CALCULATED STERIC CHARGES ON THE MOLECULAR SURFACES ARE USED TO INVESTIGATE THE HALOGEN BONDS FORMED BETWEEN SOME R-X MOLECULES (R= NC, NCCC, CF3CC, FCC, CF3 AND CH3, AND X=F, CL AND BR) AND AMMONIA, WATER AS WELL AS FORMALDEHYDE. IT IS SHOWN THAT THE FORMATION OF HALOGEN-BONDED COMPLEXES COULD BE REGARDED AS THE INTERACTION BETWEEN A NEGATIVE STERIC CHARGE (STERIC POTENTIAL DEPLETION) ON THE SURFACE OF HALOGEN ATOM AND A POSITIVE STERIC CHARGE (STERIC POTENTIAL ACCUMULATION) REGION OF AN ELECTRON-DONOR SITE. ...

THERE ARE SOME EVIDENCES THAT SHOW WHEN FLUORINE IS BONDEDTO A STRONG ELECTRON WITHDRAWING GROUP, IT CAN INTERACT WITH AN ELECTRON DONOR SPECIES AND FORM A WEAK NONCOVALENT BOND.BECAUSE THERE IS A POSITIVE Σ-HOLE ON THE OUTERMOST PORTION OF THE FLUORINE SURFACE, THESE INTERACTIONS ARE USUALLY CLASSIFIED AS HALOGEN BONDS. HOWEVER, OUR CALCULATIONS BASED ON THE ELECTRON DENSITY ANALYSIS, INTERACTING QUANTUM ATOM (IQA) AND NATURAL ENERGY DECOMPOSITION ANALYSIS (NEDA) APPROACHES REVEAL THAT THERE ARE SOME FUNDAMENTAL DIFFERENCES BETWEEN TRADITIONAL HALOGEN BANDS AND FLUORINE INTERACTIONS. ...

BACKGROUND: THE “TERM HALOGEN BOND” (XB) IS USED TO DESCRIBE ANY NONCOVALENTINTERACTION INVOLVING HALOGEN AS ACCEPTOR OF ELECTRON DENSITY [1]. XB IS A CONSEQUENCE OF INTERACTION BETWEEN Y AND THE Ζ-HOLE REGION OF X AND IS BELIEVED TO BE MAINLY OF THE ELECTROSTATICNATURE [2]. HEREIN, CHARACTERIZATION OF HALOGEN BONDS WERE PERFORMED USING THE TOPOLOGICAL PROPERTIES OFELECTRON DENSITY OBTAINED FROM ATOMS IN MOLECULES (AIM) ANALYSIS OF BIS (PYRIDINE) HALONIUM. (SEE FIGURE 1)METHODS: ALL STRUCTURES WERE OPTIMIZED USING GAUSSIAN 09 PROGRAM PACKAGE AT THE B3LYP/6-311++G** LEVEL. THE LANL2DZ BASIS SETS WAS EMPLOYED FORIODINE. THE TOPOLOGICAL ANALYSIS OFELECTRON DENSITY WERE COMPUTED BY THEAIM2000 PROGRAM.RESULTS: THE VALUES OF ELECTRON DENSITY RB, LAPLACIAN OF ELECTRON DENSITY D2RB, ELECTRON ENERGY DENSITY HB AND -GB/VB, WHICH IS THE RATIO OF THE KINETIC ENERGY DENSITY TO THE POTENTIAL ENERGY DENSITY AT THE BCP, ARE IN THE RANGES ILLUSTRATED IN THE TABLE 1, WITH THE SHARED-SHELL AND CLOSED-SHELL AS TWO LIMITED INTERACTIONS.

HALOGEN BOND IS AN INTERACTION THAT OCCUR BETWEEN A HALIDE (X) IN ONE MOLECULE (R-X) AND AN ELECTRON-RICH SITE IN A NEARBY LEWIS BASE (Y−R’) [1]. HALOGEN AND HYDROGEN BONDS HAVE THE SAME PROPERTIES, SUCH THAT THE FORMER MAY ALSO BE USED IN THE STRUCTURE OF ARTIFICIAL PROTEINS AND NUCLEOTIDES [2]. IN THIS WORK, INDIVIDUAL INTERACTIONS IN HALOGEN (CL AND BR)- BONDED DNA BASE PAIRS CONTAINING MODIFIED GUANINE, CYTOSINE, ADENINE AND THYMINE NUCLEOSIDES HAVE BEEN ESTIMATED USING ELECTRON CHARGE DENSITIES CALCULATED AT THE HALOGEN BOND CRITICAL POINTS BY THE ATOMS IN MOLECULES (AIM) METHOD [3]. ALL STRUCTURES WERE OPTIMIZED BY THE B3LYP METHOD IN CONJUNCTION WITH THE 6-31G* BASIS SET FOR ALL ATOMS WITH THE EXCEPTION OF IODINE THAT THE MIDIX BASIS SET WAS EMPLOYED. THE ESTIMATED INDIVIDUAL HALOGEN BOND (XB) ENERGIES HAVE BEEN STUDIED ON THE BASE OF BOND DISTANCES AND BOND ANGLES. THE RESULTS SHOW THAT INDIVIDUAL HALOGEN BOND ENERGIES ARE STRONGER, WHEN THE BOND DISTANCES ARE SHORTER AND ALSO BOND ANGLES ARE NEARER TO 180O. ACCORDING TO TABLE 1, THE MOST STRENGTH HALOGEN BOND CORRESPONDS TO BR-CONTAINING COMPLEXES IN BOTH DG:DC (N-BR…O) AND DA: DT (N…BR-N) CASES.

BACKGROUND: HALOGEN BOND PLAYS A CRUCIAL ROLE IN THE FIELD OF MOLECULAR RECOGNITION, CRYSTAL ENGINEERING AND BIOLOGICAL SYSTEMS. THE ENERGY OF HALOGEN BOND (XB) IS AN IMPORTANT SUBJECT IN CHEMISTRY AND BIOCHEMISTRY [1], WHICH CAN BE CALCULATED BY THE SUPRA-MOLECULAR METHOD. THE THEORY OF ATOMS IN MOLECULES (AIM) HAS OFFERED A VALUABLE TOOL TO UNDERSTAND THE CONCEPT OF CHEMICAL BOND AND ITS STRENGTH IN TERM OF ELECTRON DENSITY. IN THE PRESENT WORK, THE FORMATION OF HALOGEN BOND BETWEEN ALKYLHALIDE AND NITROGEN ATOM IN AMMONIA HAVE BEEN STUDIED.METHODS: THE MOLECULAR STRUCTURES OF ALL COMPLEXES AND MONOMERS HAVE BEEN OPTIMIZEDAT THE MP2/6- 311++G (D, P) LEVEL OF THEORY AND THEIR COMPLEXATION ENERGY WERE CALCULATED. ALL OF TOPOLOGICAL PROPERTIES OF THE ELECTRON DENSITY OF VARIOUS COMPLEXES WERE OBTAINED FROM THE WFN FILES AT THE SAME LEVEL OF THEORY.RESULTS: FIRST, THE INTERACTION ENERGIES WITHOUT AND WITH THE BSSE (BASIS SET SUPERPOSITION ERROR) CORRECTION WERE CALCULATED. THEN, AIM ANALYSES ARE USED TO DETERMINE THE PRESENCE OF BOND CRITICAL POINT (BCP) OF THE INTRAMOLECULAR BOND IN EACH OF COMPLEXES. FURTHERMORE, ALL OF TOPOLOGICAL PROPERTIES AND INTEGRATED ATOMIC PROPERTIES WERE OBTAINED.CONCLUSION: IN THE PRESENT WORK, LINEAR CORRELATIONS BETWEEN THE HALOGEN BOND ENERGY AND ALL OF TOPOLOGICAL PROPERTIES, SUCH AS ELECTRON DENSITY, ITS LAPLACIAN AND VARIOUS INTEGRATED ATOMIC PROPERTIES WERE FOUND. ADDITIONALLY, THERE ARE GOOD RELATIONSHIPS BETWEEN BONDING ENERGY WITH GEOMETRICAL AND SPECTROSCOPIC PARAMETERS. ACCORDING TO THESE CORRELATIONS, WE CAN EASILY ESTIMATE THE HALOGEN BOND ENERGY IN COMPLEX BIOLOGICAL SYSTEMS.