NCImilano: an electron-density-based code for the study of noncovalent interactions

2013 ◽  
Vol 46 (5) ◽  
pp. 1513-1517 ◽  
Author(s):  
Gabriele Saleh ◽  
Leonardo Lo Presti ◽  
Carlo Gatti ◽  
Davide Ceresoli
Keyword(s):  
Solid State ◽  
Gas Phase ◽  
Noncovalent Interactions ◽  
Real Space ◽  
Quantum Mechanical ◽  
Solid State Electron ◽  
X Ray ◽  
Reduced Density Gradient ◽  
Reduced Density ◽  
First Time

NCImilano, a Fortran90 code for applying the reduced density gradient (RDG) descriptor to a real-space study of noncovalent interactions, is presented. This code has been specifically designed for the X-ray charge density community, as it can deal with both gas-phase and solid-state electron densities as evaluated by popular multipolar (XD2006) and Gaussian-based quantum mechanical (Gaussian03/09,CRYSTAL) computational platforms. Moreover, it implements for the first time the possibility of plotting energy densities over RDG isosurfaces.

The X-ray constrained wavefunction of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions

2020 ◽  
Vol 76 (5) ◽  
pp. 802-814
Author(s):  
Juan F. Van der Maelen ◽  
Mario Ceroni ◽  
Javier Ruiz
Keyword(s):  
Source Function ◽  
Noncovalent Interactions ◽  
Intramolecular Interactions ◽  
X Ray ◽  
Interacting Quantum Atoms ◽  
Reduced Density Gradient ◽  
Type C ◽  
Reduced Density ◽  
High Degree

The synthesis and X-ray structure determination of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex (1) are described. The C—Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C—H...Br—C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.

An insight to the noncovalent interactions in two triamine based mononuclear iron(III) Schiff base complexes with special emphasis on the formation of Br•••π halogen bonding

CrystEngComm ◽  
2021 ◽  
Author(s):  
Shouvik Chattopadhyay ◽  
Tanmoy Basak ◽  
Antonio Frontera
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Schiff Base Complexes ◽  
X Ray ◽  
Mononuclear Iron

Two mononuclear iron(III) complexes, [FeL1Cl]∙CH3CN (1) and [FeL2(N3)] (2) {H2L1= N,N′-bis(5-chlorosalicylidene)diethylenetriamine and H2L2= N,N′-bis(5-bromosalicylidene)diethylenetriamine}, have been synthesized and characterized by X-ray crystallographic studies. In the solid state, there are strong...

Bis(1-phenyl-1-propyne) complexes of tungsten(II): crystal structures of [WI2(CO)(NCR)(η2-MeC2Ph)2] (R = Me, Et, or Ph)

2001 ◽  
Vol 79 (3) ◽  
pp. 263-271
Author(s):  
Paul K Baker ◽  
Michael GB Drew ◽  
Deborah S Evans
Keyword(s):  
Carbon Monoxide ◽  
Solid State ◽  
Crystal Structures ◽  
Octahedral Geometry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Alkyne Complexes ◽  
First Time

Reaction of [WI2(CO)3(NCMe)2] with two equivalents of 1-phenyl-1-propyne (MeC2Ph) in CH2Cl2, and in the absence of light, gave the bis(1-phenyl-1-propyne) complex [WI2(CO)(NCMe)(η2-MeC2Ph)2] (1) in 77% yield. Treatment of equimolar quantities of 1 and NCR (R = Et, i-Pr, t-Bu, Ph) in CH2Cl2 afforded the nitrile-exchanged products, [WI2(CO)(NCR)(η2-MeC2Ph)2] (2-5) (R = Et (2), i-Pr (3), t-Bu (4), Ph (5)). Complexes 1, 2, and 5 were structurally characterized by X-ray crystallography. All three structures have the same pseudo-octahedral geometry, with the equatorial sites being occupied by cis and parallel alkyne groups, which are trans to the cis-iodo groups. The trans carbon monoxide and acetonitrile ligands occupy the axial sites. In structures 1 and 2, the methyl and phenyl substituents of the 1-phenyl-1-propyne ligands are cis to each other, whereas for the bulkier NCPh complex (5), the methyl and phenyl groups are trans to one another. This is the first time that this arrangement has been observed in the solid state in bis(alkyne) complexes of this type.Key words: bis(1-phenyl-1-propyne), carbonyl, nitrile, diiodo, tungsten(II), crystal structures.

CsOH and its Lighter Homologues – a Comparison

2014 ◽  
Vol 69 (11-12) ◽  
pp. 1229-1236
Author(s):  
Matthias Wörsching ◽  
Constantin Hoch
Keyword(s):  
Gas Phase ◽  
Room Temperature ◽  
Structure Type ◽  
Alkali Metal Hydroxide ◽  
X Ray ◽  
Raman Spectroscopic ◽  
Cesium Hydroxide ◽  
Free Ion ◽  
The One ◽  
First Time

Abstract Cesium hydroxide, CsOH, was for the first time characterised on the basis of single-crystal data. The structure is isotypic to the one of the room-temperature modification of NaOH and can be derived from the NaCl structure type thus allowing the comparison of all alkali metal hydroxide structures. Raman spectroscopic investigations show the hydroxide anion to behave almost as a free ion as in the gas phase. The X-ray investigations indicate possible H atom positions.

Structural studies of organoboron compounds. LVI. 1-Benzyl-7-methyl-3,5-diphenyl-2,4,6-trioxa-1-azonia-3-bora-5-boratabicyclo[3.3.0]octane and 1,4,6,9-tetramethyl-2,7-diphenyl-3,8,11,12-tetraoxa-1,6-diazonia-2,7-diboratatricyclo[5.3.1.12,6]dodecane

1992 ◽  
Vol 70 (11) ◽  
pp. 2809-2817 ◽  
Author(s):  
Wolfgang Kliegel ◽  
Gottfried Lubkowitz ◽  
Steven J. Rettig ◽  
James Trotter
Keyword(s):  
Solid State ◽  
Gas Phase ◽  
Phenylboronic Acid ◽  
Direct Methods ◽  
Structural Studies ◽  
Triclinic Space Group ◽  
Full Matrix ◽  
X Ray ◽  
Molar Ratios ◽  
New Type

The preparation of the N-(2-hydroxypropyl)-N-alkylhydroxylamines, 6a (R = CH3) and 6b (R = CH2Ph), and their reactions with phenylboronic acid are described. Regardless of the molar ratios of reactants employed, the reaction with 6b leads to the 1:2 condensate 1-benzyl-7-methyl-3,5-diphenyl-2,4,6-trioxa-1-azonia-3-bora-5-boratabicyclo[3.3.0]octane, 7, while that with 6a gives rise to the 1:1 condensate 1,4,6,9-tetramethyl-2,7-diphenyl-3,8,11,12-tetraoxa-1,6-diazonia-2,7-diboratatricyclo[5.3.1. 12,6]dodecane, 11 (the cyclic BONBON dimer of 4,6-dimethyl-2-phenyl-1,3-dioxa-4-aza-2-boracyclohexane, 9). Compounds 7 and 11 both crystallize in the triclinic space group [Formula: see text]: for 7; a = 13.126(1), b = 15.337(1), c = 10.9469(5) Å, α = 91.727(5), β = 104.647(5), γ = 72.922(7)°, Z = 4; and for 11; a = 9.0807(4), b = 9.1653(3), c = 6.4876(2) Å, α = 97.708(3), β = 108.830(3), γ = 89.188(4)°, Z = 1. The structures were solved by direct methods and were refined by full-matrix least-squares procedures to R = 0.038 and 0.032 for 5879 and 1827 reflections with I ≥ 3σ(F2), respectively. Compound 7 has the expected bicyclic pyroboronate structure, but represents the first reported N-substituted example of this type of compound. Bond lengths involving boron in 7 are (C) O—B(sp3) = 1.428(2) and 1.420(2), (B)O—B(sp3) = 1.472(2) and 1.468(2), N—B(sp3) = 1.737(2) and 1.762(2), C(phenyl)—B(sp3) = 1.588(2) and 1.584(2), (N)O—B(sp2) = 1.402(2) and 1.404(2), (B)O—B(sp2) = 1.331(2) and 1.329(2), C(phenyl)—B(sp2) = 1.555(3) and 1.553(2) Å. The X-ray analysis establishes a centrosymmetric, twofold N → B coordinated, dimeric structure in the solid state for 11 in which each B—O—N segment of a central six-membered BONBON ring is bridged by an O—C—C moiety. Compound 11 represents the first fully characterized example of a new type of "BONBON" compound. Bond distances involving the boron atom are (N)O—B = 1.465(1), (C)O—B = 1.428(1), N—B = 1.695(2), and C(phenyl)—B = 1.607(2) Å. Spectroscopic evidence indicates that in solution and in the gas phase this material exists predominantly as the monomer 9.

Niobium-bearing arsenides and germanides from elemental mixtures not involving niobium: a new twist to an old problem in solid-state synthesis

2018 ◽  
Vol 74 (5) ◽  
pp. 623-627 ◽  
Author(s):  
Sviatoslav Baranets ◽  
Hua He ◽  
Svilen Bobev
Keyword(s):  
High Temperature ◽  
Solid State ◽  
Diffraction Data ◽  
Alkaline Earth ◽  
Alkaline Earth Metals ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Temperature Reactions ◽  
First Time ◽  
Synthetic Work

Three isostructural transition-metal arsenides and germanides, namely niobium nickel arsenide, Nb0.92(1)NiAs, niobium cobalt arsenide, NbCoAs, and niobium nickel germanide, NbNiGe, were obtained as inadvertent side products of high-temperature reactions in sealed niobium containers. In addition to reporting for the very first time the structures of the title compounds, refined from single-crystal X-ray diffraction data, this article also serves as a reminder that niobium containers may not be suitable for the synthesis of ternary arsenides and germanides by traditional high-temperature reactions. Synthetic work involving alkali or alkaline-earth metals, transition or early post-transition metals, and elements from groups 14 or 15 under such conditions may yield Nb-containing products, which at times could be the major products of such reactions.

scholarly journals The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 455 ◽  
Author(s):  
Saikat Seth
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Noncovalent Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Mixed Ligand ◽  
Binding Energies ◽  
Zigzag Chain ◽  
X Ray ◽  
Π Interactions

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

Sodium Alanate Dehydrogenation Properties Enhanced by MnTiO3 Nanoparticles

2020 ◽  
Vol 15 (2) ◽  
pp. 197-203
Author(s):  
Yujie Sun ◽  
Xia Yang ◽  
Yue Huang ◽  
Jianquan Li ◽  
Xinghua Cen ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrogen Desorption ◽  
Test Results ◽  
X Ray Diffraction ◽  
X Ray ◽  
Sodium Alanate ◽  
State Ceramic ◽  
Solid State Ceramic Route ◽  
Ceramic Route ◽  
First Time

In this study, we investigated the influence of MnTiO3 nanoparticles additive on hydrogen released performance of NaAlH4 for the first time. The MnTiO3 nanoparticles were successfully synthesized using conventional solid-state ceramic route. It was found that the hydrogen released performance of NaAlH4 can be significantly improved by the addition of MnTiO3 nanoparticles. Meantime, the composite of NaAlH4 doped 5 wt% MnTiO3 possessed excellent dehydrogenation properties, the onset dehydrogenation temperature was only 70.6 °C, reduced by about 105 °C in comparison with the pristine NaAlH4, and approximately 5.01 wt% of hydrogen could be released from composite with temperature heated to 220 °C. The isothermal dehydrogenation test results indicated that the amount of hydrogen released by NaAlH4-5 wt% MnTiO3 composite could reach 4.4 wt% under 200 °C within 25 min. According to the analysis of X-ray diffraction, the presence of MnTiO3 nanoparticles did not alter the overall dehydrogenation pathway of NaAlH4, and the Al3 Ti phases formed after dehydrogenation, which enhanced hydrogen desorption performances of NaAlH4 .

Configurations and conformations of glycosyl sulfoxides

2010 ◽  
Vol 88 (11) ◽  
pp. 1154-1174 ◽  
Author(s):  
Hong Liang ◽  
Micheline MacKay ◽  
T. Bruce Grindley ◽  
Katherine N. Robertson ◽  
T. Stanley Cameron
Keyword(s):  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Lone Pair ◽  
Azido Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Comparison Of The Results ◽  
P Type

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

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