Model protein excited states: MRCI calculations with large active spaces vs CC2 method.

Benchmarking calculations on excited states of models of phenylalanine protein chains are presented to assess the ability of alternative methods to the standard and most commonly used multiconfigurational wave function-based method, the complete active space self-consistent field (CASSCF), in recovering the non-dynamical correlation for systems that become not affordable by the CASSCF. The exploration of larger active spaces beyond the CASSCF limit is benchmarked through three strategies based on the reduction in the number of determinants: the restricted active space self-consistent field, the generalized active space self-consistent field (GASSCF), and the occupation-restricted multiple active space (ORMAS) schemes. The remaining dynamic correlation effects are then added by the complete active space second-order perturbation theory and by the multireference difference dedicated configuration interaction methods.

Recent developments in the general atomic and molecular electronic structure system.

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory.

Quasi-Atomic Bond Analyses in the Sixth Period: II. Bond Analyses of Cerium Oxides.

The role of the 4f orbitals in bonding is examined for the molecules cerium monoxide and cerium dioxide that have cerium formally in the +2 and +4 oxidation states, respectively. It is shown that the 4f orbitals are used primarily for polarization of the 5d orbitals when cerium is in the lower oxidation state, while the 4f orbitals play a significant role in chemical bonding via 5d/4f hybridization when cerium is in the +4 oxidation state.

Quasi-Atomic Bond Analyses in the Sixth Period: I. Relativistic Accurate Atomic Minimal Basis Sets for the Elements Cesium to Radon.

Full-valence relativistic accurate atomic minimal basis set (AAMBS) orbitals are developed for the sixth-row elements from cesium to radon, including the lanthanides. Saturated primitive atomic basis sets are developed and subsequently used to form the AAMBS orbitals. By virtue of the use of a saturated basis, properties computed based on the AAMBS orbitals are basis set independent.

Ab Initio Molecular Orbital Study of the First Four Si/C Alternately Substituted Annulenes.

The ground and low-lying excited states of four alternating Si/C annulenes, H Si C with n = 4, 6, 8, and 10, have been investigated by ab initio molecular orbital methods and compared to those of their all-carbon and all-silicon analogues. In the ground state, all of the Si/C-mixed annulenes, except for the largest 10-membered annulene (HSiC), assume equal-bond-length structures by adopting a closed-shell electronic structure in the possible highest symmetry. For the largest HSiC, the trend of the bond delocalization still remains but the circular structure is considerably distorted and nonplanar due to severe angle strain.

Spin-Orbit Coupling Constants in Atoms and Ions of Transition Elements: Comparison of Effective Core Potentials, Model Core Potentials, and All-Electron Methods.

The spin-orbit coupling constants (SOCC) in atoms and ions of the first- through third-row transition elements were calculated for the low-lying atomic states whose main electron configuration is [ nd] ( q = 1-4 and 6-9, n = the principal quantum number), using four different approaches: (1) a nonrelativistic Hamiltonian used to construct multiconfiguration self-consistent field (MCSCF) wave functions utilizing effective core potentials and their associated basis sets within the framework of second-order configuration interaction (SOCI) to calculate spin-orbit couplings (SOC) using one-electron Breit-Pauli Hamiltonian (BPH), (2) a nonrelativistic Hamiltonian used to construct MCSCF wave functions utilizing model core potentials and their associated basis sets within the framework of SOCI to calculate SOC using the full BPH, (3) nonrelativistic and spin-independent relativistic Hamiltonians used to construct MCSCF wave functions utilizing all-electron (AE) basis sets within the framework of SOCI to calculate SOC using the full BPH, and (4) a relativistic Hamiltonian given by the exact two-component (X2C) transformation for construction of Kramers-restricted relativistic configuration interaction wave functions. In this investigation, these four approaches are referred to as ECP, MCP, AE, and X2C methods, respectively. The ECP, MCP, and AE methods are so-called two-step approaches (TSA), while the X2C method is a one-step approach (OSA).

Hybrid Correlation Energy (HyCE): An Approach Based on Separate Evaluations of Internal and External Components.

A novel hybrid correlation energy (HyCE) approach is proposed that determines the total correlation energy via distinct computation of its internal and external components. This approach evolved from two related studies. First, rigorous assessment of the accuracies and size extensivities of a number of electron correlation methods, that include perturbation theory (PT2), coupled-cluster (CC), configuration interaction (CI), and coupled electron pair approximation (CEPA), shows that the CEPA(0) variant of the latter and triples-corrected CC methods consistently perform very similarly.

Effect of Boron Clusters on the Ignition Reaction of HNO and Dicynanamide-Based Ionic Liquids.

Many ionic liquids containing the dicynamide anion (DCA, formula N(CN)) exhibit hypergolic ignition when exposed to the common oxidizer nitric acid. However, the ignition delay is often about 10 times longer than the desired 5 ms for rocket applications, so that improvements are desired. Experiments in the past decade have suggested both a mechanism for the early reaction steps and also that additives such as decaborane can reduce the ignition delay.

Relativistic ab Initio Accurate Atomic Minimal Basis Sets: Quantitative LUMOs and Oriented Quasi-Atomic Orbitals for the Elements Li-Xe.

Valence virtual orbitals (VVOs) are a quantitative and basis set independent method for extracting chemically meaningful lowest unoccupied molecular orbitals (LUMOs). The VVOs are formed based on a singular value decomposition (SVD) with respect to precomputed and internally stored ab initio accurate atomic minimal basis sets (AAMBS) for the atoms. The occupied molecular orbitals and VVOs together form a minimal basis set that can be transformed into orthogonal oriented quasi-atomic orbitals (OQUAOs) that provide a quantitative description of the bonding in a molecular environment.

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces.

Electronic Polarization Effect of the Water Environment in Charge-Separated Donor-Acceptor Systems: An Effective Fragment Potential Model Study.

The electronic polarization (POL) of the surrounding environment plays a crucial role in the energetics of charge-separated systems. Here, the mechanism of POL in charge-separated systems is studied using a combined quantum mechanical and effective fragment potential (QM/EFP) method. In particular, the POL effect caused by charge separation (CS) is investigated at the atomic level by decomposition into the POL at each polarizability point.

The MICE facility - a new tool to study plant-soil C cycling with a holistic approach.

Plant-soil interactions are recognized to play a crucial role in the ecosystem response to climate change. We developed a facility to disentangle the complex interactions behind the plant-soil C feedback mechanisms. The MICE ('Multi-Isotope labelling in a Controlled Environment') facility consists of two climate chambers with independent control of the atmospheric conditions (light, CO, temperature, humidity) and the soil environment (temperature, moisture).

Threshold Ionization and Spin-Orbit Coupling of Ceracyclopropene Formed by Ethylene Dehydrogenation.

A Ce atom reaction with ethylene was carried out in a laser-vaporization metal cluster beam source. Ce(C2H2) formed by hydrogen elimination from ethylene was investigated by mass-analyzed threshold ionization (MATI) spectroscopy, isotopic substitutions, and relativistic quantum chemical computations. The theoretical calculations include a scalar relativistic correction, dynamic electron correlation, and spin-orbit coupling.

Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids (BPCA).

Fire-derived, pyrogenic carbon (PyC), sometimes called black carbon (BC), is the carbonaceous solid residue of biomass and fossil fuel combustion, such as char and soot. PyC is ubiquitous in the environment due to its long persistence, and its abundance might even increase with the projected increase in global wildfire activity and the continued burning of fossil fuel. PyC is also increasingly produced from the industrial pyrolysis of organic wastes, which yields charred soil amendments (biochar).

Heavy Element Effects in the Diagonal Born-Oppenheimer Correction within a Relativistic Spin-Free Hamiltonian.

Methodologies beyond the Born-Oppenheimer (BO) approximation are nowadays important to explain high precision spectroscopic measurements. Most previous evaluations of the BO correction are, however, focused on light-element molecules and based on a nonrelativistic Hamiltonian, so no information about the BO approximation (BOA) breakdown in heavy-element molecules is available. The present work is the first to investigate the BOA breakdown for the entire periodic table, by considering scalar relativistic effects in the Diagonal BO correction (DBOC).

Infrared Spectroscopy and Structure of (NO)(n) Clusters.

Nitrogen oxide clusters (NO)n have been studied in He droplets via infrared depletion spectroscopy and by quantum chemical calculations. The ν1 and ν5 bands of cis-ON-NO dimer have been observed at 1868.2 and 1786.

Valence Virtual Orbitals: An Unambiguous ab Initio Quantification of the LUMO Concept.

Unlabelled: Many chemical concepts hinge on the notion of an orbital called the lowest unoccupied molecular orbital, or LUMO. This hypothetical orbital and the much more concrete highest occupied molecular orbital (HOMO) constitute the two "frontier orbitals", which rationalize a great deal of chemistry. A viable LUMO candidate should have a sensible energy value, a realistic shape with amplitude on those atoms where electron attachment or reduction or excitation processes occur, and often an antibonding correspondence to one of the highest occupied MOs.

A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. II. Strongly Correlated MCSCF Wave Functions.

A methodology is developed for the quantitative identification of the quasi-atomic orbitals that are embedded in a strongly correlated molecular wave function. The wave function is presumed to be generated from configurations in an internal orbital space whose dimension is equal to (or slightly larger) than that of the molecular minimal basis set. The quasi-atomic orbitals are found to have large overlaps with corresponding orbitals on the free atoms.

A Comprehensive Analysis in Terms of Molecule-Intrinsic Quasi-Atomic Orbitals. IV. Bond Breaking and Bond Forming along the Dissociative Reaction Path of Dioxetane.

The quantitative analysis of molecular density matrices in terms of oriented quasi-atomic orbitals (QUAOs) is shown to yield detailed conceptual insight into the dissociation of dioxetane on the basis of ab initio wave functions. The QUAOs persist and can be followed throughout the reaction path. The kinetic bond orders and the orbital populations of the QUAOs quantitatively reveal the changes of the bonding interactions along the reaction path.

A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. III. The Covalent Bonding Structure of Urea.

The analysis of molecular electron density matrices in terms of quasi-atomic orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.

Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method.

Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms.

Model space diabatization for quantum photochemistry.

Diabatization is a procedure that transforms multiple adiabatic electronic states to a new representation in which the potential energy surfaces and the couplings between states due to the electronic Hamiltonian operator are smooth, and the couplings due to nuclear momentum are negligible. In this work, we propose a simple and general diabatization strategy, called model space diabatization, that is applicable to multi-configuration quasidegenerate perturbation theory (MC-QDPT) or its extended version (XMC-QDPT). An advantage over previous diabatization schemes is that dynamical correlation calculations are based on standard post-multi-configurational self-consistent field (MCSCF) multi-state methods even though the diabatization is based on state-averaged MCSCF results.

Transformation and stabilization of pyrogenic organic matter in a temperate forest field experiment.

Pyrogenic organic matter (PyOM) decomposes on centennial timescale in soils, but the processes regulating its decay are poorly understood. We conducted one of the first studies of PyOM and wood decomposition in a temperate forest using isotopically labeled organic substrate, and quantified microbial incorporation and physico-chemical transformations of PyOM in situ. Stable-isotope (¹³C and ¹⁵N) enriched PyOM and its precursor wood were added to the soil at 2 cm depth at ambient (N0) and increased (N+) levels of nitrogen fertilization.

Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method.

The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree-Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen.