Exciting flavins: Absorption spectra and spin–orbit coupling in light–oxygen–voltage (LOV) domains

Flavins are central molecular chromophores for many photobiological processes. In this paper, several aspects of the photophysics and photochemistry of lumiflavin in a (protein) environment will be studied with the help of quantum chemical methods. In a first part of the paper, we present vertical singlet excitation energies for lumiflavin (a molecule of the isoalloxazin type), using time-dependent density functional theory (TD-DFT) in conjunction with the B3LYP hybrid functional. When calculated for isolated species, TD-DFT excitation energies are generally blue-shifted relative to the experimental absorption spectra of isoalloxazines in solution, or in a protein environment. We develop four different models to account for environmental effects, with special emphasis on the LOV1 domain of Chlamydomonas reinhardtii. It is found that the two lowest, allowed singlet excitations are sensitive to the polarizability of an environment, to hydrogen bonds, and to geometrical constraints imposed by the surrounding protein. All of this brings theory and experiment in better agreement.

In the second part of the paper the light-induced adduct formation in LOV domains, between the chromophore and a neighbouring cystein unit is investigated. Energies along a model “reaction path” are calculated on the DFT/B3LYP and MCQDPT2 level of theories. A transition state for a H-transfer between the mercapto (SH–) group of cystein, and the N(5) position of flavin is found. The reaction requires spin–orbit coupling between the S₀ and the T₁ states of the system. Spin–orbit coupling constants between S₀ and T₁ are calculated, and found to be in the range of several tens of cm⁻¹ after the transition state was passed. A biradical intermediate was observed along the reaction path.     

Spin–orbit coupling of spin‐frustrated systems

We have investigated the effects of spin–orbit (SO) interactions on noncollinear molecular magnetism by combining the classical Dzyaloshinsky–Moriya (DM) model and ab initio generalized spin orbital (GSO) method. We have derived an estimation scheme of the magnetic anisotropy energy (MAE) and the Dzyaloshinsky vector based on the SO first‐order perturbation theory (SOPT1) for GSO Hartree–Fock (GHF) solutions. We found that the fundamental results of GHF‐SOPT1 method can be reproduced by diagonalizing the core Hamiltonian plus SO terms, and that the spin topologies of odd‐ring systems can be determined by the topological indices of the singly occupied molecular orbitals. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Two‐component calculations of spin–orbit effects for a van der Waals molecule Rn2

Electronic structures of the weakly bound Rn₂ were calculated by the two‐component Møller–Plesset second‐order perturbation and coupled‐cluster methods with relativistic effective core potentials including spin–orbit operators. The calculated spin–orbit effects are small, but depend strongly on the size of basis sets and the amount of electron correlations. Magnitudes of spin–orbit effects on D_e (0.7–3.0 meV) and R_e (−0.4∼−2.2 Å) of Rn₂ are comparable to previously reported values based on configuration interaction calculations. A two‐component approach seems to be a promising tool to investigate spin–orbit effects for the weak‐bonded systems containing heavy elements. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 139–143, 1999     

Development of spin‐orbit coupling for stochastic configuration interaction techniques

To perform spin‐orbit coupling calculations on atoms and molecules, good zeroth‐order wavefunctions are necessary. Here, we present the software development of the Monte Carlo Configuration Interaction (MCCI) method, to enable calculation of such properties, where MCCI iteratively constructs a multireference wavefunction using a stochastic procedure. In this initial work, we aim to establish the efficacy of this technique in predicting the splitting of otherwise degenerate energy levels on a range of atoms and small diatomic molecules. It is hoped that this work will subsequently act as a gateway toward using this method to investigate singlet‐triplet interactions in larger multireference molecules. We show that MCCI can generate very good results using highly compact wavefunctions compared to other techniques, with no prior knowledge of important orbitals. Higher‐order relativistic effects are neglected and spin‐orbit coupling effects are incorporated using first‐order degenerate perturbation theory with the Breit‐Pauli Hamiltonian and effective nuclear charges in the one‐electron operator. Results are obtained and presented for B, C, O, F, Si, S, and Cl atoms and OH, CN, NO, and C₂ diatomic radicals including spin‐orbit coupling constants and the relative splitting of the lowest energy degenerate state for each species. Convergence of MCCI to the full configuration interaction result is demonstrated on the multireference problem of stretched OH. We also present results from the singlet‐triplet interaction between the and both the and states of the O₂ molecule. © 2017 Wiley Periodicals, Inc.     

Ab initio calculations of the ground and excited states of the ZrN molecule including spin‐orbit effects

The electronic structures with spin‐orbit effects of the zirconium nitride ZrN molecule are investigated by the methods of multireference single and double configuration interaction. The potential energy curves are calculated along with the spectroscopic constants for the lowest‐lying 34 spin‐orbit states Ω in ZrN. A good agreement is displayed by comparing the calculated spectroscopic constants with those available experimentally. The permanent dipole moments are calculated along with the vibrational energies. New results are obtained in this work for 29 spin‐orbit states and their spectroscopic constants calculated. © 2015 Wiley Periodicals, Inc.     

Spin‐orbit ab initio and density functional theory investigation of bismuth monoboronyl,BiBO

The molecular properties of bismuth monoboronyl, BiBO, were investigated using high‐level ab initio and density functional theory calculations by including the effect of spin‐orbit coupling (SOC). SOC does not cause any change in the Bi? B bond length of BiBO, by contrast it causes significant elongation of the Bi? B bond of BiBO^?, by ～0.03 Å. The Bi? B bond length of BiBO^? that is calculated by considering SOC is almost identical to that of BiBO; this result is consistent with a recent experimental study. The term values of excited states of BiBO calculated by including SOC are in good agreement with the experimental results. One excited state which was not assigned in the previous experimental study is the Ω = 0⁺ state generated by strong SOC. In the theoretical calculations on molecules containing 6p‐block elements, including SOC is crucial for obtaining results that are consistent with the corresponding experimental results.     

Ab initio study of spin–orbit interaction in the ground electronic states of XH (X = C, Si, Ge and Sn) molecules

Electronic structure and spectroscopic properties for the ground electronic states of CH, SiH, GeH and SnH molecules were obtained using the multiconfigurational self-consistent field followed by spin–orbit multireference multistate perturbation theory. Spin–orbit splitting calculations for ground states of the four molecules were carried out with model core potential (MCP) and all-electron (AE) methods. MCP results are compared with corresponding AE values to estimate the accuracy of the saving cost MCP calculations. The potential energy curves, calculated for the Ω states CH(X₁²Π_1/2 and X₂²Π_3/2), SiH(X₁²Π_1/2 and X₂²Π_3/2), GeH(X₁²Π_1/2 and X₂²Π_3/2) and SnH(X₁²Π_1/2 and X₂²Π_3/2) using the MCP method, were fitted to analytical potential energy function using Murrell–Sorbie potential energy function. Based on the analytical potential energy function, force constants and spectroscopic constants for the Ω states were obtained.     

Ab initio calculation of the Dzyaloshinskii–Moriya parameters: Spin–orbit GSO‐HF,DFT, and CI approaches

We present ab initio methods to determine the Dzyaloshinskii–Moriya (DM) parameter, which provides the anisotropic effects of noncollinear spin systems. For this purpose, we explore various general spin orbital (GSO) approaches, such as Hartree–Fock (HF), density functional theory (DFT), and configuration interaction (CI), with one‐electron spin–orbit coupling (SOC1). As examples, two simple D_3h‐symmetric models, H₃ and B(CH₂)₃, are examined. Implications of the computational results are discussed in relation to as isotropic and anisotropic interactions of molecular‐based magnets. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A full‐pivoting algorithm for the Cholesky decomposition of two‐electron repulsion and spin‐orbit coupling integrals

A significant reduction in the computational effort for the evaluation of the electronic repulsion integrals (ERI) in ab initio quantum chemistry calculations is obtained by using Cholesky decomposition (CD), a numerical procedure that can remove the zero or small eigenvalues of the ERI positive (semi)definite matrix, while avoiding the calculation of the entire matrix. Conversely, due to its antisymmetric character, CD cannot be directly applied to the matrix representation of the spatial part of the two‐electron spin‐orbit coupling (2e‐SOC) integrals. Here, we present a computational strategy to achieve a Cholesky representation of the spatial part of the 2e‐SOC integrals, and propose a new efficient CD algorithm for both ERI and 2e‐SOC integrals. The proposed algorithm differs from previous CD implementations by the extensive use of a full‐pivoting design, which allows a univocal definition of the Cholesky basis, once the CD δ threshold is made explicit. We show that is the upper limit for the errors affecting the reconstructed 2e‐SOC integrals. The proposed strategy was implemented in the ab initio program Computational Emulator of Rare Earth Systems (CERES), and tested for computational performance on both the ERI and 2e‐SOC integrals evaluation. © 2017 Wiley Periodicals, Inc.     

Use of the normal coordinates in variational and perturbative ab initio handling of the vibronic and spin–orbit couplings in Π electronic states of linear tetra‐atomic molecules

Avariational and a perturbative approach are developed to handle the combined effect of the vibronic and spin–orbit couplings in Π electronic states of tetra‐atomic molecules with linear equilibrium geometry. Both of them are based on the use of the normal vibrational bending coordinates. The perturbative treatment is carried out via two schemes for partition of the model Hamiltonian: In the first, the spin–orbit coupling term is treated as a perturbation; in the second, it is included in the zeroth‐order Hamiltonian. It is demonstrated that both perturbative approaches lead to the same second‐order formulae when the spin–orbit coupling constant is small compared to the bending frequency, but much larger than the splitting of potential surfaces upon bending. These approaches are used to calculate the vibronic and spin–orbit structure in the X²Π electronic state of HCCS by employing the ab initio‐computed potential energy surfaces. Complete numerical equivalence of the results obtained with the present variational approach and those generated by the algorithms employing internal vibrational coordinates is demonstrated. The restrictions concerning the applicability of the perturbative approaches are discussed in terms of the agreement between the results obtained by means of them with those generated in the corresponding variational computations. The general reliability of the model employed is checked by comparing the theoretical results with the available experimental data. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

All‐electron relativistic computations on the low‐lying electronic states,bond length,and vibrational frequency of CeF diatomic molecule with spin–orbit coupling effects

Ab initio all‐electron computations have been carried out for Ce⁺ and CeF, including the electron correlation, scalar relativistic, and spin–orbit coupling effects in a quantitative manner. First, the n‐electron valence state second‐order multireference perturbation theory (NEVPT2) and spin–orbit configuration interaction (SOCI) based on the state‐averaged restricted active space multiconfigurational self‐consistent field (SA‐RASSCF) and state‐averaged complete active space multiconfigurational self‐consistent field (SA‐CASSCF) wavefunctions have been applied to evaluations of the low‐lying energy levels of Ce⁺ with [Xe]4f¹5d¹6s¹ and [Xe]4f¹5d² configurations, to test the accuracy of several all‐electron relativistic basis sets. It is shown that the mixing of quartet and doublet states is essential to reproduce the excitation energies. Then, SA‐RASSCF(CASSCF)/NEVPT2 + SOCI computations with the Sapporo(‐DKH3)‐2012‐QZP basis set were carried out to determine the energy levels of the low‐lying electronic states of CeF. The calculated excitation energies, bond length, and vibrational frequency are shown to be in good agreement with the available experimental data. © 2018 Wiley Periodicals, Inc.     

Description of excited states in [Re(Imidazole)(CO)3(Phen)]+ including solvent and spin‐orbit coupling effects: Density functional theory versus multiconfigurational wavefunction approach

The low‐lying electronic excited states of [Re(imidazole)(CO)₃(phen)]⁺ (phen = 1,10‐phenanthroline) ranging between 420 nm and 330 nm have been calculated by means of relativistic spin‐orbit time‐dependent density functional theory (TD‐DFT) and wavefunction approaches (state‐average‐CASSCF/CASPT2). A direct comparison between the theoretical absorption spectra obtained with different methods including SOC and solvent corrections for water points to the difficulties at describing on the same footing the bands generated by metal‐to‐ligand charge transfer (MLCT), intraligand (IL) transition, and ligand‐to‐Ligand‐ charge transfer (LLCT). While TD‐DFT and three‐roots‐state‐average CASSCF (10,10) reproduce rather well the lowest broad MLCT band observed in the experimental spectrum between 420 nm and 330 nm, more flexible wavefunctions enlarged either by the number of roots or by the number of active orbitals and electrons destabilize the MLCT states by introducing IL and LLCT character in the lowest part of the absorption spectrum. © 2016 Wiley Periodicals, Inc.     

First example of the correlated calculation of the one‐bond tellurium–carbon spin–spin coupling constants: Relativistic effects,vibrational corrections,and solvent effects

This work reports on the comprehensive calculation of the NMR one‐bond spin–spin coupling constants (SSCCs) involving carbon and tellurium, ¹J(¹²⁵Te,¹³C), in four representative compounds: Te(CH₃)₂, Te(CF₃)₂, Te(C?CH)₂, and tellurophene. A high‐level computational treatment of ¹J(¹²⁵Te,¹³C) included calculations at the SOPPA level taking into account relativistic effects evaluated at the 4‐component RPA and DFT levels of theory, vibrational corrections, and solvent effects. The consistency of different computational approaches including the level of theory of the geometry optimization of tellurium‐containing compounds, basis sets, and methods used for obtainig spin–spin coupling values have also been discussed in view of reproducing the experimental values of the tellurium–carbon SSCCs. Relativistic corrections were found to play a major role in the calculation of ¹J(¹²⁵Te,¹³C) reaching as much as almost 50% of the total value of ¹J(¹²⁵Te,¹³C) while relativistic geometrical effects are of minor importance. The vibrational and solvent corrections account for accordingly about 3–6% and 0–4% of the total value. It is shown that taking into account relativistic corrections, vibrational corrections and solvent effects at the DFT level essentially improves the agreement of the non‐relativistic theoretical SOPPA results with experiment. © 2016 Wiley Periodicals, Inc.     

The adiabatic‐to‐diabatic transformation angle and the berry phase for coupled jahn–teller/renner–teller systems: The F + H2 as a case study

The approach to calculate improved, two‐state, adiabatic‐to‐diabatic transformation angles (also known as mixing angles), presented before (see Das et al., J Chem Phys 2010, 133, 084107), was used here while studying the F + H₂ system. However, this study is characterized by two new features: (a) it is the first of its kind in which is studied the interplay between Renner–Teller (RT) and Jahn–Teller (JT) nonadiabatic coupling terms (NACT); (b) it is the first of its kind in which is reported the effect of an upper singular RT‐NACT on a lower two‐state (JT) mixing angle. The fact that the upper NACT is singular (it is shown to be a quasi‐Dirac δ‐function) enables a semi‐analytical solution for this perturbed mixing angle. The present treatment, performed for the F + H₂ system, revealed the existence of a novel parameter, η, the Jahn–Renner coupling parameter (JRCP), which yields, in an unambiguous way, the right intensity of the RT coupling (as resembled, in this case, by the quasi‐Dirac δ‐function) responsible for the fact that the final end‐of‐the contour angle (identified with the Berry phase) is properly quantized. This study implies that the numerical value of this parameter is a pure number (independent of the molecular system): η = $ 2\sqrt 2 /\pi $ (= 0.9003) and that there is a good possibility that this value is a novel characteristic molecular constant for a certain class of tri‐atomic systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Open‐chain unsaturated selanyl sulfides: stereochemical structure and stereochemical behavior of their 77Se–1H spin–spin coupling constants

Stereochemical structure of nine Z‐2‐(vinylsulfanyl)ethenylselanyl organyl sulfides has been investigated by means of experimental measurements and second‐order polarization propagator approach calculations of their ¹H–¹H, ¹³C–¹H, and ⁷⁷Se–¹H spin–spin coupling constants together with a theoretical conformational analysis performed at the MP2/6‐311G** level. All nine compounds were shown to adopt the preferable skewed s‐cis conformation of their terminal vinylsulfanyl group, whereas the favorable rotational conformations with respect to the internal rotations around the C–S and C–Se bonds of the internal ethenyl group are both skewed s‐trans. Stereochemical trends of ⁷⁷Se–¹H spin–spin coupling constants originating in the geometry of their coupling pathways and the selenium lone pair effect were rationalized in terms of the natural J‐coupling analysis within the framework of the natural bond orbital approach. Copyright © 2012 John Wiley & Sons, Ltd.     

Nonadiabatic quantum dynamics of Br2 in solid Ar: A four-dimensional study of the B to C state predissociation

Quantum dynamics simulations are performed for a diatomics-in-molecules based model of Br₂ in solid Ar which incorporates four nuclear degrees of freedom and four electronic states. The nuclear motions comprise two large amplitude coordinates describing the Br₂ bond distance and an effective symmetry-preserving matrix mode. Two symmetry-lowering harmonic modes are added in the spirit of linear vibronic coupling theory. Initiating the dynamics on the B state by means of an ultrafast laser pulse, nonadiabatic transitions to the two degenerate C states are monitored and the effect of vibrational preexcitation in the electronic ground state is investigated.     

The ultraviolet photodissociation of DCl: H/D isotope effects on the Cl(P) atom spin–orbit branching

The photodissociation of jet-cooled DCl molecules subsequent to excitation in the long-wavelength tail of the first UV absorption band (A¹Π₁←X¹Σ⁺) has been investigated at five wavelengths in the range 200–220 nm. Ground state Cl(²P_3/2) and spin–orbit excited Cl^*(²P_1/2) photofragments were monitored using (2+1) resonance enhanced multiphoton ionization in a time-of-flight mass spectrometer. The product branching fractions are reported and compared with previous experimental results and high-level quantum mechanical calculations for HCl and DCl. A significant H/D isotope effect in the branching fractions is found at all the studied wavelengths, in quantitative agreement with recent theoretical predictions.     

A theoretical structural analysis of the factors that affect 1JNH, 1hJNH and 2hJNN in N–H···N hydrogen‐bonded complexes

Calculations of ¹ J_NH, ^1h J_NH and ^2h J_NN spin–spin coupling constants of 27 complexes presenting N–H·N hydrogen bonds have allowed to analyze these through hydrogen‐bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, ? 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states ‘proton‐in‐the‐middle’ is considerable. Copyright © 2008 John Wiley & Sons, Ltd.     

A quantum chemical calculation on Fe(CO)5 revealing the operation of the Dewar–Chatt–Duncanson model

A nonstandard computational scheme has been applied to calculate Fe(CO)₅ with the aim to illustrate the operation of the Dewar–Chatt–Duncanson model by computation. A full configuration interaction (CI) calculation in an active space has been performed. The active space is built from naturally localized molecular orbitals (NLMOs) localized in bond regions or forming lone pairs. For selecting this active space, Weinhold's perturbation theory formulated in the natural bond orbital (NBO) space has been applied. Bonding, lone pair, and antibond NBOs exhibiting large interaction energies serve to define the active space. The actually applied active space, however, comprises NLMOs that are close in shape to the NBOs indicated by perturbation theory. Thus, a CI calculation with localized orbitals has been performed meeting the classical reasoning of chemists that is often based on local bonding concepts. The computational scheme yields the Lewis structure for Fe(CO)₅ whose energy is identical to the Hartree–Fock energy. The Lewis energy comprises CO → Fe σ‐electron transfer (ET) and CO ← Fe electron back donation (BD). This Lewis energy gets lowered by localized correlation energy contributions caused by ET processes where electrons are back donated from the Fe d‐lone pairs into the CO ligands. Thus, electron correlation within the selected active space is dominated by electron BD. Energies and electron populations of the NBOs support the notion that electrons are preferentially back donated into the equatorial CO ligands. Weights of local Slater determinants, determining the correlation energy, also point to a predominant BD into the equatorial CO ligands. Correlation energy increments resulting from electron BD into single antibond orbitals of the CO ligands have been calculated. These energy quantities also demonstrate that BD into the equatorial CO ligands is more energy lowering than BD into the axial CO ligands. © 2012 Wiley Periodicals, Inc.     

Quantum chemical study of IrFn (n = 1–7) clusters: An investigation of superhalogen properties

In present investigation, the interactions of iridium (Ir) atom with fluorine (F) atoms have been studied using the density functional theory. Up to seven F atoms were able to bind to a single Ir atom which resulted in increase of electron affinities successively, reaching a peak value of 7.85 eV for IrF₇. The stability and reactivity of these clusters were analyzed by calculating highest occupied molecular orbital (HOMO)–LUMO gaps, molecular orbitals and binding energies of these clusters. The unusual properties of these clusters are due to the involvement of inner shell 5d‐electrons, which not only allows IrF_n clusters to belong to the class of superhalogens but also shows that its valence can exceed the nominal value of 2. © 2012 Wiley Periodicals, Inc.