ABSTRACT
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
Subject(s)
Quantum Theory , Software , Monte Carlo MethodABSTRACT
Taking long-range electrostatic effects into account in classical and hybrid quantum mechanics-molecular mechanics (QM/MM) simulations is necessary for an accurate description of the system under study. We have recently developed a method, termed long-range electrostatic corrections (LREC), for monopolar QM/MM calculations. Here, we present an extension of LREC for multipolar/polarizable QM/MM simulations within the LICHEM software package. Reaction barriers and QM-MM interaction energies converge with a LREC cutoff between 20 and 25 Å, in agreement with our previous results. Additionally, the LREC approach for the QM-MM interactions can be smoothly combined with standard shifting or Ewald summation methods in the MM calculations. We recommend the use of QM(LREC)/MM(PME), where the QM region is treated with LREC and the MM region is treated with particle mesh Ewald (PME) summation. This combination is an excellent compromise between simplicity, speed, and accuracy for large QM/MM simulations.
ABSTRACT
Treatment of NiCl2(dme) and NiBr2(dme) (dme = dimethoxyethane) with 2 equiv of LiOR (OR = OC(t)Bu2Ph) forms the distorted trigonal planar complexes [NiLiX(OR)2(THF)2] (THF = tetrahydrofuran) 5 (X = Cl) and 6 (X = Br). The reaction of CuX2 (X = Cl, Br) with 2 equiv of LiOR affords the Cu(I) product Cu4(OR)4 (7). The same product can be obtained using the Cu(I) starting material CuCl. NMR studies indicated that the reduction of Cu(II) to Cu(I) is accompanied by the oxidation of the alkoxide RO(-) to form the alkoxy radical RO(â¢), which subsequently forms tert-butyl phenyl ketone by ß-scission. Treatment of compounds 1-4 ([M2Li2Cl2(OR)4], M = Cr-Co) with thallium hexafluorophosphate allowed the isolation of the distorted tetrahedral complexes of the form M(OR)2(THF)2 for M = Mn (8), Fe (9), and Co (10). Cyclic voltammetry performed on compounds 8-10 demonstrated irreversible oxidations for all complexes, with the iron complex 9 being the most reducing. Complex 9 shows a reactivity toward PhIO and Ph3SbS to form the corresponding dinuclear iron(III) complexes Fe2(O)(OR)4(THF)2 (11) and Fe2(S)(OR)4(THF)2 (12), respectively. X-ray structural studies were performed, showing that the Fe-O-Fe angle for complex 11 is 176.4(1)° and that the Fe-S-Fe angle for complex 12 is 164.83(3)°.
ABSTRACT
The vibrational spectroscopy of the nitrate-water isotopologues is studied in the O-H and O-D stretching regions using temperature-dependent infrared multiple photon dissociation spectroscopy combined with calculations of the anharmonic spectra. At a temperature of 15 K a series of discrete peaks is observed in the IRMPD spectra of NO3(-)·H2O, NO3(-)·HDO, and NO3(-)·D2O. This structure is considerably more complex than predicted by harmonic calculations. A signal is only observed in the hydrogen-bonded O-H (O-D) stretching region, characteristic of a double hydrogen-bond donor binding motif. With increasing temperature, the peaks broaden, leading to a quasi-continuous absorption from 3150 to 3600 cm(-1) (2300-2700 cm(-1)) for NO3(-)·H2O (NO3(-)·D2O) and, above 100 K, an additional band in the free O-H (O-D) stretching region, suggesting the population of complexes containing only a single hydrogen bond at higher internal energies. Vibrational configuration interaction calculations confirm that much of the structure observed in the IRMPD spectra derives from progressions in the water rocking mode resulting from strong cubic coupling between the O-H (O-D) stretch and water rock degrees of freedom. The spectra of both NO3(-)·H2O and NO3(-)·D2O display a strong peak that does not derive from the water rock progression but results instead from a Fermi resonance between the O-H (O-D) stretch and H-O-H (D-O-D) bend overtone. Additional insight into the nature of the O-H (O-D) stretch and water rocking coupling in these complexes is provided by an effective Hamiltonian that allows for the cubic coupling between the O-H stretch and water rock degrees of freedom.