De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. Coordination isomerism

The ground state coordination isomers for 30 different trigonal bipyramidal transition metal complexes have been predicted using different levels of quantum mechanics: semiempirical (PM3(tm)), ab initio (MP2//HF), pure (BPW91) and hybrid (B3PW91) density functional theory (DFT) methods. For species where these methods failed to reproduce crystallographic data, hybrid quantum mechanics/molecular mechanics (QM/MM) methods were used to study more exact experimental models. Literature deficiencies regarding ground state multiplicity of these species were supplemented by spin predictions using previously tested PM3(tm) methods. Geometry optimization calculations were performed for each possible coordination isomer. The predicted ground state minima provided by the different methods are compared to each other and with crystallographic data. Pure DFT functionals outperformed hybrid functionals and MP2//HF. The very rapid PM3(tm) parameterization method provided accurate predictions in comparison to other levels of theory. An integrated MM/PM3(tm)/DFT de novo scheme accurately reproduced crystallographic data for species where the individual methods failed.     

De novo structural prediction of transition metal complexes: application to technetium

De novo structural prediction of transition metal complexes is investigated. Technetium complexes are chosen given their importance in medical imaging and nuclear waste remediation and for the chemical diversity they display. A new conformational searching algorithm (LIGB) for transition metals is described that allows one to search for different conformational and geometric isomers within a single simulation. In the preponderance of cases, both conformational searching techniques (LIGB and high-temperature molecular dynamics/simulated annealing) provide comparable results, while LIGB is superior for macrocyclic complexes. A genetic algorithm-optimized PM3(tm) parametrization for Tc is compared with the standard implementation and found to yield a significant improvement in predictive ability for the most prevalent Tc structural motifs. The utility of a coupled molecular mechanics-semiempirical quantum mechanics protocol is demonstrated for very rapid, efficient, and effective de novo prediction of transition metal complex geometries.     

Activation Energy and Transition State Determination of the Olefin Insertion Process of Metallocene Catalysts Using a Semiempirical Molecular Orbital Calculation

The transition state of the olefin insertion process of metallocene catalysts can be determined by adopting the semiempirical PM3 model. In computational chemistry, the computational methods most employed are the ab initio method and density functional theory, which are very time consuming. The semiempirical molecular orbital method requires much less computational resources than the above methods. However, the accuracy and reliability of the semiempirical molecular orbital method remains to be determined. The PM3 model is the most recently developed the semiempirical molecular orbital method and can also be applied to transition metal calculations. This study is intended to investigate the reliability of computational results determined using semiempirical PM3 model on metallocene catalysts through comparison with published results on the density functional theory (DFT). The saddle point finding procedure is adopted to find the transition state of the ethylene insertion process of metallocene catalysts. Results on the geometry and energy trends of the ethylene insertion process of metallocene catalysts determined using the PM3 model are in good agreement with the DFT results. In addition, the saddle point of the potential energy surface of ethylene insertion is verified in accordance with the eigenvalue of the vibrational frequency spectrum. Correct eigenvalues indicate that the correct saddle point of the potential energy surface of ethylene insertion has been successfully located. Hence, the eigenvalue of the vibrational frequency spectrum is a valuable reference in terms of saddle point justification. Computational results and vibrational frequency spectrum analysis demonstrate that the PM3 model can be used to locate the correct saddle point of the potential energy surface. The results obtained using the PM3 model confirm that the eigenvalue of the transition state lies nearly on the vibrational frequency spectrum. The eigenvalues are also analyzed, providing a valuable reference for further studies of the transition state of olefin insertion of metallocene catalysts. The activation energies for the olefin insertion reaction are also studied for evaluation of the catalyst.     

Investigating the structural and electronic properties of nitrile hydratase model iron(III) complexes using projected unrestricted Hartree-Fock (PUHF) calculations

Important structural and mechanistic details concerning the non-heme, low-spin Fe(III) center in nitrile hydratase (NHase) remain poorly understood. We now report projection unrestricted Hartree-Fock (PUHF) calculations on the spin preferences of a series of inorganic complexes in which Fe(III) is coordinated by a mixed set of N/S ligands. Given that many of these compounds have been prepared as models of the NHase metal center, this study has allowed us to evaluate this computational approach as a tool for future calculations on the electronic structure of the NHase Fe(III) center itself. When used in combination with the INDO/S semiempirical model, the PUHF method correctly predicts the experimentally observed spin state for 12 of the 13 Fe(III)-containing complexes studied here. The one compound for which there is disagreement between our theoretical calculations and experimental observation exhibits temperature-dependent spin behavior. In this case, the failure of the PUHF-INDO/S approach may be associated with differences between the structure of the Fe(III) complex present under the conditions used to measure the spin preference and that observed by X-ray crystallography. A preliminary analysis of the role of the N/S ligands and coordination geometry in defining the Fe(III) spin preferences in these complexes has also been undertaken by computing the electronic properties of the lowest energy Fe(III) spin states. While any detailed interpretation of our results is constrained both by the limited set of well-characterized Fe(III) complexes used in this study and by the complicated dependence of Fe(III) spin preference upon metal-ligand interactions and coordination geometry, these PUHF-INDO/S calculations support the hypothesis that the deprotonated amide nitrogens coordinating the metal stabilize the low-spin Fe(III) ground state seen in NHase. Strong evidence that the sulfur ligands exclusively define the Fe(III) spin state preference by forming metal-ligand bonds with significant covalent character is not provided by these computational studies. This might, however, reflect limitations in modeling these systems at the INDO/S level of theory.     

ADF Studies of Neutral Small C_n(n=3～6)High-symmetry Clusters

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Molecular Modeling of Bioorganometallic Compounds: Thermodynamic Properties of Molybdocene–Glutathione Complexes and Mechanism of Peptide Hydrolysis

The computational study of bioinorganic complexes between transition metals and flexible ligands is still challenging, given that, besides requiring extensive conformational searches, the treatment of metal–ligand bonds demands the application of quantum chemical methods. Herein, the adducts formed between molybdocene, which exhibits antitumor activity and reacts with thiol groups to give stable water‐soluble complexes, and the tripeptide glutathione, which is a major source of biological thiols, are studied. Conformational searches are performed using the semiempirical PM6 method followed by geometry optimizations and single‐point calculations using density functional theory methods. In addition, molecular dynamics simulations of the molybdocene–glutathione complex involved in the regioselective hydrolysis of the Cys–Gly linkage are performed in explicit solvent. The reactive process is also studied theoretically on cluster models of both the molybdocene‐bound and the free peptide.     

Semiempirical configuration interaction calculations for ru‐centered dyes*

Computational investigation of the photochemical properties of transition‐metal‐centered dyes typically involves optimization of the molecular structure followed by calculation of the UV/visible spectrum. At present, these steps are usually carried out using density functional theory (DFT) and time‐dependent DFT calculations. Recently, we demonstrated that semiempirical methods with appropriate parameterization could yield geometries that were in very good agreement with DFT calculations, allowing large sets of molecules to be screened quickly and efficiently. In this article, we modify a configuration interaction (CI) method based on a semiempirical PM6 Hamiltonian to determine the UV/visible absorption spectra of Ru‐centered complexes. Our modification to the CI method is based on a scaling of the two‐center, two‐electron Coulomb integrals. This modified, PM6‐based method shows a significantly better match to the experimental absorption spectra versus the default configuration interaction method (in MOPAC) on a training set of 13 molecules. In particular, the modified PM6 method blue‐shifts the location of the metal‐to‐ligand charge‐transfer (MLCT) peaks, in better agreement with experimental and DFT‐based computational results, correcting a significant deficiency of the unmodified method. Published 2018. This article is a U.S. Government work and is in the public domain in the USA     

Semiempirical NDDO/MC calculations of the excited states of the chromate ion

A new semiempirical method of calculating the excited states of transition metal complexes is developed. This technique uses the configuration interaction and semiempirical NDDO/MC methods to obtain the ground state of a set of Slater type valence spd-orbitals chosen from the optical spectra of transition metals together with the corresponding core integrals. The method is tested in calculations of the electronically excited states of the chromate ion. Good agreement with the experimental energies of vertical transitions and the results of ab initio calculations is achieved.     

Would the pseudocoordination centre method be appropriate to describe the geometries of lanthanide complexes?

The correct prediction of the ground-state geometries of lanthanide complexes is an important step in the development of efficient light conversion molecular devices (LCMD). Considering this, we evaluate here the capability of semiempirical approaches and ab initio effective core potential (ECP) methodology in reproducing the coordination polyhedron geometries of lanthanide complexes. Initially, we compare the facility of two semiempirical approaches: Pseudocoordination centre method (PCC) and Sparkle model. In the first step, we considered only high-quality crystallographic structures and included 633 complexes, and in the last step, we compare the capability of two semiempirical approaches with ab initio/ECP calculations. Because this last methodology was found to be computationally very demanding, we further used a subset containing 91 high-quality crystallographic structures. A total of 91 ab initio full geometry optimizations were performed. Our results suggest that only the semiempirical Sparkle model (hundreds of times faster) present accuracy similar to what can be obtained by present-day ab initio/ECP full geometry optimization calculations on such lanthanide complexes. In addition, it further indicates that the PCC approach has a poor prediction related to the coordination polyhedron geometries of lanthanide complexes.     

Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system.     

Density matrix renormalization group calculations on relative energies of transition metal complexes and clusters

The accurate first-principles calculation of relative energies of transition metal complexes and clusters is still one of the great challenges for quantum chemistry. Dense lying electronic states and near degeneracies make accurate predictions difficult, and multireference methods with large active spaces are required. Often density functional theory calculations are employed for feasibility reasons, but their actual accuracy for a given system is usually difficult to assess (also because accurate ab initio reference data are lacking). In this work we study the performance of the density matrix renormalization group algorithm for the prediction of relative energies of transition metal complexes and clusters of different spin and molecular structure. In particular, the focus is on the relative energetical order of electronic states of different spin for mononuclear complexes and on the relative energy of different isomers of dinuclear oxo-bridged copper clusters.     

Comparison of AM1 and PM3 semiempirical to ab initio methods in the study of Diels-Alder reactions of butadiene and cyclopentadiene with cyanoethylenes

Assuming a concerted synchronous mechanism with one transition state of the Diels-Alder reactions, the structures of the transition states and the activation energies for the reactions of butadiene and cyclopentadiene with cyanoethylenes were calculated by AM1 and PM3 semiempirical methods. The structural parameters were compared with those obtained by high level Gaussian calculations, whereas the activation energies were compared both with the ab initio calculations and those obtained experimentally. The structural properties calculated with PM3 methods are in general in better agreement with the ab initio calculations. The low level ab initio calculations are in many cases worse than the semiempirical methods. All predicted activation energies with both semiempirical methods are up to 300% higher than the experimental values. The predicted reactivity is also opposite to the experimental data. Only the very high level Gaussian calculations are in good correlation with experimental results. The predicted selectivity of the reaction is also opposite to the experimental facts. Two explanations are offered for this discrepancy: AM1 and PM3 methods cannot handle the calculation of the concerted Diels-Alder transition states and are not recommended to be used for that purpose, or this Diels-Alder reaction is not concerted but is stepwise.     

Prediction of geometries and interaction energies of complexes formed by small molecules using semiempirical and ab initio methods

The accuracy of the semiempirical quantum mechanics methods (AM1 and PM3), and the ab initio methods (6-31G^** and MP2/6-31G^**) in predicting intermolecular geometries and interaction energies have been evaluated by detailed studies of 17 bimolecular complexes formed by small molecules. Comparisons between calculated and experimental geometries for 12 complexes are presented. It was found that AM1 gave reasonably good predictions of the geometries of complexes such as CH₄ · CH₄, which have very weak interactions, but it is not as good as other methods in predicting intermolecular geometry for complexes where hydrogen bonding interactions play an important role. This is consistent with its inability to reproduce the charge transfer in the formation of hydrogen bonds in these complexes.

PM3 is able to predict intermolecular geometries for most complexes, including those with hydrogen bonding; its major flaw is its tendency to overestimate the strength of the interactions between hydrogen atoms. Care should be taken therefore in using PM3 to study complicated molecular systems with multiple hydrogen atom interactions and the method's weakness in handling complexes in which electrostatic forces are important should also be noted.

Among ab initio methods, both the 6-31G^** and the MP2/6-31G^** were found to outperform AM1 and PM3 in prediction of intermolecular geometry. Both of these ab initio methods showed excellent consistency in geometry prediction for most of the complexes studied, although MP2/6-31G^** is better than 6-31G^**. It is noted that the MP2/6-31G^** did not produce the correct geometry for the CO₂· HF complex.

For 12 complexes for which experimental geometry data are available, AM1, PM3, 6-31G^**, and MP2/6-31G^** successfully predicted the geometry in 10, 12, 12, and 11 cases, respectively. The average errors given by AM1 in the predicted intermolecular distances were 0.264, 0.272, 0.091, and 0.061 Å, respectively. In comparison to the ab initio methods, AM1 and PM3 commonly underestimated the molecular interaction energy in such complexes by ˜ 1–2 kcal mol⁻¹.     

Am1 and pm3 transition structure for the hydride transfer. A model of reaction catalyzed by dihydrofolate reductase

The transition state structure for the hydride transfer in dihydrofolate reductase, DHFR, enzyme has been calculated with analytical gradients at semiempirical levels: AM1 and PM3. The geometry, electronic structure and transition vector components are qualitatively semiempirical level independent. Comparing the transition structures for the hydride transfer step in models of liver alcohol dehydrogenase, formate dehydrogenase, lactate dehydrogenase, and glutathione reductase, the geometries of these stationary points are transferable and invariant. The topology of the transition structures in these enzymes resembles the one calculated in this paper.     

Ab initio and direct quasiclassical-trajectory study of the F+CH4-->HF+CH3 reaction

We present an electronic structure and dynamics study of the F+CH4-->HF+CH3 reaction. CCSD(T)/aug-cc-pVDZ geometry optimizations, harmonic-frequency, and energy calculations indicate that the potential-energy surface is remarkably isotropic near the transition state. In addition, while the saddle-point F-H-C angle is 180 degrees using MP2 methods, CCSD(T) geometry optimizations predict a bent transition state, with a 153 degrees F-H-C angle. We use these high-quality ab initio data to reparametrize the parameter-model 3 (PM3) semiempirical Hamiltonian so that calculations with the improved Hamiltonian and employing restricted open-shell wave functions agree with the higher accuracy data. Using this specific-reaction-parameter PM3 semiempirical Hamiltonian (SRP-PM3), we investigate the reaction dynamics by propagating quasiclassical trajectories. The results of our calculations using the SRP-PM3 Hamiltonian are compared with experiments and with the estimates of two recently reported potential-energy surfaces. The trajectory calculations using the SRP-PM3 Hamiltonian reproduce quantitatively the measured HF vibrational distributions. The calculations also agree with the experimental HF rotational distributions and capture the essential features of the excitation function. The results of the SRP semiempirical Hamiltonian developed here clearly improve over those using the two prior potential-energy surfaces and suggest that reparametrization of semiempirical Hamiltonians is a promising strategy to develop accurate potential-energy surfaces for reaction dynamics studies of polyatomic systems.     

Spectroscopic and theoretical studies on nickel(II) complex of maleonitriledithiolate and 2,2'-bipyridine

The complete IR spectra of the title complex Ni(mnt)(bpy) (mnt=maleonitriledithiolate, bpy=2,2'-bipyridine) and a new method to analyze vibrational spectra for such a complicated metal complex are reported in this paper. The molecular geometry, binding, electronic structure and spectroscopic property of it have been studied in detail by theoretical calculations. The geometry optimization from PM3 calculations give that this molecule is of a planar structure with the symmetry point group C(2v) and its ground state is the spin triplet state. The vibrational and electronic spectra were calculated by PM3 and ZINDO/S methods, respectively. The scientific method of analyzing vibrational spectra is established herein by giving main fixed points and pivotal vibrational units. Besides the regular symbols, the new defined symbols eta and M play an important role in describing the vibration modes accurately and vividly.     

A sobering assessment of small‐molecule force field methods for low energy conformer predictions

We have carried out a large scale computational investigation to assess the utility of common small‐molecule force fields for computational screening of low energy conformers of typical organic molecules. Using statistical analyses on the energies and relative rankings of up to 250 diverse conformers of 700 different molecular structures, we find that energies from widely used classical force fields (MMFF94, UFF, and GAFF) show unconditionally poor energy and rank correlation with semiempirical (PM7) and Kohn–Sham density functional theory (DFT) energies calculated at PM7 and DFT optimized geometries. In contrast, semiempirical PM7 calculations show significantly better correlation with DFT calculations and generally better geometries. With these results, we make recommendations to more reliably carry out conformer screening.     

Electronic absorption spectra of amino substituted anthraquinones and their interpretation using the ZINDO/S and AM1 methods

Electronic absorption spectra of 1,2-diamino-9,10-anthraquinone (12DAAQ), 1,4-diamino-9,10-anthraquinone (14DAAQ), 1,5-diamino-9,10-anthraquinone (15DAAQ), and 2,6-diamino-9,10-anthraquinone (26DAAQ) are investigated. Molecular geometries of the amino anthraquinones in the ground state are optimized using the semiempirical ZINDO/1 and AM1 methods without imposing any symmetry constraints. The ground state geometries of all the molecular systems are found to be planar. For interpretation of the spectra, ZINDO/S-CI and AM1-CI calculations employing singly excited configuration using the completely optimized geometry are carried out. Such calculations on the electronic spectra of amino anthraquinones are carried out for the first time. On the basis of these calculations, the assignment of the spectra are successfully made.     

Ability of fullerenes to act as η6 ligands in transition metal complexes. A comparative PM3(tm)–density functional theory study

High‐quality DFT calculations are employed to estimate the arene exchange energies for reactions of general formula: For C₆₀ and C₇₀ complexes of Cr(CO)₃, full geometry optimizations at the DFT level using moderately large basis sets were performed, while for the other systems a hybrid approach was developed in which the geometries were obtained at the PM3(tm) level and the energetics were evaluated at the DFT level. C₇₀ is shown to be a slightly better arene ligand than C₆₀; however, no enhancements of arene‐like bonding capabilities are seen for C₇₈ and C₈₄ relative to C₇₀. Explicit calculation of a series of exchange energies at the DFT level using both DFT and PM3(tm) geometries demonstrates that PM3(tm) geometries are sufficiently accurate for the calculation of energetics at a higher theoretical level, but PM3(tm) calculations are inadequate for a quantitative assessment of exchange energies. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1881–1886, 2001