How does the NMR thermometer work? Application of combined quantum molecular dynamics and GIPAW calculations into the study of lead nitrate

Lead nitrate is an inorganic salt, commonly used for the accurate temperature determination in the solid state NMR spectroscopy, due to the strong temperature dependence of the ²⁰⁷Pb chemical shift. As the reason for this phenomenon remained unknown, the main purpose of this study was to explain this temperature dependence at the molecular level. To achieve this, combined CASTEP geometry optimization, quantum molecular dynamics at chosen temperatures and GIPAW NMR computations were performed. Due to the previous literature reports on inaccuracy in the calculation of ²⁰⁷Pb NMR parameters using GIPAW, a large emphasis was put on the optimization of computational method. The application of quantum molecular dynamics provided the simulation of the temperature-dependent vibrational motions and enabled to accurately compute the changes in the value of Pb δ_iso resulting from them. © 2018 Wiley Periodicals, Inc.     

Spectroscopic investigations (FTIR,UV-VIS,NMR) and DFT calculations on the molecular structure of Nω-Nitro-L-arginine

The spectroscopic properties of N_ω-nitro-l-arginine were investigated by FT-IR, UV-VIS, and ¹H NMR spectra. Geometrical parameters and energies were calculated using the density functional theory (DFT) B3LYP method with the 6-311G basis set. Geometrical optimization of the molecule has been performed, vibrational spectra have been calculated, and fundamental vibrations have been determined from the total energy distribution (TED) of the vibrational modes. The HOMO-LUMO analysis is carried out for various electric fields (0.0–0.025 A^?1). The HOMO-LUMO gap is decreased while increasing the electric field. The calculated quantum chemical parameters are calculated and correlated to the inhibition efficiency, A Mullliken population was also important for determining local reactivity by indicating reactive centers and identifying potential nucleophilic and electrophilic attack sites. Charge transfer occurs inside the compound based on the HOMO LUMO gap. Calculations of DFT were evaluated in their ability to predict inhibition efficiency.     

Does Gd@C82 have an anomalous endohedral structure? Synthesis and single crystal X-ray structure of the carbene adduct

We report here the results on single crystal X-ray crystallographic analysis of the Gd@C82 carbene adduct (Gd@C82(Ad), Ad = adamantylidene). The Gd atom in Gd@C82(Ad) is located at an off-centered position near a hexagonal ring in the C2v-C82 cage, as found for M@C82 (M = Sc and La) and La@C82(Ad). Theoretical calculation also confirms the position of the Gd atom in the X-ray crystal structure.     

What is the best DFT functional for vibronic calculations? A comparison of the calculated vibronic structure of the S1-S0 transition of phenylacetylene with cavity ringdown band intensities

The sensitivity of vibronic calculations to electronic structure methods and basis sets is explored and compared to accurate relative intensities of the vibrational bands of phenylacetylene in the S(1)(A(1)B(2)) ← S(0)(X(1)A(1)) transition. To provide a better measure of vibrational band intensities, the spectrum was recorded by cavity ringdown absorption spectroscopy up to energies of 2000 cm(-1) above the band origin in a slit jet sample. The sample rotational temperature was estimated to be about 30 K, but the vibrational temperature was higher, permitting the assignment of many vibrational hot bands. The vibronic structure of the electronic transition was simulated using a combination of time-dependent density functional theory (TD-DFT) electronic structure codes, Franck-Condon integral calculations, and a second-order vibronic model developed previously [Johnson, P. M.; Xu, H. F.; Sears, T. J. J. Chem. Phys. 2006, 125, 164331]. The density functional theory (DFT) functionals B3LYP, CAM-B3LYP, and LC-BLYP were explored. The long-range-corrected functionals, CAM-B3LYP and LC-BLYP, produced better values for the equilibrium geometry transition moment, but overemphasized the vibronic coupling for some normal modes, while B3LYP provided better-balanced vibronic coupling but a poor equilibrium transition moment. Enlarging the basis set made very little difference. The cavity ringdown measurements show that earlier intensities derived from resonance-enhanced multiphoton ionization (REMPI) spectra have relative intensity errors.     

Can TD‐DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case

By using calculations rooted in the time dependent density functional theory (TD-DFT) we have investigated how the lowest energy excited states of a face-to-face pi-stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S(1))(2). TD-PBE0, TD-LC-omegaPBE, and TD-M05-2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al. (J Chem Phys 2006, 125, 231102), predicting that (S(1))(2) has a minimum for R approximately 3 A, with a binding energy of approximately 0.5 eV, whereas TD-B3LYP, TD-CAM-B3LYP, and TD-PBE understimate the binding energy. However, independently of the functional employed, no low-energy spurious charge transfer transitions are predicted by TD-DFT calculations, also when a nonsymmetric dimer is investigated, providing encouraging indications for the use of TD-DFT for studying the excited state of pi-stacked nucleobases.     

Insight and performance of LC-DFT vs DFT in the NMR shielding and chemical shift calculations: Case of CHClCH?CF3

Fifteen density functional theory (DFT) methods and fifteen long-range corrected density functional theory (LC-DFT) methods were used in the present work to assess nuclear magnetic resonance parameters such as nuclear shielding constant (NSC), nuclear chemical shift (NCS), and nuclear anisotropic shielding constant (NAS). These different methods were associated with the full basis set 6-311++G(3df,3pd). The gauge-independent atomic orbital was used for the calculation of nuclear shielding tensors of the nuclei contained in the stereoisomers cis- and trans-CHClCHCF₃. Thus, the effects of LC are clearly observed for heavy nuclei (¹³C, ¹⁹F, ³⁵Cl). The results of NSC, NCS, and NAS from DFT are better described than LC-DFT with regard to the KT3 method. Moreover, the results from the LC-DFT are better described than the standard DFT with regard to CCSD(T). Based on the latter method used as the benchmark, the NSCs of nuclei are well fitted by the competitive functionals LC-TPSSTPSS and LC-PKZBPKZB. In the particular case of the trans-isomer, mPWPKZB was found to be the best method. For the NCSs, the more accurate methods include the latter two LC functionals and the non-LC functionals TPSSTPSS and mPWPKZB. The accuracy of NAS depends strongly on the nuclei. Thus, CAM-B3LYP describes it well for ¹⁹F and LC-PKZBPKZB for ³⁵Cl. The rest of nuclei are well fitted by all the methods except ¹³C₁ and ¹³C₂, which are better reproduced by the LC-DFT except the LC-PKZBPKZB, LC-TPSSTPSS, and CAM-B3LYP functionals.     

How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? The case of the divide-and-conquer method

The authors have developed a fragmentation-based linear-scaling electronic structure calculation strategy named the divide-and-conquer (DC) method, which has been implemented into the Gamess program package. Although there are many sorts of fragmentation-based linear-scaling schemes, most of them require the charge and spin multiplicity of each fragment a priori. Therefore, their applications to delocalized and/or open-shell systems have been limited. However, the DC method is a notable exception because the distribution of electrons in the entire system is automatically determined by the universal Fermi level. In this perspective, the authors have summarized the performance of the linear-scaling self-consistent field (SCF) and post-SCF calculations of delocalized and/or open-shell systems based on the DC method. Furthermore, some future prospects of the method have been discussed.     

A new building block for electroactive organic materials? Synthesis, cyclic voltammetry, single crystal X-ray structure, and DFT treatment of a unique boron-based viologen

A boronium-based paraquat analog undergoes reductions at more negative potentials than paraquat itself, making it a promising building block for electroactive materials.     

How reliable are GIAO calculations of 1H and 13C NMR chemical shifts? A statistical analysis and empirical corrections at DFT (PBE/3z) level

Reliability of calculated (1)H and (13)C NMR chemical shifts for various classes of organic compounds obtained with gauge-invariant atomic orbital (GIAO) approach has been studied at the PBE/3ζ level (as implemented in PRIRODA code) using linear regression analysis with experimental data. Empirical corrections for the calculated chemical shifts δ(H,calc) = δ(PBE/3ζ) - 0.08 ppm (RMS 0.18 ppm, MAD 0.66 ppm) and δ(C,calc) = δ(PBE/) (3) (ζ) - 6.35 ppm (RMS 3.09 ppm, MAD 9.42 ppm) have been developed using the sets of 263 and 308 experimental values for (1)H and (13)C chemical shifts, respectively. The confidence intervals of NMR chemical shifts at 95% confidence probability are δ(H,calc) ± 0.35 ppm for (1)H and δC,calc) ± 6.05 ppm for (13)C.     

Synthesis and structure of 1-benzyl-5-amino-1H-tetrazole in the solid state and in solution: Combining X-ray diffraction, 1H NMR,FT–IR,and UV–Vis spectra and DFT calculations

Compound 1-benzyl-5-amino-1H-tetrazole (BAT) was synthesized and characterized by ¹H NMR, FT–IR, and UV–Vis spectroscopies and elemental (CHNS) analysis. The crystal structure was further elucidated by single-crystal X-ray diffraction. Density functional theory (DFT) calculations with B3LYP and PBE1PBE functionals of the BAT were performed to provide structural and spectroscopic information and guide spectral assignments. The compound crystallizes in monoclinic primitive system space group P2(1)/c with a = 14.91 Å, b = 5.12 Å, c = 11.19 Å, V = 852 Å³, Z = 4, R₁ = 0.0428 at 298 K. The structure exhibits intermolecular hydrogen bonds of the type N–H(amino)···N(tetrazole). Simultaneous hydrogen bonds between amino···tetrazole and tetrazole···amino establish a dimeric intermolecular structure, whereas another hydrogen bond between the remaining H atom of the amino group and the other N atoms of the tetrazole ring extends the structure into another dimension. The crystal structure of BAT is properly reproduced by DFT calculations only when a dimeric or tetrameric model is employed in the modeling. Comparisons between experimental and calculated spectral properties suggest that the monomeric form of BAT is dominant in aprotic, polar, hydrogen-bonding solvents, such as DMSO and DMF.     

Does the A.T or G.C base-pair possess enhanced stability? Quantifying the effects of CH...O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations

An empirically based relationship between overall complex stability (-DeltaG degrees ) and various possible component interactions is developed to probe the question of whether the A.T/U and G.C base-pairs exhibit enhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approach suggests ca. 2-2.5 kcal mol-1 in additional stability for A.T owing to a group interaction containing a CH...O contact. Pairing geometry and the role of the CH...O interaction in the A.T base-pair were also probed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicated that Hoogsteen geometry is preferred over Watson-Crick geometry in A.T by ca. 1 kcal mol-1. Factors that might contribute to the preference for Hoogsteen geometry are a shorter CH...O contact, a favorable alignment of dipoles, and greater distances between secondary repulsive sites. The CH...O interaction was also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initio calculations support the result of the phenomenological approach that the A.T base-pair does have enhanced stability relative to hydrogen-bonded complexes with just N-H...N and N-H...O hydrogen bonds.     

X-ray crystal structures of Ru3(μ-H)(μ-C,N-C5H4N)(CO)10-n (P i Pr3) n,n=0,1: A A case of the hydride following the Phosphine?

The reaction ofRu₃(-H)(-C,N-C₅H₄N)(CO)₁₀ (1) with Pt(P ⁱ Pr₃)(nb)₂ {nb = bicyclo-[2.2.1]hept-2-ene} does not afford any Ru-Pt mixed metal clusters, but gives instead the mono-substituted phosphine derivative Ru₃(-H) (-C,N-C₅H₄N)(CO)₉(P ⁱ Pr₃) (2) as the sole isolable product. Single crystal X-ray studies have been carriedout on 1 and 2. Crystal data for 1: monoclinic, space group P2₁/c,a = 16.9637(10) A,b = 7.6632(5) Á,c = 17.4058(11) Á, = 117.214(5)°,V = 2009.0(2) Á³,R(R _w) = 0.022 (0.034) for 3090 independent absorption corrected data. Crystal data for 2: triclinic, space group P,a = 9.3389(5) Á,b = 11.4376(6) Á,c = 15.1781(8) Á, = 76.454(4), = 79.900(5), = 67.428(5)°,V = 1448.8(2) Á³ R(R _w ) = 0.024 (0.034) for 4564 independent absorption corrected data. In cluster 1 the Ru-Ru bonds are in the range 2.8462(4)-2.8986(4) Á. The hydride and-pyridyl ligand bridge the same Ru-Ru vector, and the Ru(-H) bridge is symmetric, with Ru-H = 1.78(4) and 1.77(4) Á. In cluster 2 the Ru-Ru distances show a greater ranger 2.7267(3)-3.0604(3) Á. The phosphine ligand is bonded to the Ru atom which is not involved in the-pyridyl bridge. In contrast to 1, the hydride and-pyridyl ligands in 2 bridge different Ru-Ru vectors and the resultant Ru(-H)Ru bridge is asymmetric, with Ru-H = 1.70(4) and 1.89(4) Á.     

Does the molecular structure of CaH2 affect the dihydrogen bonding in CaH2 … HY (Y = CH3, C2H3, C2H, CN, and NC) complexes? A quantum chemistry study using MP2 and B3LYP methods

Second-order M ller-Plesset(MP2) and density functional theory(DFT) calculations have been carried out in order to investigate the structures and properties of dihydrogen-bonded CaH 2 HY(Y = CH 3,C 2 H 3,C 2 H,CN,and NC) complexes.Our calculations revealed two possible structures for CaH 2 in CaH 2 HY complexes:linear(I) and bent(II).The bond lengths,interaction energies,and strengths for H H interactions obtained by both MP2 and B3LYP methods are quite close to each other.It was found that the interaction energy decreases with increasing electron density at the Ca-H bond critical point.Atom-in-molecule(AIM) results show that for all of Ca-H H-Y interactions considered here,the Laplacian of the electron density at the H H bond critical point is positive,indicating the electrostatic nature of these Ca-H H-Y dihydrogen bonded systems.     

The series of molecular conductors and superconductors ET4[AFe(C2O4)3]·PhX (ET = bis(ethylenedithio)tetrathiafulvalene; (C2O4)2- = oxalate; A+ = H3O+, K+; X = F, Cl, Br, and I): influence of the halobenzene guest molecules on the crystal structure and superconducting properties

An extensive series of radical salts formed by the organic donor bis(ethylenedithio)tetrathiafulvalene (ET), the paramagnetic tris(oxalato)ferrate(III) anion [Fe(C(2)O(4))(3)](3-), and halobenzene guest molecules has been synthesized and characterized. The change of the halogen atom in this series has allowed the study of the effect of the size and charge polarization on the crystal structures and physical properties while keeping the geometry of the guest molecule. The general formula of the salts is ET(4)[A(I)Fe(C(2)O(4))(3)]·G with A/G = H(3)O(+)/PhF (1); H(3)O(+)/PhCl (2); H(3)O(+)/PhBr (3), and K(+)/PhI (4), (crystal data at room temperature: (1) monoclinic, space group C2/c with a = 10.3123(2) ?, b = 20.0205(3) ?, c = 35.2732(4) ?, β = 92.511(2)°, V = 7275.4(2) ?(3), Z = 4; (2) monoclinic, space group C2/c with a = 10.2899(4) ?, b = 20.026(10) ?, c = 35.411(10) ?, β = 92.974°, V = 7287(4) ?(3), Z = 4; (3) monoclinic, space group C2/c with a = 10.2875(3) ?, b = 20.0546(15) ?, c = 35.513(2) ?, β = 93.238(5)°, V = 7315.0(7) ?(3), Z = 4; (4) monoclinic, space group C2/c with a = 10.2260(2) ?, b = 19.9234(2) ?, c = 35.9064(6) ?, β = 93.3664(6)°, V = 7302.83(18) ?(3), Z = 4). The crystal structures at 120 K evidence that compounds 1-3 undergo a structural transition to a lower symmetry phase when the temperature is lowered (crystal data at 120 K: (1) triclinic, space group P1 with a = 10.2595(3) ?, b = 11.1403(3) ?, c = 34.9516(9) ?, α = 89.149(2)°, β = 86.762(2)°, γ = 62.578(3)°, V = 3539.96(19) ?(3), Z = 2; (2) triclinic, space group P1 with a = 10.25276(14) ?, b = 11.15081(13) ?, c = 35.1363(5) ?, α = 89.0829(10)°, β = 86.5203(11)°, γ = 62.6678(13)°, V = 3561.65(8) ?(3), Z = 2; (3) triclinic, space group P1 with a = 10.25554(17) ?, b = 11.16966(18) ?, c = 35.1997(5) ?, α = 62.7251(16)°, β = 86.3083(12)°, γ = 62.7251(16)°, V = 3575.99(10) ?(3), Z = 2; (4) monoclinic, space group C2/c with a = 10.1637(3) ?, b = 19.7251(6) ?, c = 35.6405(11) ?, β = 93.895(3)°, V = 7128.7(4) ?(3), Z = 4). A detailed crystallographic study shows a change in the symmetry of the crystal for compound 3 at about 200 K. This structural transition arises from the partial ordering of some ethylene groups in the ET molecules and involves a slight movement of the halobenzene guest molecules (which occupy hexagonal cavities in the anionic layers) toward one of the adjacent organic layers, giving rise to two nonequivalent organic layers at 120 K (compared to only one at room temperature). The structural transition at about 200 K is also observed in the electrical properties of 1-3 and in the magnetic properties of 1. The direct current (dc) conductivity shows metallic behavior in salts 1-3 with superconducting transitions at about 4.0 and 1.0 K in salts 3 and 1, respectively. Salt 4 shows a semiconductor behavior in the temperature range 300-50 K with an activation energy of 64 meV. The magnetic measurements confirm the presence of high spin S = 5/2 [Fe(C(2)O(4))(3)](3-) isolated monomers together with a Pauli paramagnetism, typical of metals, in compounds 1-3. The magnetic properties can be very well reproduced in the whole temperature range with a simple model of isolated S = 5/2 ions with a zero field splitting plus a temperature independent paramagnetism (Nα) with the following parameters: g = 1.965, |D| = 0.31 cm(-1), and Nα = 1.5 × 10(-3) emu mol(-1) for 1, g = 2.024, |D| = 0.65 cm(-1), and Nα = 1.4 × 10(-3) emu mol(-1) for 2, and g = 2.001, |D| = 0.52 cm(-1), and Nα = 1.5 × 10(-3) emu mol(-1) for 3.