Joseph Ivanic

Direct configuration interaction and multiconfigurational self-consistent-field method for multiple active spaces with variable occupations. I. Method

In order to reduce the number of ineffective configurations in a priori generated configuration spaces, a direct configuration interaction method has been developed which limits the electron occupations of orbital groups making up a total active space. A wave function is specified by first partitioning an active space into an unrestricted number of orbital groups and second by providing limiting values, in the form of minima and maxima, for the electron occupancies of each group. The configuration interaction problem corresponding to all possible determinants satisfying these conditions is solved in a fully direct manner by the use of Slater–Condon expressions in conjunction with single and double replacements. This configuration interaction approach, termed occupation restricted multiple active space-configuration interaction, has also been linked with orbital optimization programs to produce the occupation restricted multiple active space-self consistent field method.

Direct configuration interaction and multiconfigurational self-consistent-field method for multiple active spaces with variable occupations. II. Application to oxoMn(salen) and N2O4

In a previous paper, a new direct configuration interaction method for multiple active spaces with variable occupations was described. The present article illustrates how this method may be applied to the oxoMn(salen) complex and the N2O4 molecule. In the first application it is shown how complete-active-space self-consistent-field wave functions of the oxoMn(salen) system may be approximated by a drastically reduced number of configurations with negligible loss of accuracy in terms of energetics. In the second application, to N2O4, it is demonstrated how the fully optimized reaction space wave function may be approximated and also how the recovery of dynamic correlation effects may be achieved. The best predictions of the structure (rNN=1.743 A, rNO=1.189 A, ∠(ONO)=134.4°) and binding energy (De=16.0 kcal/mol) are both in very good agreement with experiment (rNN=1.756, rNO=1.191, ∠(ONO)=134.46°, De=16.3 kcal/mol).

Solvent-Induced Shifts in Electronic Spectra of Uracil

Highly accurate excitation spectra are predicted for the low-lying n-π* and π-π* states of uracil for both the gas phase and in water employing the complete active space self-consistent field (CASSCF) and multiconfigurational quasidegenerate perturbation theory (MCQDPT) methods. Implementation of the effective fragment potential (EFP) solvent method with CASSCF and MCQDPT enables the prediction of highly accurate solvated spectra, along with a direct interpretation of solvent shifts in terms of intermolecular interactions between solvent and solute. Solvent shifts of the n-π* and π-π* excited states arise mainly from a change in the electrostatic interaction between solvent and solute upon photoexcitation. Polarization (induction) interactions contribute about 0.1 eV to the solvent-shifted excitation. The blue shift of the n-π* state is found to be 0.43 eV and the red shift of the π-π* state is found to be -0.26 eV. Furthermore, the spectra show that in solution the π-π* state is 0.4 eV lower in energy than the n-π* state.

Electronic Structure Analysis of the Ground-State Potential Energy Curve of Be2

The recently measured ground-state potential energy curve of the diatomic beryllium molecule is reproduced to within an accuracy of 20 cm(-1) by a full valence configuration interaction calculation based on augmented correlation-consistent double-, triple-, and quadruple-zeta basis sets, followed by a two-tier extrapolation to the complete basis set limit and complemented by a configuration interaction estimate of the core and core-valence correlations. The origin of binding in Be(2) as well as the unusual shape of its potential energy curve is elucidated by an in-depth analysis of the contributions of the various components of this wave function to the bonding process. Beyond the bonding region, the 6/8 London dispersion interaction is recovered.

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

Single base substitutions constitute the most frequent type of human gene mutation and are a leading cause of cancer and inherited disease. These alterations occur non-randomly in DNA, being strongly influenced by the local nucleotide sequence context. However, the molecular mechanisms underlying such sequence context-dependent mutagenesis are not fully understood. Using bioinformatics, computational and molecular modeling analyses, we have determined the frequencies of mutation at G•C bp in the context of all 64 5′-NGNN-3′ motifs that contain the mutation at the second position. Twenty-four datasets were employed, comprising >530,000 somatic single base substitutions from 21 cancer genomes, >77,000 germline single-base substitutions causing or associated with human inherited disease and 16.7 million benign germline single-nucleotide variants. In several cancer types, the number of mutated motifs correlated both with the free energies of base stacking and the energies required for abstracting an electron from the target guanines (ionization potentials). Similar correlations were also evident for the pathological missense and nonsense germline mutations, but only when the target guanines were located on the non-transcribed DNA strand. Likewise, pathogenic splicing mutations predominantly affected positions in which a purine was located on the non-transcribed DNA strand. Novel candidate driver mutations and tissue-specific mutational patterns were also identified in the cancer datasets. We conclude that electron transfer reactions within the DNA molecule contribute to sequence context-dependent mutagenesis, involving both somatic driver and passenger mutations in cancer, as well as germline alterations causing or associated with inherited disease.

A Systematic Multireference Perturbation-Theory Study of the Low-Lying States of SiC3

The three known lowest-energy isomers of SiC(3), two cyclic singlets (2s and 3s) and a linear triplet (1t), have been reinvestigated using multireference second-order perturbation theory (MRPT2). The dependence of the relative energies of the isomers upon the quality of the basis sets and the sizes of the reference active spaces is explored. When using a complete-active-space self-consistent-field reference wave function with 12 electrons in 11 orbitals [CASSCF (12, 11)] together with basis sets that increase in size up to the correlation-consistent polarized core-valence quadruple zeta basis set (cc-pCVQZ), the MRPT2 method consistently predicts the linear triplet to be the most stable isomer. A new parallel direct determinant MRPT2 code has been used to systematically explore reference spaces that vary in size from CASSCF (8,8) to full optimized reaction space [FORS or CASSCF (16,16)] with the cc-pCVQZ basis. It is found that the relative energies of the isomers change substantially as the active space is increased. At the best level of theory, MRPT2 with a full valence FORS reference, the 2s isomer is predicted to be more stable than 3s and 1t by 4.7 and 2.2 kcal/mol, respectively.

In Vivo Activation of Duocarmycin–Antibody Conjugates by Near-Infrared Light

Near-IR photocaging groups based on the heptamethine cyanine scaffold present the opportunity to visualize and then treat diseased tissue with potent bioactive molecules. Here we describe fundamental chemical studies that enable biological validation of this approach. Guided by rational design, including computational analysis, we characterize the impact of structural alterations on the cyanine uncaging reaction. A modest change to the ethylenediamine linker (N,N′-dimethyl to N,N′-diethyl) leads to a bathochromic shift in the absorbance maxima, while decreasing background hydrolysis. Building on these structure–function relationship studies, we prepare antibody conjugates that uncage a derivative of duocarmycin, a potent cytotoxic natural product. The optimal conjugate, CyEt-Pan-Duo, undergoes small molecule release with 780 nm light, exhibits activity in the picomolar range, and demonstrates excellent light-to-dark selectivity. Mouse xenograft studies illustrate that the construct can be imaged in vivo prior to uncaging with an external laser source. Significant reduction in tumor burden is observed following a single dose of conjugate and near-IR light. These studies define key chemical principles that enable the identification of cyanine-based photocages with enhanced properties for in vivo drug delivery.

Decoding Nitric Oxide Release Rates of Amine-Based Diazeniumdiolates

Amine-based diazeniumdiolates (NONOates) have garnered widespread use as nitric oxide (NO) donors, and their potential for nitroxyl (HNO) release has more recently been realized. While NO release rates can vary significantly with the type of amine, half-lives of seconds to days under physiological conditions, there is as yet no way to determine a priori the NO or HNO production rates of a given species, and no discernible trends have manifested other than that secondary amines produce only NO (i.e., no HNO). As a step to understanding these complex systems, here we describe a procedure for modeling amine-based NONOates in water solvent that provides an excellent correlation (R(2) = 0.94) between experimentally measured dissociation rates of seven secondary amine species and their computed NO release activation energies. The significant difference in behavior of NONOates in the gas and solvent phases is also rigorously demonstrated via explicit additions of quantum mechanical water molecules. The presented results suggest that the as-yet unsynthesized simplest amine-based NONOate, the diazeniumdiolated ammonia anion [H2N-N(O)═NO(-)], could serve as an unperturbed HNO donor. These results provide a step forward toward the accurate modeling of general NO and/or HNO donors as well as for the identification of tailored prodrug candidates.

High-level theoretical study of the NO dimer and tetramer: Has the tetramer been observed?

The ground-state properties of (NO)(2) and (NO)(4) have been investigated using multireference second-order perturbation theory (MRMP2) and include a two-tier extrapolation to the complete basis set (CBS) limit. For the NO dimer the MRMP2(18,14)/CBS predicted structure, binding energy (with respect to 2NO; D(e) = 3.46 kcal/mol), and dipole moment (u(e) = 0.169 D) are in excellent agreement with experimental measurements (D(e) = 2.8-3.8 kcal/mol; u(e) = 0.171 D). Additionally, three of four intermolecular anharmonic MRMP2(18,14)/CBS-estimated frequencies (143 cm(-1), 238 cm(-1), 421 cm(-1)) are in excellent agreement with recent gas-phase experimental measurements (135 cm(-1), 239 cm(-1), 429/428 cm(-1)); however, the predicted value of 151 cm(-1) for the out-of-plane torsion (A(2)) is elevated compared to recent experimental estimates of 97-117 cm(-1). Our finding that this infrared-forbidden vibration is also predicted to have an extremely low Raman activity (0.04 Å/amu at the MP2/QZ level of theory) conflicts with Raman measurements of a strong intensity for a low frequency band; however, these studies were performed for low temperature solid and liquid phases. Probing the possibility of the presence of higher order clusters we investigated the stability of (NO)(4) and discovered three isomers, each resembling pairs of dimers, that were stable to dissociation to 2(NO)(2), with the lowest-energy isomer (C(i) structure) having a predicted binding energy almost identical to that of the dimer. Computed vibrational frequencies of the C(i) isomer indicate that the 12 highest-frequency modes resemble barely shifted NO dimer-combined bands while the 13th highest-frequency mode at ~100 cm(-1) is exclusive to (NO)(4). Moreover, this tetramer-unique vibration is infrared inactive but has a very high predicted Raman activity of some 24 Å/amu. Guided by the theoretical results, we reexamined and reassigned experimental Raman and infrared data going back to 1951 and determined that our best predictions of vibrational frequencies of (NO)(2) and (NO)(4) are consistent with experimental observations. We thus postulate the existence and observation of (NO)(4).