The Role of Nitrogen-Rich Moieties in the Selection of Arginine's Tautomeric Form at Different Temperatures.

It is well known that the guanidinium group in Arginine plays an important role in noncovalent interactions. However, its role is not well documented since the selection of its global minimum structure is still controversial. The main difficulties on obtaining accurate results lie on:  neutral Arginine can occur in 3 forms, two of which are canonical and one is zwitterion; each form has degenerate enantiomers D- and L-; its numerous degrees of freedom make it challenging to perform a thorough study; the short-range interactions require higher levels of theory to correctly describe them. Thus, we have performed a meticulous global minimum search. We performed optimizations of the systems at the PBE0 /Def2TZVP level of theory and single point calculations at the DLPNO-CCSD(T)/Def2TZVP level with zero-point corrections at PBE0 /Def2TZVP. We also analyzed Thermal Populations and IR Spectra of the systems to fully understand Arginine's behavior. The results show the energy minima structures strongly rely on its internal nitrogen-rich groups.

Relative Populations and IR Spectra of Cu38 Cluster at Finite Temperature Based on DFT and Statistical Thermodynamics Calculations.

The relative populations of Cu38 isomers depend to a great extent on the temperature. Density functional theory and nanothermodynamics can be combined to compute the geometrical optimization of isomers and their spectroscopic properties in an approximate manner. In this article, we investigate entropy-driven isomer distributions of Cu38 clusters and the effect of temperature on their IR spectra. An extensive, systematic global search is performed on the potential and free energy surfaces of Cu38 using a two-stage strategy to identify the lowest-energy structure and its low-energy neighbors. The effects of temperature on the populations and IR spectra are considered via Boltzmann factors. The computed IR spectrum of each isomer is multiplied by its corresponding Boltzmann weight at finite temperature. Then, they are summed together to produce a final temperature-dependent, Boltzmann-weighted spectrum. Our results show that the disordered structure dominates at high temperatures and the overall Boltzmann-weighted spectrum is composed of a mixture of spectra from several individual isomers.

Effects of Temperature on Enantiomerization Energy and Distribution of Isomers in the Chiral Cu13 Cluster.

In this study, we report the lowest energy structure of bare Cu13 nanoclusters as a pair of enantiomers at room temperature. Moreover, we compute the enantiomerization energy for the interconversion from minus to plus structures in the chiral putative global minimum for temperatures ranging from 20 to 1300 K. Additionally, employing nanothermodynamics, we compute the probabilities of occurrence for each particular isomer as a function of temperature. To achieve that, we explore the free energy surface of the Cu13 cluster, employing a genetic algorithm coupled with density functional theory. Moreover, we discuss the energetic ordering of isomers computed with various density functionals. Based on the computed thermal population, our results show that the chiral putative global minimum strongly dominates at room temperature.

Theoretical Prediction of Structures, Vibrational Circular Dichroism, and Infrared Spectra of Chiral Be4B8 Cluster at Different Temperatures.

Lowest-energy structures, the distribution of isomers, and their molecular properties depend significantly on geometry and temperature. Total energy computations using DFT methodology are typically carried out at a temperature of zero K; thereby, entropic contributions to the total energy are neglected, even though functional materials work at finite temperatures. In the present study, the probability of the occurrence of one particular Be4B8 isomer at temperature T is estimated by employing Gibbs free energy computed within the framework of quantum statistical mechanics and nanothermodynamics. To identify a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surfaces is carried out using a multi-level multistep global genetic algorithm search coupled with DFT. In addition, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The total VCD/IR spectra as a function of temperature are computed using each isomer's probability of occurrence in a Boltzmann-weighted superposition of each isomer's spectrum. Additionally, we present chemical bonding analysis using the adaptive natural density partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11- Flux-Ional Cluster.

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11- clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11- clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations' temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer's infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.

Bonding and Mobility of Alkali Metals in Helicenes.

In this work, we analyze the interactions of alkali metal cations with [6]- and [14]helicene and the cation mobility of therein. We found that the distortion of the carbon skeleton is the reason that some of the structures which are local minima for the smallest cations are not energetically stable for K+ , Rb+ , and Cs+ . Also, the most favorable complexes are those where the cation is interacting with two rings forming a metallocene-like structure, except for the largest cation Cs+ , where the distortion provoked by the size of the cation destabilizes the complex. As far as mobility is concerned, the smallest cations, particularly Na+ , are the ones that can move most efficiently. In [6]helicene, the mobility is limited by the capture of the cation forming the metallocene-like structure. In larger helicenes, the energy barriers for the cation to move are similar both inside and outside the helix. However, complexes with the cation between two layers are more energetically favored so that the movement will be preferred in that region. The bonding analysis reveals that interactions with no less than 50 % of orbital contribution are taking place for the series of E+ -[6]helicene. Particularly, the complexes of Li+ show remarkable orbital character (72.5-81.6 %).

A Spinning Umbrella: Carbon Monoxide and Dinitrogen Bound MB12- Clusters (M = Co, Rh, Ir).

Strong binding of carbon monoxide (CO) and dinitrogen (N2) by MB12- (M = Co, Rh, Ir) clusters results in a spinning umbrella-like structure. For OCMB12- and NNMB12- complexes, the bond dissociation energy values range within 50.3-67.7 kcal/mol and 25.9-35.7 kcal/mol, respectively, with the maximum value obtained in Ir followed by that in Co and Rh analogues. COMB12- complex is significantly less stable than the corresponding C-side bonded isomer. The associated dissociation processes for OCMB12- and NNMB12- into CO or N2 and MB12- are highly endergonic in nature at 298 K, implying their high thermochemical stability with respect to dissociation. In OCMB12- and NNMB12- complexes, the C-O and N-N bonds are found to be elongated by 0.022-0.035 Å along with a large red-shift in the corresponding stretching frequencies, highlighting the occurrence of bond activation therein toward further reactivity due to complexation. The obtained red-shift is explained by the dominance of L←M π-back-donation (L = CO, OC, NN) over L→M σ-donation. The binding of L enhances the energy barrier for the rotation of the inner B3 unit within the outer B9 ring by 0.4-1.8 kcal/mol, which can be explained by a reduction in the distance of the longest bond between inner B3 and outer B9 rings upon complexation. A good correlation is found between the change in rotational barrier relative to that in MB12- and the energy associated with the L→M σ-donation. Born-Oppenheimer molecular dynamics simulations further support that the M-L bonds in the studied systems are kinetically stable enough to retain the original forms during the internal rotation of inner B3 unit.

The cubyl cation rearrangements.

Born-Oppenheimer molecular dynamics simulations and high-level ab initio computations predict that the cage-opening rearrangement of the cubyl cation to the 7H(+)-pentalenyl cation is feasible in the gas phase. The rate-determining step is the formation of the cuneyl cation with an activation barrier of 25.3 kcal mol(-1) at the CCSD(T)/def2-TZVP//MP2/def2-TZVP level. Thus, the cubyl cation is kinetically stable enough to be formed and trapped at moderate temperatures, but it may be rearranged at higher temperatures.

Nonclassical 21-Homododecahedryl Cation Rearrangement Revisited.

The degenerate rearrangement in the 21-homododecahedryl cation (1) has been studied via density functional theory computations and Born-Oppenheimer Molecular Dynamics simulations. Compound 1 can be described as a highly fluxional hyperconjugated carbocation. Complete scrambling of 1 can be achieved by the combination of two unveiled barrierless processes. The first one is a "rotation" of one of the six-membered rings via a 0.8 kcal·mol(-1) barrier, and the second one is a slower interconvertion between two hyperconjomers via an out-of-plane methine bending (ΔG(⧧) = 4.0 kcal·mol(-1)).

Dynamical behavior of Borospherene: A Nanobubble.

The global minimum structure of borospherene (B40) is a cage, comprising two hexagonal and four heptagonal rings. Born-Oppenheimer Molecular Dynamics simulations show that continuous conversions in between six and seven membered rings take place. The activation energy barrier for such a transformation is found to be 14.3 kcal · mol(-1). The completely delocalized σ- and π-frameworks, as well as the conservation of the bonding pattern during rearrangement, facilitate the dynamical behavior of B40. B40 is predicted to act as a support-free spherical two-dimensional liquid at moderate temperature. In other words, B40 could be called as a nanobubble.

The 9-homocubyl cation rearrangement revisited.

Complexity of the potential energy surface of the 9-homocubyl cation is revealed by Born-Oppenheimer molecular dynamics simulations and high ab initio levels. The stereospecific automerizations observed experimentally involve bridged ions, which have either an aromatic or an anti-aromatic character. New pathways leading to more stable isomers are unveiled.

Stop rotating! One substitution halts the B1919⁻ motor.

The B19(-) anion and other boron species have been dubbed 'Wankel motors' for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B19(-) is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB18 species is shown computationally to enforce bond localization.

B18(2-): a quasi-planar bowl member of the Wankel motor family.

A quasi-planar member of the so-called 'Wankel motor' family, B18(2-), is found. This boron cluster is an electronically stable dianion and a concentric doubly σ- and π-aromatic system. The inner B6 unit in B18(2-) undergoes quasi-free rotation inside the perimeter of the B12 ring. The absence of any localized σ-bond between the inner ring and the peripheral boron atoms makes the system fluxional.

Carbo-cages: a computational study.

Inspired by their geometrical perfection, intrinsic beauty, and particular properties of polyhedranes, a series of carbo-cages is proposed in silico via density functional theory computations. The insertion of alkynyl units into the C-C bonds of polyhedranes results in a drastic lowering of the structural strain. The induced magnetic field shows a significant delocalization around the three-membered rings. For larger rings, the response is paratropic or close to zero, suggesting a nonaromatic behavior. In the carbo-counterparts, the values of the magnetic response are shifted with respect to their parent compounds, but the aromatic/nonaromatic character remains unaltered. Finally, Born-Oppenheimer molecular dynamics simulations at 900 K do not show any drastic structural changes up to 10 ps. In the particular case of a carbo-prismane, no structural change is perceived until 2400 K. Therefore, although carbo-cages have enthalpies of formation 1 order of magnitude higher than those of their parent compounds, their future preparation and isolation should not be discarded, because the systems are kinetically stable, explaining why the similar systems like carbo-cubane have already been synthesized.

Re-examination of the C(6)Li(6) structure: to be, or not to be symmetric.

The potential energy surface of C6 Li6 was re-examined and a new non-symmetric global minimum was found. The new structure can be described as three C2 (2-) fragments strongly aggregated through lithium bridges. At high temperatures, fluxionality is perceived instead of dissociation. At 600 and 900 K, the BOMD simulations show that the lithium mobility is high, indicating that the cluster behaves in a liquid-like manner (BOMD=Born-Oppenheimer molecular dynamics).

CBe5E- (E = Al, Ga, In, Tl): planar pentacoordinate carbon in heptaatomic clusters.

A series of clusters with the general formula CBe(5)E(-) (E = Al, Ga, In, Tl) are theoretically shown to have a planar pentacoordinate carbon atom. The structures show a simple and rigid topological framework-a planar EBe(4) ring surrounding a C center, with one of the ring Be-Be bonds capped in-plane by a fifth Be atom. The system is stabilized by a network of multicenter σ bonds in which the central C atom is the acceptor, and π systems as well by which the C atom donates charge to the Be and E atoms that encircle it.

Can an eight π-electron bare ring be planar?

Here we explore in silico an alternative to make planar eight π-electron bare ring systems with substitutions of some cyclooctatetraene ring carbon atoms by heavier group 14 elements. We found that the most stable eight membered rings with formulae C(4)Si(4)H(8), C(4)Ge(4)H(8), and C(4)Sn(4)H(8) have a perfect planar structure, enhancing delocalization energy as compared to cot.

Unravelling phenomenon of internal rotation in B13+ through chemical bonding analysis.

We describe and explain the fluxionality of B(13)(+). The chemical bonding analysis shows that the inner triangle of B(13)(+) is bound to the peripheral ring by delocalized bonds only, allowing a quasi-free rotation of the inner ring.

Shorter still: compressing C-C single bonds.

How short can a C-C single bond get? The bonding in a set of molecules that are related structurally to previously synthesized or theoretically examined systems with short C-C bonds is investigated. According to calculations, a single C-C bond could be compressed to 1.313 Å! To the best of our knowledge, this is the shortest single C-C bond reported to date. This shortening is a consequence of a change in the C-C-C bond angle, θ, to minimize strain in the cages and an effort to offset the tension in the surrounding bridges.