The existence of uneven hexagon and heptagon on the surface of the borospherene B40 cage allows its interaction with transition metal–organic fragments to form complexes. Based on density functional ...theory calculations, the sandwich complex C5H5ScB40 was studied. Results show that when the B7-heptagon of B40 sandwiched with Sc, the isomer had the lowest energy. Detailed structural characterization and bonding analyses for the lowest energy isomer Cs C5H5ScB40 (1) show that both non-covalent and covalent interactions were present between Sc and C5H5 and B40. B40 can act as an inorganic ligand to bond with transition metals, in which the boron atoms that deviate from the heptagon play an important role in the bonding. At the same time, the IR, Raman, and UV–vis absorption spectra of Cs C5H5ScB40 (1) were theoretically simulated, and the findings can provide some theoretical guidance for future experimental synthesis.
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•Detailed conformational analysis of solvated l-DOPA in acidic conditions using MD and DFT.•Obtaining state-of-the-art VOA spectra of l-DOPA in an acidic aqueous solution.•Refined ...conformer ratios based on experimental data, thus improving simulation accuracy.•Paving the way for future research on deuterated l-DOPA analogs.
l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l-DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l-DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l-DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l-DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs.
This article presents a method for extracting the optical constants of homogeneous isotropic materials using the infrared spectra of that material. The method is based on using the harmonic ...oscillator model of molecular polarizability to obtain optical constants, then calculating the spectrum, comparing the calculated spectrum to an experimental spectrum of the material, and adjusting the model parameters until a close fit between the spectra is obtained. Corrections that need to be made to the experimental spectra in order to remove instrumental distortions are also briefly described. The remainder of the article centers on describing how the optical constants can be used to simulate spectra of that material in different experimental arrangements and the benefits that spectral simulations afford to experimentalists.
Based on extensive global minimum searches augmented with first-principles theory calculations, we predict herein the first boron-based perfect tetrahedral clusters
T
d
B
16
P
4
(
2
) and
T
d
B
16
As
...4
(
3
) which, as aromatic non-metal analogs of the experimentally observed
T
d
Au
20
(2003,
Science
299
, 864), all contain a truncated
T
d
B
16
(
1
) cage at the center effectively stabilized by four trivalent non-metal atoms (P, As) at the corners. Detailed natural bonding orbital (NBO) and adaptive natural density partitioning (AdNDP) bonding analyses indicate that the valences of all the trivalent component atoms in these tetrahedral clusters are fully satisfied, rendering spherical aromaticity and extra stability to the systems. The IR, Raman, and photoelectron spectra (PES) of the concerned species are theoretically simulated to facilitate their characterizations in future experiments.
Graphical Abstract
This chapter summarizes the core concepts underlying the simulation of EPR spectra from biological samples in the solid state, from a user perspective. The key choices and decisions that have to be ...made by a user when simulating an experimental EPR spectrum are outlined. These include: the choice of the simulation model (the network of spins and the associated spin Hamiltonian), the dynamic regime (solid, liquid, slow motion), the level of theory used in the simulation (matrix diagonalization, perturbation theory, etc.), the treatment of orientational order and disorder (powder, crystal, partial ordering), the inclusion of the effects of structural disorder (strains), the effects of other line broadening mechanisms (unresolved hyperfine couplings, relaxation), and the inclusion of experimental distortions (field modulation, power saturation, filtering). Additionally, the salient aspects of utilizing least-squares fitting algorithms to aid the analysis of experimental spectra with the help of simulations are outlined. Although drawing from the experience gained from implementing EasySpin and from interacting with EasySpin's user base, this chapter applies to any EPR simulation software.
Pulmonary surfactant exhibits phase coexistence over a wide range of surface pressure and temperature. Less is known about the effect of temperature on pulmonary surfactant models. Given the lack of ...studies on this issue, we used electron paramagnetic resonance (EPR) and nonlinear least–squares (NLLS) simulations to investigate the thermotropic phase behavior of the matrix that mimics the pulmonary surfactant lipid complex, i.e., the lipid mixture composed of dipalmitoyl phosphatidylcholine (DPPC), palmitoyl–oleoyl phosphatidylcholine (POPC) and palmitoyl–oleoyl phosphatidylglycerol (POPG). Irrespective of pH, the EPR spectra recorded from 5°C to 25°C in the DPPC/POPC/POPG (4:3:1) model membrane contain two spectral components corresponding to lipids in gel-like and fluid-like phases, indicating a coexistence of two domains in that range. The temperature dependence of the distribution of spin labels between the domains yielded nonlinear van't Hoff plots. The thermodynamic parameters evaluated were markedly different for DPPC and for the ternary DPPC/POPC/POPG (4:3:1) membranes and exhibited a dependence on chemical environment. While enthalpy and entropy changes for DPPC were always positive and presented a quadratic behavior with temperature, those of the ternary mixture were linearly dependent on temperature and changed from negative to positive values. Despite that, enthalpy-entropy compensation takes place in the two systems. The thermotropic process associated with the coexistence of the two domains is entropically–driven in DPPC and either entropically– or enthalpically–driven in the pulmonary surfactant membrane depending on the pH, ionic strength and temperature. The significance of these results to the structure and function of the pulmonary surfactant lipid matrix is discussed.
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•An EPR/NLLS method to study the thermodynamics of coexisting domains is proposed.•Nonlinear van't Hoff behavior was found for the coexisting membrane domains.•The thermodynamic parameters were modulated by temperature, pH, and ionic strength.•Enthalpy-entropy compensation takes place in coexisting domains of model membranes.
The difference between the functioning of the human non-visual and photopic systems has elicited the need for complex in situ measurements or time-consuming multi-spectral simulations to accurately ...predict the non-visual luminous content of the indoor environment. As such methodologies are time-consuming, the aim of the present study was to determine whether such complex methodologies are needed. The issue was studied through simulations of four cardinally oriented identical offices located in Ljubljana, Slovenia. Each was studied using orange, grey and blue walls. Diurnal luminous conditions were studied under clear, hazy and overcast skies on December, March and June 21st. The non-visual content was evaluated using novel metrics, the Autonomy of Circadian Potential and Circadian Autonomy, which assess temporal circadian luminous content. Diurnal results were used to construct climate-based spectral months to evaluate the monthly non-visual potential of the studied offices. Furthermore, simulations addressed the question of whether the requirements of the non-visual system might contradict the visual comfort of indoor environments. The results show that compliance with non-visual requirements for indoor spaces with spectrally neutral surfaces or those in shades of blue could be assessed using photopic methodologies. However, this is not true for spaces characterised by orange and red materials.
The newly discovered cage-like borospherene
D
2
d
B
40
with two η
6
-B
6
hexagons and four η
7
-B
7
heptagons on the surface may serve as an effective multi-dentate ligand to coordinate transition ...metals. Based upon extensive density functional theory calculations, we present herein the possibility of the exohedral complex series (C
6
H
6
Cr)
n
&B
40
(n = 1–6) with n Cr centres sandwiched between the central η
6/7
-B
40
unit and n planar η
6
-C
6
H
6
ligands. C
6
H
6
Cr fragments in (C
6
H
6
Cr)
n
&B
40
occupy the η
6
-B
6
hexagonal coordination site atop the B
40
cage first, the four neighboring η
7
-B
7
heptagons on the waist next, and finally the η
6
-B
6
hexagon at the bottom, forming a multinuclear complex series effectively stabilized by n C
6
H
6
Cr fragments. The two η
6
-B
6
hexagons and four η
7
-B
7
heptagons on the spherical surface of B
40
can be practically viewed as six independent coordination sites to coordinate Cr centers with almost the same coordination energies. Detailed bonding analyses indicate that the eclipsed
C
2
v
C
6
H
6
Cr&B
40
(
1
-
1
) possesses a coordination bonding pattern similar to that of dibenzenechromium, with the B
40
ligand inheriting the σ + π double delocalization bonding pattern of the parent borospherene. The IR, Raman, and UV–vis absorption spectra of
C
2
v
C
6
H
6
Cr&B
40
(
1
-
1
) are theoretically simulated to facilitate its future experimental characterization.
