Degree Of Molecules Research Articles

Ring kinematics‐informed conformation space exploration

AbstractConformational searches and ML‐driven geometry predictions (e.g., AlphaFold) work in the space of molecule's degrees of freedom. When dealing with cycles, cyclicity constraints impose complex interdependence between them, so that arbitrary changes of cyclic dihedral angles lead to heavy distortions of some bond lengths and valence angles of the ring. This renders navigation through conformational space of cyclic molecules to be very challenging. Inverse kinematics is a theory that provides a mathematically strict solution to this problem. It allows one to identify degrees of freedom for any polycyclic molecule, that is, its dihedral angles that can be set independently from each other. Then for any values of degrees of freedom, inverse kinematics can reconstruct the remaining dihedrals so that all rings are closed with given bond lengths and valence angles. This approach offers a handy and efficient way for constructing and navigating conformational space of any molecule using either naïve Monte‐Carlo sampling or sophisticated machine learning models. Inverse kinematics can considerably narrow the conformational space of a polycyclic molecule to include only cyclicity‐preserving regions. Thus, it can be viewed as a physical constraint on the model, making the latter obey the laws of kinematics, which govern the rings conformations. We believe that inverse kinematics will be universally used in the ever‐growing field of geometry prediction of complex interlinked molecules.This article is categorized under: Structure and Mechanism > Molecular Structures Data Science > Artificial Intelligence/Machine Learning Data Science > Chemoinformatics

Deep Learning-Assisted Investigation of Electric Field-Dipole Effects on Catalytic Ammonia Synthesis.

External electric fields can modify binding energies of reactive surface species and enhance catalytic performance of heterogeneously catalyzed reactions. In this work, we used density functional theory (DFT) calculations-assisted and accelerated by a deep learning algorithm-to investigate the extent to which ruthenium-catalyzed ammonia synthesis would benefit from application of such external electric fields. This strategy allows us to determine which electronic properties control a molecule's degree of interaction with external electric fields. Our results show that (1) field-dependent adsorption/reaction energies are closely correlated to the dipole moments of intermediates over the surface, (2) a positive field promotes ammonia synthesis by lowering the overall energetics and decreasing the activation barriers of the potential rate-limiting steps (e.g., NH2 hydrogenation) over Ru, (3) a positive field (>0.6 V/Å) favors the reaction mechanism by avoiding kinetically unfavorable N≡N bond dissociation over Ru(1013), and (4) local adsorption environments (i.e., dipole moments of the intermediates in the gas phase, surface defects, and surface coverage of intermediates) influence the resulting surface adsorbates' dipole moments and further modify field-dependent reaction energetics. The deep learning algorithm developed here accelerates field-dependent energy predictions with acceptable accuracies by five orders of magnitudes compared to DFT alone and has the capacity of transferability, which can predict field-dependent energetics of other catalytic surfaces with high-quality performance using little training data.

The effect of twisted D–D–π–A configuration on electron transfer and photo-physics characteristics

ABSTRACTTwo D–D–π–A organic dyes (M45, M46) with dithieno[3,2-b:2′,3′-d]pyrrole (DTP) units as election donors in two perpendicular directions, were investigated using density functional theory (DFT) and time-dependent DFT. The ground-state geometries, the absorption, the electronic structures, the charge density difference and molecular electrostatic potential were obtained. To simulate a more realistic performance, all calculations were based on gas condition and dichloromethane solvent. Photoelectric parameters were evaluated by the following factors: the light harvesting efficiency, electron injection driving force, the excited lifetime and vertical dipole moment. Meanwhile, the polarisability and hyperpolarisability were investigated to further explain the relationship between non-linear optical properties and efficiency. The direction of the DTP obviously affects the twisted degree of molecule, forming a better coplanarity on the donor 2 of M45, which results in stronger charge transfer interactions. Furthermore, M45 possesses significant advantages in geometric structure, absorption band and intramolecular charge transfer mechanism. These critical parameters supported the higher performance of M45 in comparison with M46. Moreover, four dyes were designed by the substitution of donor 2, which further verify the influence of the twisted donor 2 on electron transfer and photoelectric properties of D–D–π–A configuration.

Excess molar volumes and excess isentropic compressibilities of liquid mixtures formed by tetrahydropyran, piperidine and cyclic ketones at temperature from 293.15 to 308.15 K.

The densities, ρ, ρ123 and speeds of sound, u, u123 of binary Tetrahydropyran (1)+Piperidine (2) and ternary Tetrahydropyran (1)+Piperidine (2)+Cyclohexanone or Cycloheptanone (3) mixtures have been measured over the whole range of mole fraction at 293.15, 298.15, 303.15, 308.15K and atmospheric pressure. The observed data have been utilized to determine excess molar volumes, (VE)12, V123E and excess isentropic compressibilities, (κSE)12, (κSE)123 for the binary and ternary liquid mixtures respectively. The (VE)12, V123E and (κSE)12, (κSE)123 data have been fitted to Redlich-Kister equation to determine binary as well as ternary adjustable parameters along with standard deviations. The Moelywn-Huggins concept of interaction between the surfaces of the binary mixture constituents has been extended (Graph theory) to evaluate excess molar volumes and excess isentropic compressibilities of ternary mixtures using the concept of connectivity parameter of third degree of molecules, 3ξ (which deals with the topology of the constituents in pure and mixed state) to obtain an expression that describe well the measured data.

EXPERIMENTAL EVALUATION OF TOTAL HYDROGEN CAPACITY FOR FULLERITE C<sub>60</sub>

The fullerene is the fourth allotropic modification of carbon and its properties, as volume, gravimetric and electrochemical capacities, are in excess of many similar properties of metal hydrides and hydrocarbons. The solution of the problem of the reversible hydrogenation of each carbon atom in the frame of fullerene molecule will allow to create the hydrogen storage with the capacity up to 7.7 wt.% H. A series of experiments have been conducted to evaluate the full hydrogenation of fullerite C 60 ; hydrofullerenes have been produced experimentally with the variable content of hydrogen. The optimum regime of C 60 hydrogenation has been determined resulting in the full hydrogenation of fullerene molecule C 60 . As was apparent after the tests, the sequence of formation of hydrogenated fullerene molecule C 60 H 60 in fullerite has been going in the following order: the molecular hydrogen dissolution in octahedral interstices of fcc lattice of fullerite, the dissociation of hydrogen molecules in going from octa- to tetrahedral interstices, the interaction of hydrogen atoms with fullerene molecule. It has been demonstrated that chemisorption process of hydrogen by molecule C 60 is limited by diffusive processes in fullerite after hydrogen concentration conformed to C 60 H 36 . The spectral analysis has shown that the second stage process of chemisorption follows the compressive shell model. The suggestion of the model of processes going on at the interaction between H 2 and fullerite C 60 has been made. The mechanism for the definition of hydrogenation degree of molecule C 60 has been proposed in the present paper.

Spectroscopic determination of the relative particle densities of H2, HD, and D2 Molecules in non-equilibrium hydrogen–deuterium plasma: II. Experimental verification

The relative intensities of the Balmer series lines of hydrogen and deuterium atoms and the Q-branch lines in the Fulcher-α band system of the H2, HD, and D2 molecules were measured. These lines were emitted by non-equilibrium plasma surrounded by the cylindrical channel of an additional molybdenum electrode located between the cathode and anode of glow (in the deuterium with a minor hydrogen impurity) and arc (in a mixture of D2, H2, and Ne in comparable quantities) discharges at pressures of 6–8 Torr and current densities of 0.4 and 8.5–17 A/cm2, respectively. The measured intensity ratios and gas temperature were used for the estimation of the relative particle densities of the H2, HD, and D2 molecules in the framework of the simple models of the excitation of atoms (models 1a and 1b for the high and low values of dissociation degrees, respectively) and the rovibronic levels of isotopic molecules (model 2). The results obtained by means of models 1a and 2 were in a significant contradiction, whereas the data obtained with the use of models 1b and 2 coincided within error bars. The good agreement between two spectroscopic techniques based on two independent theoretical models and two independent sets of experimental data showed that the techniques proposed are promising for the determination of the isotopic composition of molecules in lowpressure hydrogen-deuterium plasma at least in the case of a low dissociation degree of molecules.

The nonlinear effects of sound in a liquid with relaxation losses

The nonlinear effects of sound in electrolyte with a chemical reaction are examined. The dynamic equations that govern non-wave modes in the field of intense sound are derived, and acoustic forces of vortex, entropy, and relaxation modes are determined in the cases of low-frequency sound and high-frequency sound. The difference in the nonlinear effects of sound in electrolyte and in a gas with excited vibrational degrees of molecules, are specified and discussed.

Molar Excess Volumes and Excess Isentropic Compressibilities of Ternary Mixtures Containing o-Toluidine

Molar excess volumes, V ijk E , and speeds of sound, U ijk , of o-toluidine (i) + benzene (j) + cyclohexane or n-hexane or n-heptane (k) ternary mixtures have been measured as a function of composition at 308.15 K. The observed speed of sound data have been utilized to determine the excess isentropic compressibilities, (K S E ) ijk , of the ternary (i+j+k) mixtures. The Moelywn-Huggins concept (Huggins in Polymer 12: 389–399, 1971) of connectivity between the surfaces of the binary mixture constituents has been extended to ternary mixtures (using the concept of a connectivity parameter of third degree of molecules, 3 ξ, which in turn depends on its topology) to obtain an expression that describes well the measured V ijk E and (K S E ) ijk data. The observed data have also been analyzed in terms of Flory’s theory.

2′-Deoxy-5-propynylcytidine: a nucleoside forming two solid-state conformations

The title compound, 4-amino-1-(2-deoxy-beta-D-erythropentofuranosyl)-5-(prop-1-ynyl)pyrimidin-2(1H)-one, C12H15N3O4, shows two conformations in the crystalline state which differ mainly in the glycosylic bond torsion angle and the sugar pucker. Both molecules exhibit an anti glycosylic bond conformation, with torsion angles chi = -135.0 (2) and -156.4 (2) degrees for molecules 1 and 2, respectively. The sugar moieties show a twisted C2'-endo sugar pucker (S-type), with P = 173.3 and 192.5 degrees for molecules 1 and 2, respectively. The crystal structure is characterized by a three-dimensional network that is stabilized by several intermolecular hydrogen bonds between the two conformers.

Effect of Molecular Chirality on Racemate Stability: α-Amino Acids with Nonpolar R Groups

A racemate of two opposite and resolvable enantiomers is generally assumed to be more stable than the corresponding conglomerate. Demonstrating this structure-stability relation, however, has proved difficult owing to a sampling bias (data available only for systems whose racemates are stable enough to exist) and a possible kinetic bias (racemates may be easier to crystallize than conglomerates from racemic media). As a new approach to studying the relation, we determined how the relative stability of the conglomerate and the racemate changes with the molecule's degree of chirality in a series of alpha-amino acids with nonpolar R groups. We found that the excess energy of the conglomerate over the racemate, (E(C) - E(R)), increases with the size of the R group, a measure of the molecule's chirality. If valid in general, this relation demonstrates a tendency for chiral molecules to form racemates rather than conglomerates. Because of the entropy effect on crystal stability, however, the excess free energy of the conglomerate over the racemate, (G(C) - G(R)), shows no simple relation with the degree of chirality at the temperatures of study (-3 to 180 degrees C).

1,3-Bis(2-ethoxyphenyl)imidazolidin-2-ylidene]bromo(cycloocta-1,5-diene)rhodium(I)

The title complex, [RhBr(C8H12)(C19H22N2O2)], has a distorted square-planar geometry. There are two molecules, A and B, in the asymmetric unit. The Rh-C bond distance between the N-heterocyclic ligand and the metal atom is 2.039 (2) A in molecule A and 2.042 (2) A in molecule B. The angle between the carbene heterocycle and the coordination plane is 87.56 (12) degrees in molecule A and 87.03 (11) degrees in molecule B. It is shown that the average Rh-C(COD) (COD is cyclooctadiene) distance is linearly dependent on the Rh-C(imidazolidine) distance in this type of compound. This can be ascribed to the steric hindrance produced by the packing. The crystal structure contains intramolecular C-H...O and intermolecular C-H...Br interactions.

Polymorphism and solvolysis of 2-cyano-3-[4-(N,N-diethylamino)phenyl]prop-2-enethioamide

Two new polymorph forms, (Ia) and (Ib), of the title compound, C(14)H(17)N(3)S, and its solvate with acetonitrile, C(14)H(17)N(3)S.0.25C(2)H(3)N, (Ic), have been investigated. Crystals of the two polymorphs were grown from different solvents, viz. ethanol and N,N-dimethylformamide, respectively. The polymorphs have different orientations of the thioamide group relative to the CN substituent, with s-cis and s-trans geometry of the C=C-C=S diene fragment, respectively. Compound (Ic) contains two independent molecules, A and B, with s-cis geometry, and the solvate molecule lies on a twofold axis. The core of each molecule is slightly non-planar; the dihedral angles between the conjugated C=C-CN linkage and the phenyl ring, and between this linkage and the thioamide group are 13.4 (2) and 12.0 (2) degrees in (Ia), 14.0 (2) and 18.2 (2) degrees in (Ib), 2.3 (3) and 12.7 (4) degrees in molecule A of (Ic), and 23.2 (3) and 8.1 (4) degrees in molecule B of (Ic). As a result of strong conjugation between donor and acceptor parts, the substituted phenyl rings have noticeable quinoid character. In (Ib), there exists a very strong intramolecular steric interaction (H...H = 1.95 A) between the bridging and thioamide parts of the molecule, which makes such a form less stable. In the crystal structure of (Ia), intermolecular N-H...N and N-H...S hydrogen bonds link molecules into infinite tapes along the [1-10] direction. In (Ib), such intermolecular hydrogen bonds link molecules into infinite (101) planes. In (Ic), intermolecular N-H...N hydrogen bonds link molecules A and B into dimers, which are connected via N-H...S hydrogen bonds and form infinite chains along the c direction.

Second‐order Nonlinear Optical Properties of a Series of Azulene Derivatives

AbstractThe first hyperpolarizabilities of a series of novel azulenic‐barbituric acid chromophores have been studied by using 12 excitation wavelengths, ranging from 900 to 1907 nm. The dispersion relation of the first hyperpolarizabilities of chromophors holds the same tendency as the experimental results. In addition. the static first hyperpolarizability β0 of molecules was calculated by means of the Sum‐Over‐States (SOS) expression and the two‐level formula respectively. The results show that these molecules possess large static fast hyperpolarizabilities and the β0 value increases as the donor or acceptor strength enhances; the distorted degree of molecules has also an important influence on the β0 value.

3-Cyclopropyl-1,2,4-triazolo[3,4-b]benzothiazole monohydrate.

The title structure, C11H9N3S.H2O, contains two crystallographically independent molecules, each consisting of a 1,2,4-triazolo[3,4-b]benzothiazole-fused ring fragment substituted with a cyclopropyl ring, and a water molecule. The geometry of both molecules differs slightly. Both molecules are planar within 0.041 and 0.03 A. The dihedral angle between triazole and the cyclopropyl ring is 60.0(1) and 61.7(1) degrees for molecules A and B, respectively, and the cyclopropyl ring is inclined at an angle of 2.0(1) and 1.2(1) degrees to the benzothiazole moiety for molecules A and B, respectively. The packing of the molecules is stabilized by O-H...N-type hydrogen bonds.

Bis[(E)-2-(2,4-dichloro-5-nitrostyryl)-1,3-benzothiazole] hydrate.

The title compound, bis[(E)-2-(2,4-dichloro-5-nitrostyryl)-1,3-benzothiazole] hydrate, 2C15H8Cl2N2O2S.-H2O, was obtained from the condensation of 2-methyl-benzothiazole with 2,4-dichloro-5-nitrobenzaldehyde. Single-crystal X-ray analysis showed that the asymmetric unit contains two crystallographically unique but structurally similar molecules. The dihedral angle between the benzothiazole fragment and the phenyl ring is 6.1 (4) degrees in molecule A and 19.5 (4) degrees in molecule B.

Helix-forming tendencies of amino acids depend on the restrictions of side-chain rotamer conformations: crystal structure of the tripeptide GAI in two crystalline forms.

In our attempts to design crystalline alpha-helical peptides, we synthesized and crystallized GAI (C11H21N3O4) in two crystal forms, GAI1 and GAI2. Form 1 (GAI1) Gly-L-Ala-L-Ile (C11H21N3O4.3H2O) crystals are monoclinic, space group P2(1) with a = 8.171(2), b = 6.072(4), c = 16.443(4) A, beta = 101.24(2) degrees, V = 800 A3, Dc = 1.300 g cm-3 and Z = 2, R = 0.081 for 482 reflections. Form 2 (GAI2) Gly-L-Ala-L-Ile (C11H21N3O4.1/2H2O) is triclinic, space group P1 with a = 5.830(1), b = 8.832(2), c = 15.008(2) A, alpha = 102.88(1), beta = 101.16(2), gamma = 70.72(2) degrees, V = 705 A3, Z = 2, Dc = 1.264 g cm-3, R = 0.04 for 2582 reflections. GAI1 is isomorphous with GAV and forms a helix, whereas GAI2 does not. In GAI1, the tripeptide molecule is held in a near helical conformation by a water molecule that bridges the NH3+ and COO- groups, and acts as the fourth residue needed to complete the turn by forming two hydrogen bonds. Two other water molecules form intermolecular hydrogen bonds in stabilizing the helical structure so that the end result is a column of molecules that looks like an incipient alpha-helix. GAI2 imitates a cyclic peptide and traps a water molecule. The conformation angles chi 11 and chi 12 for the side chain are (-63.7 degrees, 171.1 degrees) for the helical GAI1, and (-65.1 degrees, 58.6 degrees) and (-65.0 degrees, 58.9 degrees) for the two independent nonhelical molecules in GAI2; in GAI1, both the C gamma atoms point away from the helix, whereas in GAI2 the C gamma atom with the g+ conformation points inward to the helix and causes sterical interaction with atoms in the adjacent peptide plane. From these results, it is clear that the helix-forming tendencies of amino acids correlate with the restrictions of side-chain rotamer conformations. Both the peptide units in GAI1 are trans and show significant deviation from planarity [omega 1 = -168(1) degrees; omega 2 = -171(1) degrees] whereas both the peptide units in both the molecules A and B in GAI2 do not show significant deviation from planarity [omega 1 = 179.3(3) degrees; omega 2 = -179.3(3) degrees for molecule A and omega 1 = 179.5(3) degrees; omega 2 = -179.4(3) degrees for molecule B], indicating that the peptide planes in these incipient alpha-helical peptides are considerably bent.

Structure of an anticonvulsant N-methyl-m-bromophenylsuccinimide.

3-(3-Bromophenyl)-1-methyl-2,5-pyrrolidinedione, C11H10BrNO2, Mr = 268.11, triclinic P1, a = 11.606 (2), b = 11.832 (2), c = 10.370 (2) A, alpha = 101.84 (1), beta = 107.76 (1), gamma = 118.28 (2) degrees, V = 1085.7 (5) A3, Z = 4, Dx = 1.640 Mg m-3, lambda(Cu K alpha) = 1.54178 A, mu = 5.04 mm-1, F(000) = 536, room temperature, final R = 0.061 for 2971 observed reflections with I greater than 3 sigma(I) (of 3743 unique data). The only slight differences in conformation of the two independent molecules are in the inclination of the phenyl and five-membered rings. The torsion angle C4-C1-C11-C12 is -115.4 (4) degrees in molecule I and -131.6 (4) degrees in molecule II. The five-membered imide ring has the open-envelope conformation in molecule I [the deviation of C11 from the plane N11-C41-C21-C31 is -0.117 (3) A] and the twist conformation in molecule II [the deviations of C12 and C22 from the plane N12-C42-C32 are 0.117 (1) and -0.064 (1) respectively].

Structure of 6-oxo-1,6-dihydro-3,4'-bipyridine-5-carbonitrile hydrogen bromide

5-Cyano-6-oxo-1,6-dihydro-3,4'-bipyridinium bromide, C11H8N3O+.Br-, Mr = 278.11, triclinic, P1, a = 7.827 (2), b = 9.796 (2), c = 15.548 (4) A, alpha = 76.53 (2), beta = 75.40 (2), gamma = 74.36 (2) degrees, V = 1093.4 (4) A3, Z = 4, Dx = 1.689 Mg m-3, lambda (Mo K alpha) = 0.71073 A, mu = 3.70 mm-1, F(000) = 552, T = 293 K, R = 0.084 for 3989 observed reflections. The bipyridinium ions are planar, the C(2)-C(1)-C(1')-C(2') torsion angles being -3.3 (10) and 2.2 (11) degrees for molecules (1) and (2), respectively. The symmetry-independent bipyridinium ions are assembled in separate chains by hydrogen-bonding Br bridges [respective distances: Br(1)...N(3) 3.227 (6); Br(1)...N(4') 3.374 (6); Br(2)...N(3*) 3.263 (5); Br(2)...N(4'*) 3.540 (7) A] and by forming N...O hydrogen bonds between pyridinium NH groups and keto O atoms, the N(4')...O(4) and N(4'*)...O(4') distances being 2.835 (7) and 2.706 (7) A, respectively. These chains are connected by the series of stacking interactions with an average C...C distance of 3.5 A.

Structure of (3S)-3-tert-butyloxycarbonylamino-2-piperidone.

C10H18N2O3, Mr = 214.27, monoclinic, P2(1), a = 15.515 (2), b = 6.730 (1), c = 12.541 (2) A, beta = 113.6 (2) degrees, V = 1200.0 A3, Z = 4, Dx = 1.186 g cm-3, lambda(Mo K alpha) = 0.71069 A, mu = 0.54 cm-1, F(000) = 464, T = 295 K. The final R value for 1611 observed (3139 unique) reflections is 0.055. In both the independent molecules A and B of the asymmetric unit of the title compound, the conformation of the urethane moiety is trans. The lactam group of molecule A is non-planar, the C(9)-N(2)-C(10)-C(6) torsion angle being 12.4 (14) degrees. One main difference between molecules A and B is in the value of the phi[C(5)-N(1)-C(6)-C(10)] torsion angle [52.3 (11) degrees for molecule A while -86.5 (10) degrees for molecule B] as a consequence of a rotation of the ring relative to the tert-butyloxycarbonylamino substituent. A second major difference is the delta-lactam ring conformation which is approximate half-chair for molecule A while boat for molecule B.

Conformation of methylated amino acids: structure of 3,4-dimethoxy-alpha-methyl-DL-phenylalanine sesquihydrate.

C12H17NO4.1.5H2O, Mr = 266.3, triclinic, P1, a = 5.872 (1), b = 11.437 (2), c = 20.434 (1) A, alpha = 95.74 (1), beta = 96.91 (1), gamma = 89.18 (1) degrees, V = 1355.5 A3, Z = 4, Dm = 1.29, D chi = 1.305 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 8.3 cm-1, F(000) = 572, T = 294 K, R = 0.038 for 4006 reflections, I greater than or equal to 3 sigma(I). Both the molecules A and B in the asymmetric unit exist as zwitterions. With respect to the D enantiomer, the torsion angles psi 1 and psi 2 are +47.2 and -134.4 degrees in molecule A and +33.3 and -147.5 degrees in molecule B respectively. The torsion angles of the alpha-methyl group, NH3+ and COO- groups with respect to Cv are in molecules A and B respectively +67.2, +66.8, -174.3, -175.6, and -59.2 and -59.5 degrees. The hydrogen-bonding environment of water OW1 is trigonal nonplanar; OW2 is trigonal planar and OW3 is tetrahedral. The crystal structure is stabilized by a number of hydrogen bonds involving the amino and carboxylate groups of both molecules A and B and the water molecules.