All-Purpose Measure of Electron Correlation for Multireference Diagnostics

We present an analytical relationship between two natural orbital occupancy-based indices, I N D ¯ and INDmax, and two established electron correlation metrics: the leading term of a configuration interaction expansion, c0, and the D2 diagnostic. Numerical validation revealed that I N D ¯ and INDmax can effectively substitute for c0 and D2, respectively. These indices offer three distinct advantages: (i) they are universally applicable across all electronic structure methods, (ii) their interpretation is more intuitive, and (iii) they can be readily incorporated into the development of hybrid electronic structure methods. Additionally, we draw a distinction between correlation measures and correlation diagnostics, establishing MP2 and CCSD numerical thresholds for INDmax, which are to be used as a multireference diagnostic. Our findings further demonstrate that establishing thresholds for other electronic structure methods can be easily accomplished using small data sets.

Influence of the Nonprotein Amino Acid Mimosine in Peptide Conformational Propensities from Novel Amber Force Field Parameters

Mimosine is a nonprotein amino acid derived from plants known for its ability to bind to divalent and trivalent metal cations such as Zn²⁺, Ni²⁺, Fe²⁺, or Al³⁺. This results in interesting antimicrobial and anticancer properties, which make mimosine a promising candidate for therapeutic applications. One possibility is to incorporate mimosine into synthetic short peptide drugs. However, how this amino acid affects the peptide structure is not well understood, reducing our ability to design effective therapeutic compounds. In this work, we used computer simulations to understand this question. We first built parameters for the mimosine residue to be used in combination with two classical force fields of the Amber family. Then, we used atomistic molecular dynamics simulations with the resulting parameter sets to evaluate the influence of mimosine in the structural propensities for this amino acid. We compared the results of these simulations with homologous peptides, where mimosine is replaced by either phenylalanine or tyrosine. We found that the strong dipole in mimosine induces a preference for conformations where the amino acid rings are stacked over more extended conformations. We validated our results using quantum mechanical calculations, which provide a robust foundation for the outcome of our classical simulations.

Markov state models from hierarchical density-based assignment

Markov state models (MSMs) have become one of the preferred methods for the analysis and interpretation of molecular dynamics (MD) simulations of conformational transitions in biopolymers. While there is great variation in terms of implementation, a well-defined workflow involving multiple steps is often adopted. Typically, molecular coordinates are first subjected to dimensionality reduction and then clustered into small "microstates," which are subsequently lumped into "macrostates" using the information from the slowest eigenmodes. However, the microstate dynamics is often non-Markovian, and long lag times are required to converge the relevant slow dynamics in the MSM. Here, we propose a variation on this typical workflow, taking advantage of hierarchical density-based clustering. When applied to simulation data, this type of clustering separates high population regions of conformational space from others that are rarely visited. In this way, density-based clustering naturally implements assignment of the data based on transitions between metastable states, resulting in a core-set MSM. As a result, the state definition becomes more consistent with the assumption of Markovianity, and the timescales of the slow dynamics of the system are recovered more effectively. We present results of this simplified workflow for a model potential and MD simulations of the alanine dipeptide and the FiP35 WW domain.

Backbone flexibility of extended metal atom chains. Ab initio molecular dynamics for Cr3(dpa)4X2 (X = NCS, CN, NO3) in gas and crystalline phases

Computational study on the flexibility of chromium extended metal atom chains by ab initio molecular dynamics.

A multiconfigurational approach to the electronic structure of trichromium extended metal atom chains

Density functional theory, Complete Active Space Self-Consistent Field (CASSCF) and perturbation theory (CASPT2) methodologies have been used to explore the electronic structure of a series of trichromium Extended Metal Atom Chains (EMACS) with different capping ligands.

Structure and Magnetism of [M3]6/7+ Metal Chain Complexes from Density Functional Theory: Analysis for Copper and Predictions for Silver

The ground-state electronic structure of the trinuclear complex Cu3(dpa)4Cl2 (1), where dpa is the anion of di(2-pyridyl)amine, has been investigated within the framework of density functional theory (DFT) and compared with that obtained for other known M3(dpa)4Cl2 complexes (M = Cr, Co, Ni) and for the still hypothetical Ag3(dpa)4Cl2 compound. Both coinage metal compounds display three singly occupied x2-y2-like (delta) orbitals oriented toward the nitrogen environment of each metal atom, generating antibonding M-(N4) interactions. All other metal orbital combinations are doubly occupied, resulting in no delocalized metal-metal bonding. This is at variance with the other known symmetric M3(dpa)4Cl2 complexes of the first transition series, which all display some delocalized bonding through the metal backbone, with formal bond multiplicity decreasing in the order Cr > Co > Ni. An antiferromagnetic coupling develops between the singly occupied MOs via a superexchange mechanism involving the bridging dpa ligands. This magnetic interaction can be considered as an extension to the three aligned Cu(II) atoms of the well-documented exchange coupling observed in carboxylato-bridged dinuclear copper compounds. Broken-symmetry calculations with approximate spin projection adequately reproduce the coupling constant observed for 1. Oxidation of 1 removes an electron from the magnetic orbital located on the central Cu atom and its ligand environment; 1+ displays a much weaker antiferromagnetic interaction coupling the terminal Cu-N4 moieties via four ligand pathways converging through the x2-y2 orbital of the central metal. The silver homologues of 1 and 1+ display similar electronic ground states, but the calculated magnetic couplings are stronger by factors of about 3 and 4, respectively, resulting from a better overlap between the metal centers and their equatorial ligand environment within the magnetic orbitals.

Time-dependent density-functional approach for biological chromophores: the case of the green fluorescent protein

We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.

Electronic properties of polyoxometalates: a DFT study of alpha/beta-[XM(12)O(40)](n-) relative stability (M=W, Mo and X a main group element)

Keggin heteropolyanions [XM(12)O(40)](n-) have various isomeric structures, alpha and beta being the most common. Conventionally, the alpha structure appears to be the most stable, but calculations carried out at the DFT level for X = P(V), Si(IV), Al(III), As(V), Ge(IV), and Ga(III) and M = W(VI) and Mo(VI) show that this stability depends on several factors, particularly on the nature of the heteroatom (X) and the total charge of the cluster. In this paper, we apply the clathrate model to the Keggin molecule to carry out a fragment-interaction study to elucidate when and why the traditional relative stability of various isomers can be inverted. The fully oxidized anions that have inverted the traditional stability trend in this series are [AlW(12)O(40)](5-) and [GaW(12)O(40)](5-), both of which contain a third-group heteroatom and an overall charge of -5. beta-isomers are always more easily reduced than alpha-isomers. This experimental observation suggests that reduction favors the stability of beta-isomers and one of the most important results of this study is that the alpha/beta inversion is achieved in most cases after the second reduction. The alpha- and beta-isomers may have different properties because the energy of the LUMO, a symmetry-adapted d(xy)-metal orbital, is different.

[The effect of a peripheral androgenic blockade on plasma lipoproteins in hirsutism patients]

We studied the effect of flutamide, a peripheral androgenic blocking agent, 500 mg daily for 28 days in 7 non ovulating patients with hirsutism. Total and HDL cholesterol, triglycerides, testosterone and dehydroepiandrosterone sulphate (S-DHEA) plasma levels were measured in patients and in 6 non ovulating control women of similar age and weight. Only basal HDL levels were lower in patients than in controls (40.2 +/- 1.6 vs 51.4 +/- 3.3 mg/dl, p < 0.01). A decrease in S-DHEA levels was observed after flutamide in patients with hirsutism (3.2 +/- 0.4 to 2.1 +/- 0.4, p < 0.01) which may be attributed to the lowering of cortisol clearance induced by the drug. Total testosterone and plasma lipoproteins remained stable. Thus, peripheral androgenic blockade does not modify the decreased levels of HDL cholesterol in non ovulating patients with hirsutism.