradents are chemically more reactive than parent drug (except K3). However, the substitution of carboxymethyl radicalin K4 improved the physicochemical properties and binding affinity. ADMET calculations predict the improved pharmacokinetic and non-carcinogenic properties of all degradents. Based on physicochemical, molecular docking, and ADMET calculation, this study can be helpful to understand the biochemical activities of Ketorolac and its degradents and to design a potent analgesic drug.

Non-Covalent Interactions in Molecular Crystals: Exploring the Accuracy of the Exchange-Hole Dipole Moment Model with Local Orbitals.

We present the first implementation of the exchange-hole dipole moment (XDM) model in combination with a numerical finite-support local orbital method (the SIESTA method) for the modeling of non-covalent interactions in periodic solids. The XDM model is parametrized for both the B86bPBE and PBE functionals using double-ζ- and triple-ζ-quality basis sets (DZP and TZP). The use of finite-support local orbitals is shown to have minimal impact on the computed dispersion coefficients for van der Waals molecular dimers and small molecular solids. However, the quality of the basis set affects the accuracy of calculated dimer binding energies and molecular-crystal lattice energies quite significantly; the size of the counterpoise correction indicates that this is caused by basis-set incompleteness error. In the case of the DZP basis set, its performance for weakly bound gas-phase dimers is similar to that of a double-ζ Gaussian basis set without diffuse functions. The new XDM implementation was tested on graphite and phosphorene exfoliation, and on the X23 benchmark set of molecular-crystal lattice energies. Our results indicate that lattice energies similar to plane-wave calculations can be obtained only if the counterpoise correction is applied. Alternatively, the calculated equilibrium geometries are reasonably close to the plane-wave equivalents, and composite approaches in which a single-point plane-wave calculation is used at the XDM/DZP equilibrium geometry yield good accuracy at a significantly lower computational cost.

Spectroscopic properties of diketopyrrolopyrrole derivatives with long alkyl chains

The diketopyrrolopyrrole derivatives with long alkyl chains were synthesised and spectrally characterised. Experimental spectroscopic techniques were supplemented by the DFT calculations of equilibrium geometries, normal mode frequencies and time-dependent DFT simulated UV–vis spectra. Comparison between the symmetrical and unsymmetrical substitution of alkyl chains resulted in some changes like bathochromic shift of absorption, excitation and emission spectra, significant reduction of molar absorption coefficient in UV–vis range, increase of fluorescence quantum yield, and slight increase of fluorescence lifetimes. The influence of the length of the alkyl chain on the properties of material was also discussed. The experimental spectroscopic data together with the calculated results show that presence of the alkyl substituent at the nitrogen atom influences more on the properties of the investigated DPPs than the length of attached chain.

Unified picture for the conformation and stabilization of the O-glycosidic linkage in glycopeptide model structures

Glycoproteins play a central role in the immune response. In this study, we focus on the core of the common O-linked mucin-type glycopeptides. It has been observed that glycosylation stabilizes the protein in a stiffened, extended structure. We provide a unified picture for the conformation and stabilization of the O-glycosidic linkage using O-(2-acetylamino-2-deoxy-α- or -β-d-galacto- or -mannopyranosyl)-N-acetyl-l-serinamide model structures. We have calculated equilibrium geometries of the model structures with the B3LYP/6-31G(2df,p) method suggested in the Gaussian-4 theory. According to the relative energies, we confirm that the GalNAc-Ser linkage is more stable than its mannose analogues. The natural preference for the α-GalNAc-Ser over the β-GalNAc-Ser anomers can be explained by entropic effects. We explored the hydrogen bonding patterns on the carbohydrate unit calculating highly accurate dRPA@PBE0.25 and dRPA75 energies and found that in some cases, the acetamido group can be fixed by hydrogen bonding from the (O3Carb)H atom, but in most of the cases, it can rotate more freely. The torsion angles in the glycosidic linkage show that the linkage is stiffened more in the α-anomers and the most in the α-GalNAc-Ser structure because of the steric strains in the axial position and by two or three intramolecular hydrogen bonds. We also found that although, in our gas-phase model geometries, the peptide backbone prefers to be in a γ L-turn, a structural water molecule can stabilize a polyproline II helix of a proline-rich sequence, a β-sheet, or more likely random coils.

Tuning the spectroscopic properties of aryl carotenoids by slight changes in structure.

Two carotenoids with aryl rings were studied by femtosecond transient absorption spectroscopy and theoretical computational methods, and the results were compared with those obtained from their nonaryl counterpart, β-carotene. Although isorenieratene has more conjugated C═C bonds than β-carotene, its effective conjugation length, Neff, is shorter than of β-carotene. This is evidenced by a longer S1 lifetime and higher S1 energy of isorenieratene compared to the values for β-carotene. On the other hand, although isorenieratene and renierapurpurin have the same π-electron conjugated chain structure, Neff is different for these two carotenoids. The S1 lifetime of renierapurpurin is shorter than that of isorenieratene, indicating a longer Neff for renierapurpurin. This conclusion is also consistent with a lower S1 energy of renierapurpurin compared to those of the other carotenoids. Density functional theory (DFT) was used to calculate equilibrium geometries of ground and excited states of all studied carotenoids. The terminal ring torsion in the ground state of isorenieratene (41°) is very close to that of β-carotene (45°), but equilibration of the bond lengths within the aryl rings indicates that the each aryl ring forms its own conjugated system. This results in partial detachment of the aryl rings from the overall conjugation making Neff of isorenieratene shorter than that of β-carotene. The different position of the methyl group at the aryl ring of renierapurpurin diminishes the aryl ring torsion to ∼20°. This planarization results in a longer Neff than that of isorenieratene, rationalizing the observed differences in spectroscopic properties.

Theoretical study of spectroscopic constants and anharmonic force field of formaldehyde

The equilibrium geometries of formaldehyde are optimized with B3LYP, B3PW91 and MP2 methods employing three basis sets 6-311++G(2d,2p), aug-cc-pVTZ and cc-pVTZ, respectively, which agree well with the corresponding experimental and previous theoretical data. The best optimized geometries are obtained at the theoretical level B3LYP/6-311++G(2d,2p) basis set. Basing on the calculated equilibrium geometries, the spectroscopic constants and anharmonic force field of H 2 CO are investigated. The results show that DFT method is superior to MP2 method at the calculation of spectroscopic constants and force constants of H 2 CO . The vibration–rotation interaction constants and fundamental vibrational wave numbers of H 2 CO are firstly theoretically calculated. The Coriolis coupling constants, cubic force constants and most of quartic force constants are firstly theoretically predicted.

Synthesis and structural insights of substituted 2-iodoacetanilides and 2-iodoanilines

This study reports a simple and efficient method for the direct iodination of substituted anilines with molecular iodine and copper acetate in acetic acid producing 2-iodoacetanilies and 2-iodoanilines. Employing density functional theory (B3LYP) and MidiX basis set, computational study is performed to calculate equilibrium geometries, IR vibrational frequencies, and thermodynamic properties including change of energy, enthalpy and Gibbs free energies. The optimized geometries indicated longer C–I bond distance (2.133Å) which makes iodine slightly positive. The partial atomic charge profile and electrostatic potential further confirmed that most of the iodinated products are capable of forming a distinct “halogen bonding”. The thermodynamic properties disclosed that all iodination reactions are endothermic. Understanding the substituents’ effect, molecular frontier orbital (MO) calculations are conducted finding the HOMO, LUMO and HOMO–LUMO gaps for all compounds. The MO calculations revealed that two electron-withdrawing iodine groups have significant influence on lowering the HOMO–LUMO gap compared to one iodine group in the products.

Bonding analysis of trimethylenemethane (TMM) complexes [(CO)3M–TMM] (M = Fe, Ru, Os, Rh+). Absence of expected bond paths

Quantum chemical calculations using gradient-corrected DFT methods (BP86) using effective core potentials and TZP quality basis sets have been carried out for the complexes (CO)3M–TMM (M = Fe, Ru, Os, Rh+; TMM = trimethylenemethane). The calculated equilibrium geometries give trigonal pyramidal structures which are in good agreement with experimental results for the iron and ruthenium species. The TMM ligand adopts a pyramidal coordination of the central carbon atom which has a shorter distance to the metal atom than the terminal carbon atoms. The theoretically predicted bond dissociation energies of the TMM ligand are between 108.0 kcal/mol for the iron complex and 155.1 kcal/mol for the rhodium complex. The trend of the calculated TMM–M bond strength is Fe < Ru < Os < Rh+. The investigation of the electronic structure of the complexes (CO)3M–TMM using MO correlation diagrams and energy partitioning methods clearly shows that the metal atom is mainly bonded to the terminal carbon atoms of the TMM ligand while the bonding to the closer central carbon atom is much weaker. This is further supported by the AIM analysis which shows that the Laplacian distribution ∇2ρ(r) at the terminal carbon atoms possesses local area of charge concentration which points toward the metal atom while the Laplacian distribution at the central carbon atoms is nearly undistorted. In spite of the shape of the Laplacian distribution, there are bond paths between the metal atom and the central carbon atom but not to the terminal carbon atom which comes from the different interatomic distances. This clearly shows that the absence and the existence of a bond path are not reliable criteria for chemical bonding.

Descriptores globales y locales de la reactividad para el diseño de nuevos fármacos anticancerosos basados en cis-platino(II)

Density functional theory was used to investigate the global and local reactivity of some cis-platinum(II) complexes including anticancer drugs, such as cisplatin and carboplatin. Calculated equilibrium geometries at mPW1PW/LANL2DZ* are in close agreement with their available X-ray data. We develop three new local reactivity descriptors: atomic descriptor of philicity, atomic descriptor group and atomic descriptor of philicity group for determining chemical reactivity and selectivity of the studied complexes. This contribution on chemical reactivity allow us to establish qualitative trends, which enable our descriptors for use in rational platinum based anticancer drug design.

QUANTUM MECHANICAL CALCULATIONS OF IR SPECTRA; REACTION ENERGIES OF C-O (R-O) THERMAL BOND RUPTURE FOR CEFUROXIME PRODRUGS

PM3 calculations were carried out for the estimation vibration frequencies, IR absorption intensities, normal coordinates and some physical properties as heat of formation, dipole moment, and ΔEHOMO-LUMO ---etc. for Cefuroxime prodrugs at its calculated equilibrium geometries. Assignment of the vibrations was done depending on the picture of their modes obtained from Gaussian-03 program. Also reaction path for the breakage of the (R-O) C-O bond for all of the derivatives were calculated (in the gas phase). Comparisons were done between the total energies of their reactants, products, activation energies and transition states. The results show impossible use for some substituted organic groups as prodrugs for acidic Cefuroxime drug, whereas others show possible use as prodrugs on breakage the (R-O) C-O bond.

Coincidence momentum imaging of the Coulomb explosion of OCS induced by collision of 15keV/q Ar4+ Ar8+ ions

Ar4+ and Ar8+ ions of 15keV/q from the TMUECRIS have been used in conjunction with a triple coincidence time and position sensitive detection apparatus to observe the Coulomb explosion of OCS. By varying the projectile ion we can access several ionization channels from (1,1,1) to (2,2,2) (where (a,b,c) represents the production of fragments Oa+ + Cb+ + Sc+). In all cases the kinetic energy release peaks are equal to or greater than equilibrium geometry calculations and the distribution widths increase with increasing energy. The extent to which channels are concerted or stepwise is also determined.

AsH3 ultraviolet photochemistry: An ab initio view

Multireference configuration interaction calculations have been carried out for low-lying electronic states of AsH(3). Bending potentials for the nine lowest states of AsH(3) are obtained in C(3v) symmetry for As-H distances fixed at the ground state equilibrium value of 2.850 a(0), as well as for the minimum energy path constrained to R(1) = R(2) = R(3). The calculated equilibrium geometry and bond energy for the X (1)A(1) ground state agree very well with the previous experimental and theoretical data. It is shown that the lowest excited singlet state belongs to the (1)A(1) symmetry (in C(3v)), in contradiction to the previous calculations. This state is characterized by a planar equilibrium geometry. Asymmetric stretch potential energy surface (PES) cuts along the H(2)As-H recoil coordinate (at R(1) = R(2) = 2.850 a(0), θ = 123.9° and 90°) for numerous excited states and two-dimensional PESs for the X and à states up to the dissociation limits are obtained for the first time. The à (1)A(1), B(1)E-X (1)A(1) transition moments are calculated as well and used together with the PES data for the analysis of possible photodecay channels of arsine in its first absorption band.

Synthesis, High-Resolution Millimeter-Wave Spectroscopy, and Ab Initio Calculations of Ethylmercury Hydride

The millimeter-wave rotational spectrum of an organomercury compound, ethylmercury hydride, has been recorded and assigned for the first time. The spectroscopic study is complemented by quantum chemical calculations taking into account relativistic effects on the mercury atom. The very good agreement between theoretical and experimental molecular parameters validates the chosen ab initio method, in particular its capability to predict accurate quartic centrifugal distortion constants related to this type of compound. Estimations of the nuclear quadrupole coupling constants have less predictive power than those of the structural parameters, but are good enough to satisfy the spectroscopic needs. In addition, the orientation of the axis of the H-Hg-C bonds deduced from the experimental nuclear quadrupole coupling constants compares well with the corresponding ab initio value. From the good agreement between experimental and theoretical results, together with the observation of the six most abundant isotopes of mercury, ethylmercury hydride is unambiguously identified as the product of the chemical reaction described here, and its calculated equilibrium geometry is confirmed.